From 74a7e92bd5384936126aa518957e06c2407a4489 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sun, 19 Feb 2023 22:14:37 +0200 Subject: [PATCH] RO release (#677) --- .gitignore | 41 + generated-axioms.owl | 2 +- ro-base.json | 2903 +++++++++++---------- ro-base.obo | 815 +++--- ro-base.owl | 835 +++--- ro.json | 2265 ++++++++-------- ro.obo | 819 +++--- ro.owl | 1183 +++++---- src/ontology/generated-axioms.owl | 2 +- src/ontology/subsets/ro-causal.obo | 660 +++-- src/ontology/subsets/ro-causal.owl | 768 +++--- src/ontology/subsets/ro-chado.obo | 9 +- src/ontology/subsets/ro-chado.obo.tmp | 9 +- src/ontology/subsets/ro-developmental.obo | 660 +++-- src/ontology/subsets/ro-developmental.owl | 768 +++--- src/ontology/subsets/ro-eco.obo | 807 +++--- src/ontology/subsets/ro-eco.owl | 827 +++--- src/ontology/subsets/ro-interaction.obo | 660 +++-- src/ontology/subsets/ro-interaction.owl | 768 +++--- src/ontology/subsets/ro-mereotopology.obo | 660 +++-- src/ontology/subsets/ro-mereotopology.owl | 768 +++--- src/ontology/subsets/ro-sequence.obo | 660 +++-- src/ontology/subsets/ro-sequence.owl | 768 +++--- src/ontology/subsets/ro-time-interval.obo | 660 +++-- src/ontology/subsets/ro-time-interval.owl | 768 +++--- subsets/ro-causal.obo | 660 +++-- subsets/ro-causal.owl | 768 +++--- subsets/ro-chado.obo | 9 +- subsets/ro-chado.obo.tmp | 9 +- subsets/ro-developmental.obo | 660 +++-- subsets/ro-developmental.owl | 768 +++--- subsets/ro-eco.obo | 807 +++--- subsets/ro-eco.owl | 827 +++--- subsets/ro-interaction.obo | 660 +++-- subsets/ro-interaction.owl | 768 +++--- subsets/ro-mereotopology.obo | 660 +++-- subsets/ro-mereotopology.owl | 768 +++--- subsets/ro-sequence.obo | 660 +++-- subsets/ro-sequence.owl | 768 +++--- subsets/ro-time-interval.obo | 660 +++-- subsets/ro-time-interval.owl | 768 +++--- 41 files changed, 14659 insertions(+), 14646 deletions(-) diff --git a/.gitignore b/.gitignore index 268d2755..8855ab6a 100644 --- a/.gitignore +++ b/.gitignore @@ -9,3 +9,44 @@ src/ontology/gen-universal-from-homeomorphy.owl catalog-v001.xml .DS_Store src/ontology/ro-lastbuild.owl +.DS_Store +semantic.cache +bin/ + +*.tmp +*.tmp.obo +*.tmp.owl +*.tmp.json + +src/ontology/mirror +src/ontology/mirror/* +src/ontology/reports/* +src/ontology/ro.owl +src/ontology/ro.obo +src/ontology/ro.json +src/ontology/ro-base.* +src/ontology/ro-basic.* +src/ontology/ro-full.* +src/ontology/ro-simple.* +src/ontology/ro-simple-non-classified.* + +src/ontology/seed.txt +src/ontology/dosdp-tools.log +src/ontology/ed_definitions_merged.owl +src/ontology/ontologyterms.txt +src/ontology/simple_seed.txt +src/ontology/patterns +src/ontology/merged-ro-edit.owl + +src/ontology/target/ +src/ontology/tmp/* +!src/ontology/tmp/README.md + +src/ontology/imports/*_terms_combined.txt + +src/patterns/data/**/*.ofn +src/patterns/data/**/*.txt +src/patterns/pattern_owl_seed.txt +src/patterns/all_pattern_terms.txt + +target/ diff --git a/generated-axioms.owl b/generated-axioms.owl index 5eff3f88..4adb7c15 100644 --- a/generated-axioms.owl +++ b/generated-axioms.owl @@ -148,5 +148,5 @@ - + diff --git a/ro-base.json b/ro-base.json index 42528d7b..19f07664 100644 --- a/ro-base.json +++ b/ro-base.json @@ -35,7 +35,7 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part." @@ -52,7 +52,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -165,9 +165,6 @@ "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { @@ -179,6 +176,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -192,11 +192,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." @@ -234,7 +234,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -309,7 +309,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -367,7 +367,7 @@ "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -376,53 +376,53 @@ "type" : "PROPERTY", "lbl" : "results in developmental progression of" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002175", + "id" : "http://purl.obolibrary.org/obo/RO_0002296", "meta" : { "definition" : { - "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S", + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.", "xrefs" : [ ] }, - "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" - }, { - "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", - "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + "val" : "http://www.geneontology.org/GO.doc.development.shtml" } ] }, "type" : "PROPERTY", - "lbl" : "present in taxon" + "lbl" : "results in development of" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "id" : "http://purl.obolibrary.org/obo/RO_0002175", "meta" : { "definition" : { - "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.", + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S", "xrefs" : [ ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], + "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.geneontology.org/GO.doc.development.shtml" + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" } ] }, "type" : "PROPERTY", - "lbl" : "results in development of" + "lbl" : "present in taxon" }, { "id" : "http://purl.obolibrary.org/obo/RO_0015015", "meta" : { @@ -515,6 +515,9 @@ "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" @@ -530,9 +533,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -546,7 +546,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -559,7 +559,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -597,7 +597,7 @@ "val" : "tooth SubClassOf 'never in taxon' value 'Aves'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -616,13 +616,13 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Jennifer Deegan" + "val" : "https://orcid.org/0000-0001-9227-417X" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" @@ -653,6 +653,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" @@ -662,9 +665,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -679,15 +679,15 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "replaces" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -765,7 +765,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -783,7 +783,7 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Melissa Haendel" + "val" : "https://orcid.org/0000-0001-9114-8737" } ] }, "type" : "PROPERTY", @@ -817,7 +817,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -853,15 +853,15 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "connected to" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "FMA:85972" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" } ] }, "type" : "PROPERTY", @@ -904,7 +904,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Melissa Haendel" + "val" : "https://orcid.org/0000-0001-9114-8737" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -996,12 +996,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/date", "val" : "2021-11-05T17:30:44Z" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/oborel/obo-relations/issues/478" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "http://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/478" } ] }, "type" : "PROPERTY", @@ -1017,15 +1017,15 @@ "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "FMA:85994" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2212" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -1130,7 +1130,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" @@ -1160,11 +1160,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -1215,7 +1215,7 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1229,7 +1229,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" @@ -1264,9 +1264,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2212" }, { @@ -1275,6 +1272,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1299,7 +1299,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" @@ -1373,11 +1373,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -1414,7 +1414,7 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1511,7 +1511,7 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1542,11 +1542,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1560,6 +1560,9 @@ }, "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "false" }, { @@ -1568,9 +1571,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -1583,14 +1583,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A lump of clay and a statue" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -1654,7 +1654,7 @@ "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1675,15 +1675,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "false" @@ -1703,7 +1700,7 @@ "val" : "http://purl.obolibrary.org/obo/RO_0002494" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1718,26 +1715,11 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" } ] }, "type" : "PROPERTY", "lbl" : "regulates transport of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002253", - "meta" : { - "definition" : { - "val" : "inverse of connecting branch of", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051" - } ] - }, - "type" : "PROPERTY", - "lbl" : "has connecting branch" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002132", "meta" : { @@ -1746,14 +1728,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" @@ -1767,6 +1749,21 @@ }, "type" : "PROPERTY", "lbl" : "has fasciculating neuron projection" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "meta" : { + "definition" : { + "val" : "inverse of connecting branch of", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has connecting branch" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002375", "meta" : { @@ -1789,12 +1786,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004036", "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1819,7 +1816,7 @@ "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1839,7 +1836,7 @@ "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1867,12 +1864,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.medindia.net/glossary/venous_tributary.htm" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Deschutes River tributary_of Columbia River" @@ -1902,15 +1899,15 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that ( some ( that some Y?)))" @@ -1918,6 +1915,21 @@ }, "type" : "PROPERTY", "lbl" : "innervates" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002497", + "meta" : { + "definition" : { + "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.", + "xrefs" : [ ] + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + }, + "type" : "PROPERTY", + "lbl" : "existence ends during or before" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002013", "meta" : { @@ -1945,7 +1957,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -1954,28 +1966,13 @@ "type" : "PROPERTY", "lbl" : "developmentally contributes to" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002497", + "id" : "http://purl.obolibrary.org/obo/RO_0002014", "meta" : { "definition" : { - "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.", + "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.", "xrefs" : [ ] }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "existence ends during or before" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002014", - "meta" : { - "definition" : { - "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.", - "xrefs" : [ ] - }, - "comments" : [ "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'." ], + "comments" : [ "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "dos" @@ -1995,10 +1992,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Melissa Haendel" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GO:0001759" @@ -2008,18 +2002,21 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "induced by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" } ] }, "type" : "PROPERTY", @@ -2035,7 +2032,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" @@ -2070,7 +2067,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2088,7 +2085,7 @@ "val" : "attached to (anatomical structure to anatomical structure)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2103,7 +2100,7 @@ "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2123,26 +2120,11 @@ "val" : "Wikipedia:Insertion_(anatomy)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", "lbl" : "has muscle origin" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002493", - "meta" : { - "definition" : { - "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).", - "xrefs" : [ ] - }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "existence ends with" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002130", "meta" : { @@ -2151,6 +2133,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { @@ -2159,9 +2144,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that some Y?)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" @@ -2172,6 +2154,21 @@ }, "type" : "PROPERTY", "lbl" : "has synaptic terminal in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002493", + "meta" : { + "definition" : { + "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).", + "xrefs" : [ ] + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + }, + "type" : "PROPERTY", + "lbl" : "existence ends with" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002131", "meta" : { @@ -2205,7 +2202,7 @@ "val" : "http://dbpedia.org/property/insertion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Wikipedia:Insertion_(anatomy)" @@ -2213,6 +2210,20 @@ }, "type" : "PROPERTY", "lbl" : "has muscle insertion" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + }, + "type" : "PROPERTY", + "lbl" : "transformation of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002252", "meta" : { @@ -2242,25 +2253,11 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" } ] }, "type" : "PROPERTY", "lbl" : "regulates in other organism" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002494", - "meta" : { - "definition" : { - "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "transformation of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002008", "meta" : { @@ -2272,7 +2269,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Note from NCEAS meeting: consider changing primary label" @@ -2292,7 +2289,7 @@ "val" : "x 'cell expresses' y iff:\ncell(x)\nAND gene(y)\nAND exists some 'transcription, DNA templated (GO_0006351)'(t)\nAND t occurs_in x\nAND t has_input y" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" } ] }, "type" : "PROPERTY", @@ -2306,7 +2303,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" } ] }, "type" : "PROPERTY", @@ -2320,7 +2317,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2343,7 +2340,7 @@ "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" } ] }, "type" : "PROPERTY", @@ -2357,7 +2354,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2393,7 +2390,7 @@ "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" } ] }, "type" : "PROPERTY", @@ -2409,7 +2406,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" } ] }, "type" : "PROPERTY", @@ -2471,23 +2468,23 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some (\n\t and some (\n\t http://purl.obolibrary.org/obo/GO_0042734 and some (\n\t and some ?Y)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" } ] }, "type" : "PROPERTY", @@ -2516,6 +2513,19 @@ }, "type" : "PROPERTY", "lbl" : "curator guidance link" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" + } ] + }, + "type" : "PROPERTY", + "lbl" : "receives input from" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002001", "meta" : { @@ -2527,7 +2537,7 @@ "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -2535,19 +2545,6 @@ }, "type" : "PROPERTY", "lbl" : "aligned with" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002485", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "See notes for inverse relation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "receives input from" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002243", "meta" : { @@ -2570,6 +2567,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_2D_boundary" }, { @@ -2584,9 +2584,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has boundary" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." @@ -2598,11 +2595,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002486", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2629,7 +2626,7 @@ "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2642,11 +2639,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" } ] }, "type" : "PROPERTY", @@ -2669,11 +2666,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2683,7 +2680,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2696,7 +2693,7 @@ "val" : "http://neurolex.org/wiki/Property:DendriteLocation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2720,7 +2717,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2736,21 +2733,21 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that part_of some ( that some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -2849,7 +2846,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2947,7 +2944,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2982,7 +2979,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2996,7 +2993,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -3044,7 +3041,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -3068,7 +3065,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Bill Duncan (https://orcid.org/0000-0001-9625-1899)" + "val" : "https://orcid.org/0000-0001-9625-1899" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." @@ -3089,6 +3086,9 @@ "xrefs" : [ ] } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-2620-0345" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" }, { @@ -3100,9 +3100,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A diagnostic testing device utilizes a specimen." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-2620-0345" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-11-08T12:00:00Z" @@ -3123,7 +3120,7 @@ "val" : "starts with process that occurs in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -3132,21 +3129,39 @@ "type" : "PROPERTY", "lbl" : "has start location" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002110", + "id" : "http://purl.obolibrary.org/obo/RO_0002473", "meta" : { "definition" : { - "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. ", + "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.", "xrefs" : [ ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + }, + "type" : "PROPERTY", + "lbl" : "composed primarily of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002110", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. ", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" @@ -3156,6 +3171,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "synapsed in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" @@ -3164,43 +3185,19 @@ "type" : "PROPERTY", "lbl" : "has postsynaptic terminal in" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "id" : "http://purl.obolibrary.org/obo/RO_0000052", "meta" : { "definition" : { - "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.", + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.", "xrefs" : [ ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" + "val" : "this red color is a characteristic of this apple" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "composed primarily of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000052", - "meta" : { - "definition" : { - "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.", - "xrefs" : [ ] - }, - "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this red color is a characteristic of this apple" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this fragility is a characteristic of this vase" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is a characteristic of this vase" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "inheres_in" @@ -3244,7 +3241,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -3260,12 +3257,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "ends with process that occurs in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -3295,7 +3292,7 @@ "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." @@ -3313,7 +3310,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -3343,56 +3340,56 @@ "type" : "PROPERTY", "lbl" : "dispositional interpretation" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002233", + "id" : "http://purl.obolibrary.org/obo/RO_0002112", "meta" : { "definition" : { - "val" : "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.", + "val" : "Relation between a muscle and a motor neuron that synapses to it via a type Is bouton.", "xrefs" : [ ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "consumes" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] }, "type" : "PROPERTY", - "lbl" : "has input" + "lbl" : "synapsed_by_via_type_Is_bouton" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002112", + "id" : "http://purl.obolibrary.org/obo/RO_0002233", "meta" : { "definition" : { - "val" : "Relation between a muscle and a motor neuron that synapses to it via a type Is bouton.", + "val" : "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.", "xrefs" : [ ] }, - "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Marta Costa" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "consumes" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", - "lbl" : "synapsed_by_via_type_Is_bouton" + "lbl" : "has input" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002596", "meta" : { @@ -3435,7 +3432,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -3485,14 +3482,14 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "produces" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -3507,12 +3504,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "ABal nucleus child nucleus of ABa nucleus (in C elegans)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -3540,7 +3537,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -3580,11 +3577,11 @@ "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is subject of eating interaction with" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -3625,7 +3622,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "eaten by" @@ -3656,7 +3653,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -3710,6 +3707,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "finished by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -3755,6 +3755,31 @@ }, "type" : "PROPERTY", "lbl" : "existence ends at start of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002349", + "meta" : { + "definition" : { + "val" : "p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment.", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + }, + "type" : "PROPERTY", + "lbl" : "results in determination of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002228", + "meta" : { + "definition" : { + "val" : "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "facultative parasite of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002107", "meta" : { @@ -3765,13 +3790,13 @@ "comments" : [ "Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Marta Costa" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -3782,16 +3807,6 @@ }, "type" : "PROPERTY", "lbl" : "synapsed_via_type_II_bouton_to" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002228", - "meta" : { - "definition" : { - "val" : "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host.", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "facultative parasite of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0001018", "meta" : { @@ -3818,21 +3833,6 @@ }, "type" : "PROPERTY", "lbl" : "contained in" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002349", - "meta" : { - "definition" : { - "val" : "p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment.", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "results in determination of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0001019", "meta" : { @@ -3861,6 +3861,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -3874,6 +3877,9 @@ }, "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" }, { @@ -3884,13 +3890,10 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Marta Costa" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" } ] }, "type" : "PROPERTY", @@ -3917,10 +3920,10 @@ "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Marta Costa" + "val" : "https://orcid.org/0000-0001-5948-3092" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" } ] }, "type" : "PROPERTY", @@ -3938,18 +3941,18 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -3974,35 +3977,38 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", "lbl" : "starts with" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002345", + "id" : "http://purl.obolibrary.org/obo/RO_0002466", "meta" : { - "definition" : { - "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s.", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", - "lbl" : "exports" + "lbl" : "is commensalism" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002466", + "id" : "http://purl.obolibrary.org/obo/RO_0002345", "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s.", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", - "lbl" : "is commensalism" + "lbl" : "exports" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002587", "type" : "PROPERTY", @@ -4022,29 +4028,29 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1617-8244" + }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9990-8331" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19243617" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alexander Diehl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Lindsay Cowell" } ] }, "type" : "PROPERTY", @@ -4058,7 +4064,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -4066,16 +4072,6 @@ }, "type" : "PROPERTY", "lbl" : "develops from part of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002467", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "is mutualism" }, { "id" : "http://purl.obolibrary.org/obo/RO_0001015", "meta" : { @@ -4105,6 +4101,16 @@ }, "type" : "PROPERTY", "lbl" : "location of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002467", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is mutualism" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002226", "meta" : { @@ -4115,15 +4121,15 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Jonathan Bard, EHDAA2" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "EHDAA2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -4139,45 +4145,45 @@ "type" : "PROPERTY", "lbl" : "results in catabolism of" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002468", + "id" : "http://purl.obolibrary.org/obo/RO_0002105", "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton.", + "xrefs" : [ ] + }, + "comments" : [ "Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "is parasitism" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002105", - "meta" : { - "definition" : { - "val" : "A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton.", - "xrefs" : [ ] - }, - "comments" : [ "Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], - "basicPropertyValues" : [ { + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Marta Costa" } ] }, "type" : "PROPERTY", "lbl" : "synapsed_via_type_Ib_bouton_to" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002468", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is parasitism" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002348", "meta" : { @@ -4191,7 +4197,7 @@ "val" : "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -4210,18 +4216,18 @@ }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Marta Costa" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" } ] }, "type" : "PROPERTY", @@ -4232,7 +4238,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -4274,15 +4280,15 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" @@ -4300,32 +4306,32 @@ "type" : "PROPERTY", "lbl" : "adjacent to" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002462", + "id" : "http://purl.obolibrary.org/obo/RO_0002341", "meta" : { + "definition" : { + "val" : "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l ", + "xrefs" : [ ] + }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", - "lbl" : "subject participant in" + "lbl" : "results in transport along" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002341", + "id" : "http://purl.obolibrary.org/obo/RO_0002462", "meta" : { - "definition" : { - "val" : "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l ", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", - "lbl" : "results in transport along" + "lbl" : "subject participant in" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002583", "meta" : { @@ -4358,7 +4364,7 @@ "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -4372,14 +4378,14 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -4392,7 +4398,7 @@ "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -4410,12 +4416,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some (\n and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" } ] }, "type" : "PROPERTY", @@ -4430,7 +4436,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -4456,7 +4462,7 @@ "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -4470,6 +4476,9 @@ "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" }, { @@ -4481,9 +4490,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -4496,7 +4502,7 @@ "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -4509,7 +4515,7 @@ "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -4534,19 +4540,6 @@ }, "type" : "PROPERTY", "lbl" : "results in breakdown of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002344", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" - } ] - }, - "type" : "PROPERTY", - "lbl" : "results in transport to from or in" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002102", "meta" : { @@ -4556,19 +4549,16 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some (\n and some (\n and some (\n and some ?Y)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" @@ -4588,6 +4578,9 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { @@ -4601,15 +4594,18 @@ "type" : "PROPERTY", "lbl" : "starts" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002465", + "id" : "http://purl.obolibrary.org/obo/RO_0002344", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", - "lbl" : "is symbiosis" + "lbl" : "results in transport to from or in" }, { "id" : "http://purl.obolibrary.org/obo/RO_0003311", "meta" : { @@ -4620,6 +4616,16 @@ }, "type" : "PROPERTY", "lbl" : "condition exacerbated by" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002465", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is symbiosis" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002580", "type" : "PROPERTY", @@ -4630,7 +4636,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -4645,6 +4651,19 @@ }, "type" : "PROPERTY", "lbl" : "is a defining property chain axiom" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002461", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" + } ] + }, + "type" : "PROPERTY", + "lbl" : "partner in" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002340", "meta" : { @@ -4655,7 +4674,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -4670,19 +4689,6 @@ }, "type" : "PROPERTY", "lbl" : "is a defining property chain axiom where second argument is reflexive" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002461", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "partner in" }, { "id" : "http://purl.obolibrary.org/obo/RO_0003307", "meta" : { @@ -4698,6 +4704,23 @@ }, "type" : "PROPERTY", "lbl" : "ameliorates condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002459", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Anopheles is a vector for Plasmodium" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is vector for" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002217", "meta" : { @@ -4707,11 +4730,11 @@ }, "comments" : [ "Obsoleted as the inverse property was obsoleted." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "agent in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "http://purl.obolibrary.org/obo/RO_0002608" @@ -4720,23 +4743,6 @@ }, "type" : "PROPERTY", "lbl" : "obsolete actively participates in" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002459", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Anopheles is a vector for Plasmodium" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "is vector for" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002338", "meta" : { @@ -4747,7 +4753,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -4762,7 +4768,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -4777,12 +4783,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has agent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "http://purl.obolibrary.org/obo/RO_0002500" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ], "deprecated" : true }, @@ -4802,16 +4808,6 @@ }, "type" : "PROPERTY", "lbl" : "contributes to frequency of condition" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003309", - "meta" : { - "definition" : { - "val" : "A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition.", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "exacerbates condition" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002219", "meta" : { @@ -4820,11 +4816,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" @@ -4832,6 +4828,16 @@ }, "type" : "PROPERTY", "lbl" : "surrounded by" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003309", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "exacerbates condition" }, { "id" : "http://purl.obolibrary.org/obo/RO_0003308", "meta" : { @@ -4843,20 +4849,23 @@ "type" : "PROPERTY", "lbl" : "correlated with condition" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002576", + "id" : "http://purl.obolibrary.org/obo/RO_0002334", "meta" : { "definition" : { - "val" : "inverse of has skeleton", + "val" : "inverse of regulates", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "skeleton of" + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulated by (processual)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "regulated by" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002213", "meta" : { @@ -4868,12 +4877,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "positively regulates (process to process)" @@ -4891,13 +4900,28 @@ }, "type" : "PROPERTY", "lbl" : "causes condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002576", + "meta" : { + "definition" : { + "val" : "inverse of has skeleton", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + }, + "type" : "PROPERTY", + "lbl" : "skeleton of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002455", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is subject of pollination interaction with" @@ -4914,24 +4938,6 @@ }, "type" : "PROPERTY", "lbl" : "pollinates" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002334", - "meta" : { - "definition" : { - "val" : "inverse of regulates", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulated by (processual)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "regulated by" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002456", "meta" : { @@ -4939,15 +4945,15 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has polinator" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is target of pollination interaction with" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://eol.org/schema/terms/hasPollinator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -4962,7 +4968,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -5000,7 +5006,7 @@ "val" : "http://www.jbiomedsem.com/content/4/1/43" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "CLASS", @@ -5015,9 +5021,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))" @@ -5030,6 +5033,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO: add homeomorphy axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" @@ -5046,6 +5052,9 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002575", "val" : "http://purl.obolibrary.org/obo/RO_0002211" }, { @@ -5054,9 +5063,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "directly regulates (processual)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -5070,7 +5076,7 @@ "val" : "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -5085,7 +5091,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -5109,7 +5115,7 @@ "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has function realized in" @@ -5149,7 +5155,7 @@ "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" }, { "pred" : "http://purl.org/dc/terms/creator", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -5177,7 +5183,7 @@ "val" : "http://eol.org/schema/terms/HasPredator" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://polytraits.lifewatchgreece.eu/terms/PRED" @@ -5192,42 +5198,42 @@ "type" : "PROPERTY", "lbl" : "preyed upon by" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "id" : "http://purl.obolibrary.org/obo/RO_0002337", "meta" : { "definition" : { - "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.", + "val" : "A relationship that holds via some process of localization", "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has function in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is a grouping relation." } ] }, "type" : "PROPERTY", - "lbl" : "capable of part of" + "lbl" : "related via localization to" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002337", + "id" : "http://purl.obolibrary.org/obo/RO_0002216", "meta" : { "definition" : { - "val" : "A relationship that holds via some process of localization", + "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.", "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function in" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is a grouping relation." + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" } ] }, "type" : "PROPERTY", - "lbl" : "related via localization to" + "lbl" : "capable of part of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002451", "meta" : { @@ -5238,12 +5244,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "all dengue disease transmitted by some mosquito" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Add domain and range constraints" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -5258,7 +5264,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -5275,7 +5281,7 @@ "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -5323,12 +5329,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "actively involved in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://wiki.geneontology.org/index.php/Involved_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -5361,7 +5367,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" @@ -5381,7 +5387,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -5391,38 +5397,15 @@ "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" - } ] - }, - "type" : "PROPERTY", - "lbl" : "participates in a biotic-biotic interaction with" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002332", - "meta" : { - "definition" : { - "val" : "p regulates levels of c if p regulates some amount (PATO:0000070) of c", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates levels of (process to entity)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", - "lbl" : "regulates levels of" + "lbl" : "participates in a biotic-biotic interaction with" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002211", "meta" : { @@ -5434,24 +5417,24 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GO" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Hill" + "val" : "https://orcid.org/0000-0001-7476-6306" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-3837-8864" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "false" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Tanya Berardini" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "regulates (processual)" @@ -5491,11 +5474,11 @@ "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -5509,15 +5492,38 @@ }, "comments" : [ "The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate." ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-1048-5019" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is used to study" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has role in modeling" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002332", + "meta" : { + "definition" : { + "val" : "p regulates levels of c if p regulates some amount (PATO:0000070) of c", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates levels of (process to entity)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Matthew Brush" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", - "lbl" : "has role in modeling" + "lbl" : "regulates levels of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002454", "meta" : { @@ -5531,7 +5537,7 @@ "val" : "http://eol.org/schema/terms/hasHost" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -5549,7 +5555,7 @@ "val" : "negatively regulates (process to process)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" @@ -5570,7 +5576,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -5590,7 +5596,7 @@ "val" : "If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'" }, { "pred" : "http://purl.org/dc/terms/creator", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" @@ -5607,14 +5613,14 @@ }, "comments" : [ "R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C." ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-10-21T19:46:34Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/oborel/obo-relations/issues/164" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "part-of is homeomorphic for independent continuants." @@ -5631,11 +5637,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "UBERON:cjm" @@ -5656,7 +5662,7 @@ "val" : "GOC:cjm" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -5675,10 +5681,10 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0003-4639-4431" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "directly activates" @@ -5686,6 +5692,28 @@ }, "type" : "PROPERTY", "lbl" : "directly positively regulates activity of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002448", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.", + "xrefs" : [ ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + }, + "type" : "PROPERTY", + "lbl" : "directly regulates activity of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002569", "meta" : { @@ -5696,7 +5724,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -5710,7 +5738,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" @@ -5722,38 +5750,19 @@ "type" : "PROPERTY", "lbl" : "expressed in" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002448", + "id" : "http://purl.obolibrary.org/obo/RO_0002327", "meta" : { "definition" : { - "val" : "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.", - "xrefs" : [ ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "molecularly controls", - "xrefs" : [ ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" - } ] - }, - "type" : "PROPERTY", - "lbl" : "directly regulates activity of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002327", - "meta" : { - "definition" : { - "val" : "c enables p iff c is capable of p and c acts to execute p.", + "val" : "c enables p iff c is capable of p and c acts to execute p.", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "executes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "catalyzes" @@ -5772,68 +5781,67 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", "lbl" : "enables" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "id" : "http://purl.obolibrary.org/obo/RO_0002207", "meta" : { "definition" : { - "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.", + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.", "xrefs" : [ ] }, + "comments" : [ "TODO - add child relations from DOS" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "molecularly decreases activity of", + "val" : "has developmental precursor", "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002202" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly inhibits" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "FBbt" } ] }, "type" : "PROPERTY", - "lbl" : "directly negatively regulates activity of" + "lbl" : "directly develops from" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "id" : "http://purl.obolibrary.org/obo/RO_0002449", "meta" : { "definition" : { - "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.", + "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.", "xrefs" : [ ] }, - "comments" : [ "TODO - add child relations from DOS" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly decreases activity of", + "xrefs" : [ ] + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "has developmental precursor" + "val" : "https://orcid.org/0000-0003-4639-4431" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002202" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly inhibits" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "FBbt" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", - "lbl" : "directly develops from" + "lbl" : "directly negatively regulates activity of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002328", "meta" : { @@ -5843,7 +5851,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" @@ -5863,7 +5871,7 @@ "val" : "false" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -5899,43 +5907,16 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] - }, - "type" : "PROPERTY", - "lbl" : "mereotopologically related to" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002202", - "meta" : { - "definition" : { - "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y", - "xrefs" : [ ] - }, - "comments" : [ "This is the transitive form of the develops from relation" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Terry Meehan" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Melissa Haendel" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", - "lbl" : "develops from" + "lbl" : "mereotopologically related to" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002444", "meta" : { @@ -5956,11 +5937,38 @@ "val" : "http://eol.org/schema/terms/parasitizes" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", "lbl" : "parasite of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y", + "xrefs" : [ ] + }, + "comments" : [ "This is the transitive form of the develops from relation" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + }, + "type" : "PROPERTY", + "lbl" : "develops from" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002565", "meta" : { @@ -5974,7 +5982,7 @@ "val" : "" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -5992,40 +6000,17 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0003-1980-3228" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Terry Meehan" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", "lbl" : "develops into" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002566", - "meta" : { - "definition" : { - "val" : "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "causally influences (entity-centric)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" - } ] - }, - "type" : "PROPERTY", - "lbl" : "causally influences" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002445", "meta" : { @@ -6036,6 +6021,9 @@ "xrefs" : [ ] } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has parasite" }, { @@ -6044,73 +6032,67 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "parasitised by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", "lbl" : "parasitized by" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "id" : "http://purl.obolibrary.org/obo/RO_0002566", "meta" : { "definition" : { - "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)", + "val" : "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).", "xrefs" : [ ] }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0003-4639-4431" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "causally influences (entity-centric)" } ] }, "type" : "PROPERTY", - "lbl" : "developmentally related to" + "lbl" : "causally influences" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002567", + "id" : "http://purl.obolibrary.org/obo/RO_0002324", "meta" : { "definition" : { - "val" : "A relation that holds between elements of a musculoskeletal system or its analogs.", + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)", "xrefs" : [ ] }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" } ] }, "type" : "PROPERTY", - "lbl" : "biomechanically related to" + "lbl" : "developmentally related to" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002446", + "id" : "http://purl.obolibrary.org/obo/RO_0002567", "meta" : { "definition" : { - "val" : "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored.", + "val" : "A relation that holds between elements of a musculoskeletal system or its analogs.", "xrefs" : [ ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "semibiotically interacts with", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Porifiera attaches to substrate" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", - "lbl" : "participates in a abiotic-biotic interaction with" + "lbl" : "biomechanically related to" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002325", "meta" : { @@ -6120,14 +6102,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "Gene Ontology Consortium" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" @@ -6147,7 +6126,7 @@ "val" : "We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -6156,21 +6135,47 @@ "type" : "PROPERTY", "lbl" : "gene product of" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002205", + "id" : "http://purl.obolibrary.org/obo/RO_0002446", "meta" : { "definition" : { - "val" : "x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y", + "val" : "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored.", "xrefs" : [ ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "semibiotically interacts with", + "xrefs" : [ ] + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Porifiera attaches to substrate" + } ] + }, + "type" : "PROPERTY", + "lbl" : "participates in a abiotic-biotic interaction with" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002205", + "meta" : { + "definition" : { + "val" : "x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "every HOTAIR lncRNA is the gene product of some HOXC gene" @@ -6185,9 +6190,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." @@ -6200,6 +6202,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -6212,11 +6217,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Wikipedia:Antagonist_(muscle)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -6227,12 +6232,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Axiomatization to GO to be added later" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -6312,14 +6317,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-09-26T00:00:32Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" } ] }, "type" : "PROPERTY", @@ -6333,11 +6338,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" @@ -6360,40 +6365,40 @@ "type" : "PROPERTY", "lbl" : "is symmetric relational form of process class" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002320", + "id" : "http://purl.obolibrary.org/obo/RO_0002441", "meta" : { "definition" : { - "val" : "A relationship that holds via some environmental process", + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO).", "xrefs" : [ ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", - "lbl" : "evolutionarily related to" + "lbl" : "commensually interacts with" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002441", + "id" : "http://purl.obolibrary.org/obo/RO_0002320", "meta" : { "definition" : { - "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO).", + "val" : "A relationship that holds via some environmental process", "xrefs" : [ ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", - "lbl" : "commensually interacts with" + "lbl" : "evolutionarily related to" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002562", "meta" : { @@ -6417,7 +6422,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-09-26T01:08:58Z" @@ -6425,6 +6430,22 @@ }, "type" : "PROPERTY", "lbl" : "results in changes to anatomical or cellular structure" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002563", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + }, + "type" : "PROPERTY", + "lbl" : "interaction relation helper property" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002321", "meta" : { @@ -6438,7 +6459,7 @@ "val" : "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" @@ -6459,7 +6480,7 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -6477,37 +6498,46 @@ "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", "lbl" : "mutualistically interacts with" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002563", + "id" : "http://purl.obolibrary.org/obo/RO_0002322", "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." } ] }, "type" : "PROPERTY", - "lbl" : "interaction relation helper property" + "lbl" : "confers advantage in" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002564", + "id" : "http://purl.obolibrary.org/obo/RO_0002201", "meta" : { + "definition" : { + "val" : "inverse of has phenotype", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] }, "type" : "PROPERTY", - "lbl" : "molecular interaction relation helper property" + "lbl" : "phenotype of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002443", "meta" : { @@ -6518,7 +6548,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" @@ -6528,42 +6558,17 @@ } ] }, "type" : "PROPERTY", - "lbl" : "interacts with via parasite-host interaction" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002201", - "meta" : { - "definition" : { - "val" : "inverse of has phenotype", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, - "type" : "PROPERTY", - "lbl" : "phenotype of" + "lbl" : "interacts with via parasite-host interaction" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002322", + "id" : "http://purl.obolibrary.org/obo/RO_0002564", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "adapted for" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", - "lbl" : "confers advantage in" + "lbl" : "molecular interaction relation helper property" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002560", "meta" : { @@ -6588,11 +6593,11 @@ "comments" : [ "x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x." ], "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/25052702" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -6613,7 +6618,7 @@ "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "interacts with on organism level" @@ -6634,7 +6639,7 @@ "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -6644,7 +6649,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" @@ -6672,28 +6677,42 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preys upon" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is subject of predation interaction with" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Jorrit Poelen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0001-7134-3324" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-3138-4118" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.inaturalist.org/observations/2942824" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Katja Shulz" } ] }, "type" : "PROPERTY", "lbl" : "preys on" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "meta" : { + "definition" : { + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + }, + "type" : "PROPERTY", + "lbl" : "contributes to morphology of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002554", "meta" : { @@ -6717,31 +6736,17 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", "lbl" : "hyperparasitized by" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002433", - "meta" : { - "definition" : { - "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "contributes to morphology of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002312", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -6762,15 +6767,15 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", "val" : "http://purl.obolibrary.org/obo/MI_0914" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." @@ -6786,14 +6791,14 @@ "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://en.wikipedia.org/wiki/Allelopathy" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://eol.org/schema/terms/allelopathyYes" @@ -6811,7 +6816,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "regulates localization of" @@ -6835,15 +6840,15 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "inheres in part of" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -6854,7 +6859,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -6873,11 +6878,37 @@ "val" : "http://purl.obolibrary.org/obo/ECO_0000316" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", "lbl" : "genetically interacts with" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002436", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "molecularly binds with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "binds" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0915" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ECO_0000353" + } ] + }, + "type" : "PROPERTY", + "lbl" : "molecularly interacts with" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002315", "meta" : { @@ -6887,14 +6918,14 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GOC:mtg_berkeley_2013" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -6905,37 +6936,11 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", "lbl" : "has pathogen" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002436", - "meta" : { - "definition" : { - "val" : "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "molecularly binds with" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "binds" - }, { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0915" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ECO_0000353" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "molecularly interacts with" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002550", "meta" : { @@ -6954,6 +6959,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" }, { @@ -6962,9 +6970,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -6978,7 +6983,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002428" @@ -6999,6 +7004,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-06-05T17:55:39Z" @@ -7008,50 +7016,47 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/oborel/obo-relations/pull/173" - }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "Chris Mungall" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "CLASS", "lbl" : "exposure event or process" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002552", + "id" : "http://purl.obolibrary.org/obo/RO_0002431", "meta" : { "definition" : { - "val" : "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded.", + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p", "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "involved in or reguates" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" } ] }, "type" : "PROPERTY", - "lbl" : "results in ending of" + "lbl" : "involved in or involved in regulation of" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "id" : "http://purl.obolibrary.org/obo/RO_0002552", "meta" : { "definition" : { - "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p", + "val" : "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded.", "xrefs" : [ ] }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "involved in or reguates" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "OWL does not allow defining object properties via a Union" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", - "lbl" : "involved in or involved in regulation of" + "lbl" : "results in ending of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002553", "meta" : { @@ -7077,7 +7082,7 @@ "val" : "http://eol.org/schema/terms/hyperparasitoidOf" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" @@ -7101,57 +7106,57 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "executes activity in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A protein that enables activity in a cytosol." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", "lbl" : "is active in" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002547", + "id" : "http://purl.obolibrary.org/obo/RO_0002305", "meta" : { "definition" : { - "val" : "Count of number of days intervening between the start of the stage and the time of coitum.", + "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.", "xrefs" : [ ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)" + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" } ] }, "type" : "PROPERTY", - "lbl" : "start, days post coitum" + "lbl" : "causally upstream of, negative effect" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002305", + "id" : "http://purl.obolibrary.org/obo/RO_0002547", "meta" : { "definition" : { - "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.", + "val" : "Count of number of days intervening between the start of the stage and the time of coitum.", "xrefs" : [ ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "cjm" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)" } ] }, "type" : "PROPERTY", - "lbl" : "causally upstream of, negative effect" + "lbl" : "start, days post coitum" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002426", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7165,11 +7170,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -7207,7 +7212,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7224,7 +7229,7 @@ "val" : "http://purl.obolibrary.org/obo/RO_0002428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7251,7 +7256,7 @@ "val" : "May be merged into parent relation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -7282,7 +7287,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/creator", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7300,11 +7305,28 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + }, + "type" : "PROPERTY", + "lbl" : "end, months post birth" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002424", + "meta" : { + "comments" : [ "This is an exploratory relation" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions" } ] }, "type" : "PROPERTY", - "lbl" : "end, months post birth" + "lbl" : "differs in" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002303", "meta" : { @@ -7315,11 +7337,11 @@ "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y." ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-4366-3088" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Pier Buttigieg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "adapted for living in" @@ -7330,23 +7352,6 @@ }, "type" : "PROPERTY", "lbl" : "has habitat" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002424", - "meta" : { - "comments" : [ "This is an exploratory relation" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "false" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "differs in" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002545", "meta" : { @@ -7372,7 +7377,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/creator", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002411" @@ -7399,7 +7404,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7472,20 +7477,20 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "Chris Mungall" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-06-05T17:35:04Z" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "Marie Angelique Laporte" + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "Austin Meier" + "val" : "https://orcid.org/0000-0002-8461-9745" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7546,28 +7551,18 @@ }, "type" : "PROPERTY", "lbl" : "end, years post birth" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002421", - "meta" : { - "definition" : { - "val" : "A logical macro assertion whose domain is an IRI for a property", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "logical macro assertion on a property" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002300", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "May be merged into parent relation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "foramen ovale closure SubClassOf results in disappearance of foramen ovale" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -7575,6 +7570,16 @@ }, "type" : "PROPERTY", "lbl" : "results in disappearance of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002421", + "meta" : { + "definition" : { + "val" : "A logical macro assertion whose domain is an IRI for a property", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "logical macro assertion on a property" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002536", "type" : "PROPERTY", @@ -7655,7 +7660,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" @@ -7690,7 +7695,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7704,7 +7709,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "CLASS", @@ -7717,11 +7722,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002575", "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -7735,7 +7740,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair." @@ -7752,7 +7757,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence." @@ -7773,15 +7778,15 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "directly provides input for (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "directly provides input for" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7796,12 +7801,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "transitively provides input for (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" @@ -7870,7 +7875,7 @@ "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7887,7 +7892,7 @@ "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" @@ -7903,14 +7908,14 @@ "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7927,7 +7932,7 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7943,12 +7948,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "contained by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7957,15 +7962,15 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002526", "meta" : { "definition" : { - "val" : "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y.", + "val" : "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y.", "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -7975,7 +7980,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" @@ -7987,18 +7992,18 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002527", "meta" : { "definition" : { - "val" : "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y.", + "val" : "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y.", "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "disconnected from" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -8023,14 +8028,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002579", "val" : "http://purl.obolibrary.org/obo/RO_0002213" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "indirectly activates" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -8043,11 +8048,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -8060,14 +8065,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -8080,14 +8085,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" @@ -8107,7 +8112,7 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ], "deprecated" : true }, @@ -8121,11 +8126,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" @@ -8146,11 +8151,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -8167,7 +8172,7 @@ "val" : "directly produces" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "translation SubClassOf has_direct_output some protein" @@ -8183,15 +8188,15 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002524", "meta" : { "definition" : { - "val" : "x has subsequence y iff all of the sequence parts of x are sequence parts of y", + "val" : "x has subsequence y iff all of the sequence parts of y are sequence parts of x", "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" @@ -8207,11 +8212,11 @@ "meta" : { "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ], "deprecated" : true }, @@ -8241,7 +8246,7 @@ "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -8254,11 +8259,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002579", "val" : "http://purl.obolibrary.org/obo/RO_0002212" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "indirectly inhibits" @@ -8289,7 +8294,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" @@ -8322,6 +8327,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" }, { @@ -8333,9 +8341,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -8357,15 +8362,15 @@ }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Two consecutive DNA residues are sequentially adjacent" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Two exons on a processed transcript that were previously connected by an intron are adjacent" @@ -8396,15 +8401,15 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "started by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -8448,12 +8453,12 @@ }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "starts" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -8467,7 +8472,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" @@ -8488,7 +8493,7 @@ "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -8507,23 +8512,6 @@ }, "type" : "PROPERTY", "lbl" : "ectoparasite of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002512", - "meta" : { - "definition" : { - "val" : "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" - } ] - }, - "type" : "PROPERTY", - "lbl" : "ribosomal translation of" }, { "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "meta" : { @@ -8552,21 +8540,38 @@ "type" : "PROPERTY", "lbl" : "has ectoparasite" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002513", + "id" : "http://purl.obolibrary.org/obo/RO_0002512", "meta" : { "definition" : { - "val" : "inverse of ribosomal translation of", + "val" : "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y", "xrefs" : [ ] }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" } ] }, "type" : "PROPERTY", + "lbl" : "ribosomal translation of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002513", + "meta" : { + "definition" : { + "val" : "inverse of ribosomal translation of", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + }, + "type" : "PROPERTY", "lbl" : "ribosomally translates to" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002634", @@ -8601,7 +8606,7 @@ "val" : "ended by" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" @@ -8632,11 +8637,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "ends" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" @@ -8680,14 +8685,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -8739,7 +8744,7 @@ "val" : "has intermediate product" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -8768,7 +8773,7 @@ "val" : "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -8801,12 +8806,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -8819,11 +8824,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002502", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/BFO_0000169" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -8832,22 +8837,6 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002623", "type" : "PROPERTY", "lbl" : "has flowers visited by" - }, { - "id" : "http://purl.obolibrary.org/obo/valid_for_go_gp2term", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-09-22T11:05:18Z" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/subsets/" - } ] - }, - "type" : "PROPERTY", - "lbl" : "valid_for_go_gp2term" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002507", "meta" : { @@ -8857,30 +8846,46 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "determined by (system to material entity)" }, { "pred" : "http://purl.org/dc/terms/creator", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-4366-3088" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/24330602" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A coral reef environment is determined by a particular coral reef" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" - }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "Pier Buttigieg" } ] }, "type" : "PROPERTY", "lbl" : "determined by" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_gp2term", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pg" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-09-22T11:05:18Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/subsets/" + } ] + }, + "type" : "PROPERTY", + "lbl" : "valid_for_go_gp2term" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002629", "meta" : { @@ -8912,7 +8917,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "determines (material entity to system)" @@ -8930,7 +8935,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -9058,14 +9063,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Damion Dooley" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'egg white' 'has substance removed' some 'egg yolk'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" } ] }, "type" : "PROPERTY", @@ -9079,7 +9084,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Damion Dooley" + "val" : "https://orcid.org/0000-0002-8844-9165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "muffin 'has substance added' some 'baking soda'" @@ -9218,7 +9223,7 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Damion Dooley" + "val" : "https://orcid.org/0000-0002-8844-9165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "bread 'has primary substance added' some 'flour'" @@ -9236,12 +9241,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "sardine has consumer some homo sapiens" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Damion Dooley" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" } ] }, "type" : "PROPERTY", @@ -9258,7 +9263,7 @@ "val" : "sardines 'immersed in' some 'oil and mustard'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Damion Dooley" + "val" : "https://orcid.org/0000-0002-8844-9165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" @@ -9277,12 +9282,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -9332,15 +9337,15 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" } ], "deprecated" : true }, @@ -9405,7 +9410,7 @@ "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -10552,7 +10557,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -10566,7 +10571,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -10580,7 +10585,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -10594,7 +10599,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -10608,7 +10613,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -10622,7 +10627,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -10777,7 +10782,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -10794,7 +10799,7 @@ "val" : "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -10811,7 +10816,7 @@ "val" : "indirectly inhibits" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -10828,7 +10833,7 @@ "val" : "indirectly activates" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -10845,7 +10850,7 @@ "val" : "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -11019,7 +11024,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -11097,7 +11102,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -11111,7 +11116,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -11133,14 +11138,6 @@ }, "type" : "PROPERTY", "lbl" : "has driver" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004096", - "meta" : { - "comments" : [ "DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information." ], - "deprecated" : true - }, - "type" : "PROPERTY", - "lbl" : "DEPRECATED inheres in" }, { "id" : "http://purl.obolibrary.org/obo/RO_0011024", "meta" : { @@ -11150,11 +11147,19 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", "lbl" : "indirectly positively regulates quantity of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004096", + "meta" : { + "comments" : [ "DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information." ], + "deprecated" : true + }, + "type" : "PROPERTY", + "lbl" : "DEPRECATED inheres in" }, { "id" : "http://purl.obolibrary.org/obo/RO_HOM0000048", "meta" : { @@ -12164,19 +12169,6 @@ }, "type" : "PROPERTY", "lbl" : "has synaptic IO in region" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004050", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-03-14T00:03:24Z" - } ] - }, - "type" : "PROPERTY", - "lbl" : "is negative form of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0013007", "meta" : { @@ -12207,6 +12199,19 @@ }, "type" : "PROPERTY", "lbl" : "has sensory dendrite in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004050", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:24Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is negative form of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0013006", "meta" : { @@ -12307,28 +12312,28 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "Marie Angelique Laporte" + "val" : "https://orcid.org/0000-0001-6996-0040" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-8461-9745" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "Austin Meier" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7073-9172" } ] }, "type" : "PROPERTY", @@ -12342,7 +12347,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:19Z" @@ -12357,11 +12362,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004046", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:05Z" @@ -12373,11 +12378,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004049", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-14T00:03:16Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -12394,7 +12399,7 @@ "val" : "2018-03-13T23:59:29Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -12532,6 +12537,23 @@ }, "type" : "PROPERTY", "lbl" : "happens during" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004030", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:58:44Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "disease arises from alteration in structure" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002093", "meta" : { @@ -12550,23 +12572,6 @@ }, "type" : "PROPERTY", "lbl" : "ends during" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004030", - "meta" : { - "definition" : { - "val" : "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-12-26T19:58:44Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - } ] - }, - "type" : "PROPERTY", - "lbl" : "disease arises from alteration in structure" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000015", "meta" : { @@ -12605,6 +12610,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002575", "val" : "http://purl.obolibrary.org/obo/BFO_0000063" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" @@ -12621,7 +12629,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -12635,11 +12643,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-01-26T23:53:22Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002263" @@ -12656,7 +12664,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" @@ -12682,7 +12690,7 @@ "val" : "2018-01-25T23:20:13Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -12700,7 +12708,7 @@ "val" : "http://purl.obolibrary.org/obo/RO_0002263" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" @@ -12720,7 +12728,7 @@ "val" : "http://purl.obolibrary.org/obo/RO_0002264" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-01-26T23:49:51Z" @@ -12728,16 +12736,6 @@ }, "type" : "PROPERTY", "lbl" : "acts upstream of or within, negative effect" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0008508", - "meta" : { - "definition" : { - "val" : "inverse of lays eggs on", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "has eggs laid on by" }, { "id" : "http://purl.obolibrary.org/obo/RO_0004029", "meta" : { @@ -12747,7 +12745,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-26T19:50:53Z" @@ -12755,6 +12753,16 @@ }, "type" : "PROPERTY", "lbl" : "disease has feature" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008508", + "meta" : { + "definition" : { + "val" : "inverse of lays eggs on", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has eggs laid on by" }, { "id" : "http://purl.obolibrary.org/obo/RO_0008507", "meta" : { @@ -12774,7 +12782,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-26T19:45:49Z" @@ -12839,6 +12847,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" } ] }, "type" : "PROPERTY", @@ -12884,11 +12895,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004025", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "disease causes dysfunction of (disease to anatomical entity)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:58:20Z" @@ -12934,7 +12945,7 @@ "val" : "2017-11-05T03:51:09Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "disease causes disruption of (disease to process)" @@ -12976,7 +12987,7 @@ "val" : "2017-12-26T19:37:31Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -12991,12 +13002,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T04:06:02Z" @@ -13028,12 +13039,12 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:37:52Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "disease has basis in disruption of (disease to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -13056,7 +13067,7 @@ "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "di" @@ -13079,7 +13090,7 @@ "val" : "2017-11-05T03:29:32Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -13089,7 +13100,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." @@ -13135,7 +13146,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:46:07Z" @@ -13151,7 +13162,7 @@ "val" : "2017-11-05T03:20:29Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -13160,11 +13171,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004017", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:20:01Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" } ] }, "type" : "PROPERTY", @@ -13177,7 +13188,7 @@ "val" : "2017-11-05T03:26:47Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -13228,14 +13239,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.orpha.net/ORDO/Orphanet_317344" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:57:07Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" } ] }, "type" : "PROPERTY", @@ -13248,11 +13259,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:56:40Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.orpha.net/ORDO/Orphanet_317343" @@ -13272,7 +13283,7 @@ "val" : "2017-11-05T02:58:43Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.orpha.net/ORDO/Orphanet_317346" @@ -13290,12 +13301,12 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:57:43Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.orpha.net/ORDO/Orphanet_317345" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" } ] }, "type" : "PROPERTY", @@ -13306,12 +13317,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a more specific relations" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:53:08Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -13331,7 +13342,7 @@ "val" : "2017-11-05T02:56:06Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -13345,7 +13356,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:55:51Z" @@ -13369,7 +13380,7 @@ "val" : "2018-12-13T11:26:17Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -13378,11 +13389,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004006", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:46:57Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -13396,11 +13407,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:56Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -13418,7 +13429,7 @@ "val" : "2018-12-13T11:26:32Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -13468,11 +13479,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004003", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.orpha.net/ORDO/Orphanet_317343" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:45:54Z" @@ -13488,7 +13499,7 @@ "val" : "2017-11-05T02:45:37Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -13497,11 +13508,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004005", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:46:26Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" } ] }, "type" : "PROPERTY", @@ -13510,11 +13521,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004004", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:46:07Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.orpha.net/ORDO/Orphanet_317344" @@ -13526,11 +13537,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004001", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:45:20Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.orpha.net/ORDO/Orphanet_410296" @@ -13545,11 +13556,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004000", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:38:20Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a more specific relations" @@ -13562,7 +13573,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Patrick Ray" + "val" : "https://orcid.org/0000-0002-5260-9315" } ] }, "type" : "PROPERTY", @@ -13576,7 +13587,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Shawn Tan" + "val" : "https://orcid.org/0000-0001-7258-9596" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." @@ -13662,7 +13673,7 @@ "val" : "C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Patrick Ray" + "val" : "https://orcid.org/0000-0002-5260-9315" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation is not meant to capture the relation between occurrents and data." @@ -13970,6 +13981,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004047", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004005", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0004000" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002411", "pred" : "subPropertyOf", @@ -13978,10 +13993,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002016", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002017" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0004005", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0004000" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0010001", "pred" : "inverseOf", @@ -14130,14 +14141,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004028", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002410" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002381", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002488", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002490" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002381", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0001023", "pred" : "subPropertyOf", @@ -14426,14 +14437,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012006", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012004" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000022", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000011" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002230", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000022", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000011" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002590", "pred" : "subPropertyOf", @@ -14470,14 +14481,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002339", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002344" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002209", "pred" : "subPropertyOf", @@ -14634,26 +14645,26 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002455", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002442" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002252", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002375" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002466", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002465" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002252", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002375" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002263", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002264" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002310", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000007", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002310", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0011014", "pred" : "subPropertyOf", @@ -14970,14 +14981,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002533", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/RO_0002532" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002260", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000087" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002022", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002334" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002260", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000087" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000012", "pred" : "subPropertyOf", @@ -15374,14 +15385,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004006", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0004016" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002180", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002231", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002479" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002180", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013005", "pred" : "subPropertyOf", @@ -15394,10 +15405,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002088", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002091" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0004012", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0004010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002007", "pred" : "subPropertyOf", @@ -15406,6 +15413,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004024", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0004023" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004012", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0004010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002525", "pred" : "subPropertyOf", @@ -15438,6 +15449,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000062", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002087", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002090" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002085", "pred" : "inverseOf", @@ -15446,10 +15461,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002084", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002093" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002087", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002090" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0011004", "pred" : "subPropertyOf", @@ -15470,26 +15481,26 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002004", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0001018" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002458", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002476", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002258" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002458", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002438" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002233", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002006", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002130" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0001020", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0001022" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002006", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002130" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002622", "pred" : "inverseOf", @@ -15938,14 +15949,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000045", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002585", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002618", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002574" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002585", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002623", "pred" : "subPropertyOf", @@ -16146,14 +16157,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012009", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002304" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002177", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002323" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003305", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002177", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002323" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002551", "pred" : "inverseOf", @@ -16270,14 +16281,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0013003", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0013001" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002026", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002323" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002286", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002384" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002026", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002323" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000050", "pred" : "inverseOf", @@ -16314,14 +16325,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002355", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0040036" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0004015", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0004010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002256", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002258" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004015", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0004010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002254", "pred" : "inverseOf", @@ -16346,14 +16357,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002237", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002444" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002014", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002013" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000063", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002222" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002013" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002377", "pred" : "subPropertyOf", @@ -16663,17 +16674,17 @@ "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002461" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002297", + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000060", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002295" + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000050" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000065", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000000" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000060", + "sub" : "http://purl.obolibrary.org/obo/RO_0002297", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000050" + "obj" : "http://purl.obolibrary.org/obo/RO_0002295" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002331", "pred" : "subPropertyOf", @@ -16698,14 +16709,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002641", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002635" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002091", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002222" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002326", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002329" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002091", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002222" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002512", "pred" : "inverseOf", @@ -16754,14 +16765,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004002", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0004000" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002223", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004009", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002233" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002223", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002252", "pred" : "subPropertyOf", @@ -16943,7 +16954,7 @@ "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : " https://github.com/oborel/obo-relations/" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-01-04/ro-base.owl" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-02-19/ro-base.owl" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ ], @@ -17038,33 +17049,33 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000050", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000019", + "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000019" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000031", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", + "sub" : "http://purl.obolibrary.org/obo/BFO_0000019", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000019" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", + "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -17207,13 +17218,13 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_HOM0000000", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", - "pred" : "http://purl.obolibrary.org/obo/RO_HOM0000000", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", "pred" : "http://purl.obolibrary.org/obo/RO_HOM0000000", "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", + "pred" : "http://purl.obolibrary.org/obo/RO_HOM0000000", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002414", diff --git a/ro-base.obo b/ro-base.obo index e00e1627..ac913ed9 100644 --- a/ro-base.obo +++ b/ro-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: ro/releases/2023-01-04/ro-base.owl +data-version: ro/releases/2023-02-19/ro-base.owl subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -135,12 +135,12 @@ id: RO:0002310 name: exposure event or process def: "A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." [] is_a: BFO:0000015 ! process -property_value: http://purl.org/dc/terms/creator "Chris Mungall" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," xsd:string property_value: IAO:0000112 "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes." xsd:anyURI property_value: IAO:0000116 "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions." xsd:string property_value: seeAlso https://github.com/oborel/obo-relations/pull/173 xsd:anyURI -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:55:39Z [Term] @@ -148,14 +148,14 @@ id: RO:0002532 name: sequentially ordered entity def: "Any entity that is ordered in discrete units along a linear axis." [] relationship: RO:0002524 RO:0002533 ! has subsequence sequence atomic unit -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 [Term] id: RO:0002533 name: sequence atomic unit def: "Any individual unit of a collection of like units arranged in a linear order" [] is_a: RO:0002532 ! sequentially ordered entity -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair." xsd:string [Term] @@ -163,7 +163,7 @@ id: RO:0002534 name: sequence bearer def: "Any entity that can be divided into parts such that each part is an atomical unit of a sequence" [] is_a: RO:0002532 ! sequentially ordered entity -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence." xsd:string [Term] @@ -172,7 +172,7 @@ name: system def: "A material entity consisting of multiple components that are causally integrated." [] is_a: BFO:0000040 ! material entity property_value: IAO:0000116 "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.jbiomedsem.com/content/4/1/43 xsd:string [Typedef] @@ -488,7 +488,7 @@ def: "OBSOLETE A relation that holds between two neurons connected directly via comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_transitive: true is_obsolete: true @@ -500,7 +500,7 @@ def: "OBSOLETE A relation that holds between a neuron that is synapsed_to anothe comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_transitive: true is_obsolete: true @@ -512,7 +512,7 @@ def: "OBSOLETE A relation that holds between a neuron that is synapsed_by anothe comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_transitive: true is_obsolete: true @@ -647,7 +647,7 @@ id: RO:0002001 name: aligned with property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "May be obsoleted, see https://github.com/oborel/obo-relations/issues/260" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_transitive: true @@ -658,7 +658,7 @@ def: "a relation between a material entity and a 2D immaterial entity (the bound property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has boundary" xsd:string property_value: IAO:0000118 "has_2D_boundary" xsd:string property_value: RO:0001900 RO:0001901 @@ -671,14 +671,14 @@ id: RO:0002003 name: electrically_synapsed_to def: "A relation that holds between two neurons that are electrically coupled via gap junctions." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0002170 ! connected to [Typedef] id: RO:0002004 name: tracheates def: "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to)." [] -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: CARO:0000003 range: CARO:0000003 is_a: RO:0001018 ! contained in @@ -687,7 +687,7 @@ is_a: RO:0001018 ! contained in id: RO:0002005 name: innervated_by property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: CARO:0000003 range: CARO:0001001 inverse_of: RO:0002134 ! innervates @@ -696,7 +696,7 @@ inverse_of: RO:0002134 ! innervates id: RO:0002006 name: has synaptic terminal of property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0002131 ! overlaps inverse_of: RO:0002130 ! has synaptic terminal in @@ -706,7 +706,7 @@ name: bounding layer of def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" [] comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 ! material entity is_a: BFO:0000050 ! part of @@ -717,7 +717,7 @@ def: "A relation that holds between two linear structures that are approximately comment: Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. subset: ro-eco property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0002323 ! mereotopologically related to [Typedef] @@ -725,7 +725,7 @@ id: RO:0002009 name: cell expresses def: "A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g." [] property_value: http://purl.org/dc/terms/description "x 'cell expresses' y iff:\ncell(x)\nAND gene(y)\nAND exists some 'transcription, DNA templated (GO_0006351)'(t)\nAND t occurs_in x\nAND t has_input y" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: CL:0000000 is_a: RO:0002292 ! expresses @@ -733,7 +733,7 @@ is_a: RO:0002292 ! expresses id: RO:0002010 name: regulates in other organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 ! process range: BFO:0000015 ! process is_a: RO:0002418 ! causally upstream of or within @@ -743,7 +743,7 @@ id: RO:0002011 name: regulates transport of def: "A relationship that holds between a process that regulates a transport process and the entity transported by that process." [] subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 holds_over_chain: RO:0002211 RO:0002313 [Typedef] @@ -897,6 +897,7 @@ name: simultaneous with comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_transitive: true is_a: RO:0002081 ! before or simultaneous with @@ -922,7 +923,7 @@ inverse_of: RO:0002093 ! ends during id: RO:0002085 name: encompasses comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "di" xsd:string is_transitive: true is_a: RO:0002088 ! during which starts @@ -972,6 +973,7 @@ name: immediately precedes comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "ends_at_start_of" xsd:string property_value: IAO:0000118 "meets" xsd:string property_value: RO:0002575 BFO:0000063 @@ -1019,7 +1021,7 @@ id: RO:0002100 name: has soma location def: "Relation between a neuron and an anatomical structure that its soma is part of." [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 range: CARO:0000003 @@ -1033,7 +1035,7 @@ name: fasciculates with def: "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 @@ -1048,9 +1050,8 @@ name: axon synapses in def: "Relation between a neuron and some structure its axon forms (chemical) synapses in." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: RO:0002113 ! has presynaptic terminal in @@ -1063,8 +1064,8 @@ name: synapsed by def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002485 ! receives input from inverse_of: RO:0002120 ! synapsed to @@ -1076,9 +1077,9 @@ name: has plasma membrane part def: "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." [] property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Alexander Diehl" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 @@ -1093,8 +1094,8 @@ def: "A relation between a motor neuron and a muscle that it synapses to via a t comment: Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002120 ! synapsed to inverse_of: RO:0002109 ! synapsed_by_via_type_Ib_bouton @@ -1107,8 +1108,8 @@ def: "A relation between a motor neuron and a muscle that it synapses to via a t comment: Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002120 ! synapsed to inverse_of: RO:0002112 ! synapsed_by_via_type_Is_bouton @@ -1120,8 +1121,8 @@ name: synapsed_via_type_II_bouton_to def: "A relation between a motor neuron and a muscle that it synapses to via a type II bouton." [] comment: Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002120 ! synapsed to inverse_of: RO:0002108 ! synapsed_by_via_type_II_bouton @@ -1134,8 +1135,8 @@ def: "Relation between a muscle and a motor neuron that synapses to it via a typ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002103 ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" [] @@ -1147,8 +1148,8 @@ def: "Relation between a muscle and a motor neuron that synapses to it via a typ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002103 ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -1159,8 +1160,8 @@ name: has postsynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "synapsed in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -1184,8 +1185,8 @@ def: "Relation between a muscle and a motor neuron that synapses to it via a typ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002103 ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -1231,8 +1232,8 @@ def: " Relation between a neuron and an anatomical structure (including cells) t comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n ‘synapse ; GO:0045202’ that has_part some (\n ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002486 ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -1243,8 +1244,8 @@ name: dendrite synapsed in def: "Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.\n\n " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: RO:0002110 ! has postsynaptic terminal in @@ -1257,7 +1258,7 @@ name: has synaptic terminal in def: "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has synapse in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -1288,7 +1289,7 @@ name: has fasciculating neuron projection def: "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 @@ -1301,7 +1302,7 @@ name: innervates def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CARO:0001001 transitive_over: BFO:0000050 ! part of @@ -1312,7 +1313,7 @@ id: RO:0002150 name: continuous with def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 @@ -1381,7 +1382,7 @@ def: "x only in taxon y if and only if x is in taxon y, and there is no other or property_value: IAO:0000112 "lactation SubClassOf 'only in taxon' some 'Mammalia'" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints @@ -1394,8 +1395,8 @@ def: "x is in taxon y if an only if y is an organism, and the relationship betwe comment: Connects a biological entity to its taxon of origin. subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Jennifer Deegan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints @@ -1418,7 +1419,7 @@ def: "A is spatially_disjoint_from B if and only if they have no parts in common subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 @@ -1493,7 +1494,7 @@ name: has phenotype def: "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: UPHENO:0001001 is_a: RO:0016001 ! has phenotype or disease inverse_of: RO:0002201 ! phenotype of @@ -1505,7 +1506,7 @@ def: "inverse of has phenotype" [] subset: ro-eco subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_functional: true [Typedef] @@ -1514,10 +1515,10 @@ name: develops from def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] comment: This is the transitive form of the develops from relation property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_transitive: true @@ -1530,9 +1531,9 @@ name: develops into def: "inverse of develops from" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 is_transitive: true is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002387 ! has potential to develop into @@ -1544,7 +1545,7 @@ name: gene product of def: "definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\"" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000004 ! independent continuant range: BFO:0000002 ! continuant holds_over_chain: RO:0002512 RO:0002510 @@ -1558,7 +1559,7 @@ def: "x has gene product y if and only if x is a gene (SO:0000704) that particip property_value: IAO:0000112 "every HOTAIR lncRNA is the gene product of some HOXC gene" xsd:string property_value: IAO:0000112 "every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000002 ! continuant range: BFO:0000004 ! independent continuant holds_over_chain: RO:0002511 RO:0002513 @@ -1570,7 +1571,7 @@ name: expressed in def: "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" [] property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000002 ! continuant range: CARO:0000006 is_a: RO:0002330 ! genomically related to @@ -1582,10 +1583,10 @@ id: RO:0002207 name: directly develops from def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "has developmental precursor" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000119 "FBbt" xsd:string property_value: RO:0002575 RO:0002202 is_a: RO:0002202 ! develops from @@ -1621,9 +1622,9 @@ def: "p regulates q iff p is causally upstream of q, the execution of p is not c subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Hill" xsd:string -property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 +property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string @@ -1645,7 +1646,7 @@ def: "p negatively regulates q iff p regulates q, and p decreases the rate or ma subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 @@ -1661,7 +1662,7 @@ def: "p positively regulates q iff p regulates q, and p increases the rate or ma subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002211 @@ -1682,7 +1683,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" xsd:string property_value: IAO:0000116 "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants." xsd:string property_value: IAO:0000116 "TODO: add homeomorphy axiom" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 [Typedef] id: RO:0002215 @@ -1691,7 +1692,7 @@ def: "A relation between a material entity (such as a cell) and a process, in wh subset: ro-eco property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 @@ -1704,7 +1705,7 @@ is_a: RO:0002216 ! capable of part of id: RO:0002216 name: capable of part of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} @@ -1716,7 +1717,7 @@ id: RO:0002217 name: obsolete actively participates in def: "OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role" [] comment: Obsoleted as the inverse property was obsoleted. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "agent in" xsd:string is_obsolete: true replaced_by: RO:0002608 @@ -1725,7 +1726,7 @@ replaced_by: RO:0002608 id: RO:0002218 name: obsolete has active participant def: "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has agent" xsd:string is_obsolete: true replaced_by: RO:0002500 @@ -1735,7 +1736,7 @@ id: RO:0002219 name: surrounded by def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: RO:0002220 ! adjacent to inverse_of: RO:0002221 ! surrounds @@ -1753,7 +1754,7 @@ property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cy property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant @@ -1765,7 +1766,7 @@ name: surrounds def: "inverse of surrounded by" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: RO:0002220 ! adjacent to @@ -1776,7 +1777,7 @@ comment: A relation that holds between two occurrents. This is a grouping relati subset: ro-eco property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string domain: BFO:0000003 ! occurrent @@ -1789,6 +1790,7 @@ def: "inverse of starts with" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Allen" xsd:string is_a: BFO:0000050 ! part of is_a: RO:0002222 ! temporally related to @@ -1802,6 +1804,7 @@ subset: ro-eco property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string is_transitive: true is_a: BFO:0000051 ! has part @@ -1812,7 +1815,7 @@ id: RO:0002225 name: develops from part of def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002207 BFO:0000050 is_a: RO:0002202 ! develops from @@ -1821,7 +1824,7 @@ id: RO:0002226 name: develops in def: "x develops_in y if x is located in y whilst x is developing" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string domain: CARO:0000000 @@ -1847,6 +1850,7 @@ def: "inverse of ends with" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: BFO:0000050 ! part of is_a: RO:0002222 ! temporally related to inverse_of: RO:0002230 ! ends with @@ -1858,6 +1862,7 @@ def: "x ends with y if and only if x has part y and the time point at which x en subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "finished by" xsd:string is_transitive: true is_a: BFO:0000051 ! has part @@ -1869,7 +1874,7 @@ name: has start location def: "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant @@ -1882,7 +1887,7 @@ name: has end location def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant @@ -1898,7 +1903,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 ! process holds_over_chain: RO:0002224 RO:0002233 @@ -1914,7 +1919,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string holds_over_chain: RO:0002230 RO:0002234 is_a: RO:0000057 ! has participant @@ -1942,7 +1947,7 @@ is_a: RO:0002444 ! parasite of id: RO:0002238 name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] -property_value: IAO:0000117 "Bill Duncan (https://orcid.org/0000-0001-9625-1899)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: RO:0000057 ! has participant @@ -2038,7 +2043,7 @@ name: has developmental contribution from def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 holds_over_chain: BFO:0000051 RO:0002202 @@ -2051,7 +2056,7 @@ name: developmentally contributes to def: "inverse of has developmental contribution from" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002203 BFO:0000050 is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002385 ! has potential to developmentally contribute to @@ -2061,9 +2066,9 @@ id: RO:0002256 name: developmentally induced by def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string property_value: IAO:0000119 GO:0001759 xsd:string @@ -2079,7 +2084,7 @@ id: RO:0002257 name: developmentally induces def: "Inverse of developmentally induced by" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002386 ! has potential to developmentally induce @@ -2090,7 +2095,7 @@ def: "Candidate definition: x developmentally related to y if and only if there comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant @@ -2142,7 +2147,7 @@ name: developmentally replaces def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "replaces" xsd:string is_a: RO:0002258 ! developmentally preceded by @@ -2151,7 +2156,7 @@ id: RO:0002286 name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] @@ -2159,7 +2164,7 @@ id: RO:0002287 name: part of developmental precursor of property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000050 RO:0002210 is_a: RO:0002286 ! developmentally succeeded by @@ -2169,7 +2174,7 @@ name: ubiquitously expressed in def: "x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002206 ! expressed in inverse_of: RO:0002293 ! ubiquitously expresses @@ -2178,7 +2183,7 @@ id: RO:0002292 name: expresses def: "Inverse of 'expressed in'" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002330 ! genomically related to [Typedef] @@ -2187,7 +2192,7 @@ name: ubiquitously expresses def: "inverse of ubiquiotously expressed in" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002292 ! expresses [Typedef] @@ -2196,7 +2201,7 @@ name: results in developmental progression of def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 range: CARO:0000000 @@ -2211,7 +2216,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2225,7 +2230,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: RO:0002234 ! has output is_a: RO:0002295 ! results in developmental progression of @@ -2241,7 +2246,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2256,7 +2261,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2266,7 +2271,7 @@ id: RO:0002300 name: results in disappearance of property_value: IAO:0000112 "foramen ovale closure SubClassOf results in disappearance of foramen ovale" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: RO:0002552 ! results in ending of @@ -2275,7 +2280,7 @@ id: RO:0002301 name: results in developmental regression of property_value: IAO:0000112 "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: RO:0002552 ! results in ending of @@ -2284,7 +2289,7 @@ id: RO:0002302 name: is treated by substance def: "Inverse of 'is substance that treats'" [] subset: RO:0002259 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 is_a: RO:0002410 ! causally related to inverse_of: RO:0002606 ! is substance that treats @@ -2296,7 +2301,7 @@ comment: A population of xs will possess adaptations (either evolved naturally o subset: ro-eco property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Pier Buttigieg" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string domain: CARO:0001010 range: ENVO:01000254 @@ -2309,7 +2314,7 @@ def: "p is causally upstream of, positive effect q iff p is casually upstream of comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 is_a: RO:0002411 ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -2320,7 +2325,7 @@ name: causally upstream of, negative effect def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 is_a: RO:0002411 ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect @@ -2329,17 +2334,17 @@ is_a: RO:0004046 ! causally upstream of or within, negative effect id: RO:0002309 name: has exposure stimulus def: "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." [] -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 is_a: RO:0002244 ! related via exposure to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:35:04Z [Typedef] id: RO:0002312 name: evolutionary variant of -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002320 ! evolutionarily related to [Typedef] @@ -2349,7 +2354,7 @@ def: "Holds between p and c when p is a localization process (localization cover subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "regulates localization of" xsd:string is_a: RO:0002337 ! related via localization to is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2359,7 +2364,7 @@ id: RO:0002314 name: characteristic of part of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 @@ -2376,7 +2381,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string range: CARO:0000003 is_a: RO:0002295 ! results in developmental progression of @@ -2386,7 +2391,7 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure id: RO:0002320 name: evolutionarily related to def: "A relationship that holds via some environmental process" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." xsd:string [Typedef] @@ -2395,7 +2400,7 @@ name: ecologically related to def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] subset: ro-eco property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string [Typedef] @@ -2403,7 +2408,7 @@ id: RO:0002322 name: confers advantage in subset: ro-eco property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "adapted for" xsd:string range: ENVO:01000254 is_a: RO:0002321 ! ecologically related to @@ -2412,7 +2417,7 @@ is_a: RO:0002321 ! ecologically related to id: RO:0002323 name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string property_value: RO:0001900 RO:0001901 @@ -2420,7 +2425,7 @@ property_value: RO:0001900 RO:0001901 id: RO:0002324 name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] @@ -2428,9 +2433,8 @@ id: RO:0002325 name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -2444,7 +2448,7 @@ property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a het property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string is_a: RO:0002216 ! capable of part of is_a: RO:0002329 ! part of structure that is capable of @@ -2455,7 +2459,7 @@ name: enables def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string property_value: IAO:0000118 "has" xsd:string @@ -2471,14 +2475,14 @@ transitive_over: RO:0002017 ! has component activity id: RO:0002328 name: functionally related to def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string [Typedef] id: RO:0002329 name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} is_a: RO:0002328 ! functionally related to @@ -2487,7 +2491,7 @@ is_a: RO:0002328 ! functionally related to id: RO:0002330 name: genomically related to def: "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant @@ -2496,7 +2500,7 @@ range: BFO:0000002 ! continuant id: RO:0002331 name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in @@ -2510,7 +2514,7 @@ id: RO:0002332 name: regulates levels of def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 ! process @@ -2522,7 +2526,7 @@ id: RO:0002333 name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0000057 ! has participant is_a: RO:0002328 ! functionally related to @@ -2531,7 +2535,7 @@ id: RO:0002334 name: regulated by def: "inverse of regulates" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 ! process range: BFO:0000015 ! process @@ -2543,7 +2547,7 @@ id: RO:0002335 name: negatively regulated by def: "inverse of negatively regulates" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002334 ! regulated by [Typedef] @@ -2551,14 +2555,14 @@ id: RO:0002336 name: positively regulated by def: "inverse of positively regulates" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002334 ! regulated by [Typedef] id: RO:0002337 name: related via localization to def: "A relationship that holds via some process of localization" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 ! process range: BFO:0000002 ! continuant @@ -2570,7 +2574,7 @@ def: "This relationship holds between p and l when p is a transport or localizat subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002344 ! results in transport to from or in transitive_over: BFO:0000050 ! part of @@ -2581,7 +2585,7 @@ def: "This relationship holds between p and l when p is a transport or localizat subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002344 ! results in transport to from or in transitive_over: BFO:0000050 ! part of @@ -2590,14 +2594,14 @@ id: RO:0002340 name: imports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002020 ! transports [Typedef] id: RO:0002341 name: results in transport along def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to [Typedef] @@ -2605,7 +2609,7 @@ id: RO:0002342 name: results in transport across def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002021 ! occurs across is_a: RO:0002344 ! results in transport to from or in @@ -2613,7 +2617,7 @@ is_a: RO:0002344 ! results in transport to from or in id: RO:0002343 name: results in growth of property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2621,7 +2625,7 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure id: RO:0002344 name: results in transport to from or in property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to [Typedef] @@ -2629,7 +2633,7 @@ id: RO:0002345 name: exports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002020 ! transports [Typedef] @@ -2640,7 +2644,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: RO:0002295 ! results in developmental progression of @@ -2651,7 +2655,7 @@ def: "p 'results in determination of' c if and only if p is a developmental proc subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: RO:0002295 ! results in developmental progression of @@ -2681,7 +2685,7 @@ name: input of def: "inverse of has input" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0000056 ! participates in is_a: RO:0002328 ! functionally related to @@ -2691,21 +2695,21 @@ name: output of def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0000056 ! participates in is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002354 name: formed as result of -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002353 ! output of [Typedef] id: RO:0002355 name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2716,7 +2720,7 @@ def: "The relationship linking a cell and its participation in a process that re subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: RO:0002295 ! results in developmental progression of @@ -2724,14 +2728,14 @@ is_a: RO:0002295 ! results in developmental progression of id: RO:0002357 name: results in developmental induction of def: "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of [Typedef] id: RO:0002360 name: has dendrite location property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002131 ! overlaps [Typedef] @@ -2739,7 +2743,7 @@ id: RO:0002371 name: attached to def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: RO:0002170 ! connected to @@ -2749,7 +2753,7 @@ is_a: RO:0002177 ! attached to part of id: RO:0002372 name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} @@ -2760,7 +2764,7 @@ is_a: RO:0002567 ! biomechanically related to id: RO:0002373 name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} @@ -2775,8 +2779,7 @@ comment: A has_fused_element B does not imply that A has_part some B: rather tha synonym: "has fused element" BROAD [] property_value: IAO:0000112 "false" xsd:boolean property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 is_a: RO:0002156 ! derived by descent from @@ -2785,7 +2788,7 @@ id: RO:0002375 name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 @@ -2803,7 +2806,7 @@ subset: ro-eco property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string @@ -2823,7 +2826,7 @@ comment: This is both a mereotopological relationship and a relationship defined subset: ro-eco property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string @@ -2836,7 +2839,7 @@ name: anabranch of def: "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." [] subset: ro-eco property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "anastomoses with" xsd:string is_a: RO:0002377 ! distributary of disjoint_from: RO:0002382 ! proper distributary of @@ -2847,7 +2850,7 @@ id: RO:0002379 name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: RO:0002131 ! overlaps @@ -2857,7 +2860,7 @@ name: branching part of def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] subset: ro-eco property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso FMA:85994 xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 holds_over_chain: RO:0002377 RO:0002381 @@ -2872,7 +2875,7 @@ def: "x main_stem_of y if y is a branching structure and x is a channel that tra subset: ro-eco property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: BFO:0000050 ! part of is_a: RO:0002375 ! in branching relationship with @@ -2883,7 +2886,7 @@ name: proper distributary of def: "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" [] subset: ro-eco property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002377 ! distributary of [Typedef] @@ -2892,7 +2895,7 @@ name: proper tributary of def: "x proper_tributary_of y iff x tributary_of y and x does not originate from y" [] subset: ro-eco property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002376 ! tributary of [Typedef] @@ -2900,7 +2903,7 @@ id: RO:0002384 name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: RO:0002324 ! developmentally related to @@ -2910,7 +2913,7 @@ id: RO:0002385 name: has potential to developmentally contribute to def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] @@ -2918,7 +2921,7 @@ id: RO:0002386 name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] @@ -2926,7 +2929,7 @@ id: RO:0002387 name: has potential to develop into def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] @@ -2934,7 +2937,7 @@ id: RO:0002388 name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002387 ! has potential to develop into [Typedef] @@ -2943,7 +2946,7 @@ name: has direct input def: "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] property_value: IAO:0000112 "'protein catabolic process' SubClassOf has_direct_input some protein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly consumes" xsd:string property_value: IAO:0000232 "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" xsd:string holds_over_chain: RO:0002224 RO:0002400 @@ -2954,7 +2957,7 @@ id: RO:0002401 name: obsolete has indirect input comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_obsolete: true [Typedef] @@ -2963,7 +2966,7 @@ name: obsolete has direct output def: "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. " [] property_value: IAO:0000112 "translation SubClassOf has_direct_output some protein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly produces" xsd:string is_obsolete: true @@ -2972,7 +2975,7 @@ id: RO:0002403 name: obsolete has indirect output comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002411 RO:0002402 is_obsolete: true @@ -2981,7 +2984,7 @@ id: RO:0002404 name: causally downstream of def: "inverse of upstream of" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: BFO:0000062 ! preceded by is_a: RO:0002427 ! causally downstream of or within inverse_of: RO:0002411 ! causally upstream of @@ -2990,7 +2993,7 @@ inverse_of: RO:0002411 ! causally upstream of id: RO:0002405 name: immediately causally downstream of property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002087 ! immediately preceded by is_a: RO:0002404 ! causally downstream of inverse_of: RO:0002412 ! immediately causally upstream of @@ -3006,7 +3009,7 @@ replaced_by: RO:0002629 id: RO:0002407 name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 holds_over_chain: RO:0002409 RO:0002409 @@ -3028,7 +3031,7 @@ replaced_by: RO:0002630 id: RO:0002409 name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 holds_over_chain: RO:0002630 RO:0002409 @@ -3043,7 +3046,7 @@ id: RO:0002410 name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] @@ -3052,7 +3055,7 @@ name: causally upstream of def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: BFO:0000063 ! precedes is_a: RO:0002418 ! causally upstream of or within @@ -3061,7 +3064,7 @@ is_a: RO:0002418 ! causally upstream of or within id: RO:0002412 name: immediately causally upstream of def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: RO:0002090 ! immediately precedes is_a: RO:0002411 ! causally upstream of @@ -3071,7 +3074,7 @@ id: RO:0002413 name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string @@ -3084,7 +3087,7 @@ id: RO:0002414 name: transitively provides input for def: "transitive form of directly_provides_input_for" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." xsd:string property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string domain: BFO:0000015 ! process @@ -3098,7 +3101,7 @@ name: causally upstream of or within def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true is_a: RO:0002501 ! causal relation between processes @@ -3109,19 +3112,19 @@ id: RO:0002424 name: differs in comment: This is an exploratory relation property_value: IAO:0000116 "false" xsd:boolean -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions xsd:anyURI [Typedef] id: RO:0002425 name: differs in attribute of -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002424 ! differs in [Typedef] id: RO:0002426 name: differs in attribute -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: BFO:0000020 ! specifically dependent continuant is_a: RO:0002424 ! differs in @@ -3130,7 +3133,7 @@ id: RO:0002427 name: causally downstream of or within def: "inverse of causally upstream of or within" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: RO:0002501 ! causal relation between processes @@ -3139,7 +3142,7 @@ is_a: RO:0002501 ! causal relation between processes id: RO:0002428 name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002327 RO:0002211 holds_over_chain: RO:0002331 RO:0002211 is_a: RO:0002263 ! acts upstream of @@ -3149,7 +3152,7 @@ is_a: RO:0002431 ! involved in or involved in regulation of id: RO:0002429 name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002428 holds_over_chain: RO:0002327 RO:0002213 holds_over_chain: RO:0002331 RO:0002213 @@ -3159,7 +3162,7 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002430 name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 holds_over_chain: RO:0002327 RO:0002212 holds_over_chain: RO:0002331 RO:0002212 @@ -3170,7 +3173,7 @@ id: RO:0002431 name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: RO:0002264 ! acts upstream of or within is_a: RO:0002328 ! functionally related to @@ -3182,7 +3185,7 @@ name: is active in def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] synonym: "enables activity in" EXACT [] property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} is_a: RO:0002131 ! overlaps @@ -3192,7 +3195,7 @@ is_a: RO:0002328 ! functionally related to id: RO:0002433 name: contributes to morphology of def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002131 ! overlaps [Typedef] @@ -3204,7 +3207,7 @@ synonym: "in pairwise interaction with" EXACT [] property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI domain: BFO:0000040 ! material entity @@ -3216,7 +3219,7 @@ id: RO:0002435 name: genetically interacts with property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: RO:0002434 ! interacts with @@ -3226,7 +3229,7 @@ id: RO:0002436 name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 @@ -3238,7 +3241,7 @@ id: RO:0002437 name: biotically interacts with def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string @@ -3253,7 +3256,7 @@ id: RO:0002438 name: trophically interacts with def: "An interaction relationship in which the partners are related via a feeding relationship." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: RO:0002574 ! participates in a biotic-biotic interaction with @@ -3264,9 +3267,9 @@ def: "An interaction relationship involving a predation process, where the subje subset: ro-eco property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Jorrit Poelen" xsd:string -property_value: IAO:0000117 "Katja Shulz" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7134-3324 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string @@ -3279,7 +3282,7 @@ id: RO:0002440 name: symbiotically interacts with def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true @@ -3290,7 +3293,7 @@ id: RO:0002441 name: commensually interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: RO:0002440 ! symbiotically interacts with @@ -3299,7 +3302,7 @@ id: RO:0002442 name: mutualistically interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: RO:0002440 ! symbiotically interacts with @@ -3308,7 +3311,7 @@ id: RO:0002443 name: interacts with via parasite-host interaction def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: RO:0002440 ! symbiotically interacts with @@ -3319,7 +3322,7 @@ name: parasite of subset: ro-eco synonym: "direct parasite of" EXACT [] property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string is_a: RO:0002443 ! interacts with via parasite-host interaction @@ -3331,7 +3334,7 @@ id: RO:0002445 name: parasitized by subset: ro-eco synonym: "directly parasitized by" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string @@ -3345,7 +3348,7 @@ def: "A biotic interaction relationship in which one partner is an organism and subset: ro-eco synonym: "semibiotically interacts with" RELATED [] property_value: IAO:0000112 "Porifiera attaches to substrate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: RO:0002437 ! biotically interacts with @@ -3353,7 +3356,7 @@ is_a: RO:0002437 ! biotically interacts with id: RO:0002447 name: phosphorylates property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: RO:0002436 ! molecularly interacts with @@ -3362,8 +3365,8 @@ id: RO:0002448 name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002436 ! molecularly interacts with @@ -3374,8 +3377,8 @@ id: RO:0002449 name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -3386,8 +3389,8 @@ id: RO:0002450 name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -3399,14 +3402,14 @@ name: transmitted by def: "A relationship that holds between a disease and organism" [] property_value: IAO:0000112 "all dengue disease transmitted by some mosquito" xsd:string property_value: IAO:0000116 "Add domain and range constraints" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0002452 name: has symptom def: "A relation that holds between a disease or an organism and a phenotype" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: OGMS:0000031 is_a: RO:0002200 ! has phenotype @@ -3414,7 +3417,7 @@ is_a: RO:0002200 ! has phenotype id: RO:0002453 name: host of subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string is_a: RO:0002440 ! symbiotically interacts with @@ -3423,7 +3426,7 @@ id: RO:0002454 name: has host def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string is_a: RO:0002440 ! symbiotically interacts with @@ -3433,7 +3436,7 @@ name: pollinates subset: ro-eco property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string is_a: RO:0002442 ! mutualistically interacts with @@ -3443,7 +3446,7 @@ inverse_of: RO:0002456 ! pollinated by id: RO:0002456 name: pollinated by subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string @@ -3453,7 +3456,7 @@ is_a: RO:0002442 ! mutualistically interacts with id: RO:0002457 name: acquires nutrients from subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string is_a: RO:0002438 ! trophically interacts with inverse_of: RO:0002469 ! provides nutrients for @@ -3464,7 +3467,7 @@ name: preyed upon by def: "inverse of preys on" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string @@ -3476,7 +3479,7 @@ id: RO:0002459 name: is vector for subset: ro-eco property_value: IAO:0000112 "Anopheles is a vector for Plasmodium" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" xsd:string is_a: RO:0002574 ! participates in a biotic-biotic interaction with inverse_of: RO:0002460 ! has vector @@ -3485,72 +3488,72 @@ inverse_of: RO:0002460 ! has vector id: RO:0002460 name: has vector subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002461 name: partner in -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string is_a: RO:0000056 ! participates in [Typedef] id: RO:0002462 name: subject participant in -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: RO:0002461 ! partner in [Typedef] id: RO:0002463 name: target participant in -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: RO:0002461 ! partner in [Typedef] id: RO:0002464 name: helper property (not for use in curation) -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string [Typedef] id: RO:0002465 name: is symbiosis -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002563 ! interaction relation helper property [Typedef] id: RO:0002466 name: is commensalism -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002465 ! is symbiosis [Typedef] id: RO:0002467 name: is mutualism -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002465 ! is symbiosis [Typedef] id: RO:0002468 name: is parasitism -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002465 ! is symbiosis [Typedef] id: RO:0002469 name: provides nutrients for subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002438 ! trophically interacts with [Typedef] id: RO:0002470 name: eats subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: RO:0002438 ! trophically interacts with @@ -3558,7 +3561,7 @@ is_a: RO:0002438 ! trophically interacts with id: RO:0002471 name: is eaten by subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string is_a: RO:0002438 ! trophically interacts with @@ -3568,7 +3571,7 @@ id: RO:0002472 name: is evidence for def: "A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and \nthe a supports either the existence of b, or the truth value of b." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002616 ! related via evidence or inference to inverse_of: RO:0002558 ! has evidence @@ -3578,7 +3581,7 @@ name: composed primarily of def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] subset: ro-eco property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 ! material entity @@ -3590,7 +3593,7 @@ id: RO:0002476 name: child nucleus of def: "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" [] property_value: IAO:0000112 "ABal nucleus child nucleus of ABa nucleus (in C elegans)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." xsd:string domain: GO:0005634 range: GO:0005634 @@ -3600,14 +3603,14 @@ is_a: RO:0002258 ! developmentally preceded by id: RO:0002477 name: child nucleus of in hermaphrodite def: "A child nucleus relationship in which the cells are part of a hermaphroditic organism" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002476 ! child nucleus of [Typedef] id: RO:0002478 name: child nucleus of in male def: "A child nucleus relationship in which the cells are part of a male organism" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002476 ! child nucleus of [Typedef] @@ -3615,7 +3618,7 @@ id: RO:0002479 name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} @@ -3625,26 +3628,26 @@ id: RO:0002480 name: ubiquitinates def: "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" [] property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002436 ! molecularly interacts with [Typedef] id: RO:0002481 name: is kinase activity -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002482 name: is ubiquitination -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002485 name: receives input from property_value: IAO:0000116 "See notes for inverse relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002170 ! connected to inverse_of: RO:0002486 ! sends output to @@ -3652,13 +3655,13 @@ inverse_of: RO:0002486 ! sends output to id: RO:0002486 name: sends output to property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002170 ! connected to [Typedef] id: RO:0002487 name: relation between physical entity and a process or stage -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000003 ! occurrent @@ -3667,7 +3670,7 @@ range: BFO:0000003 ! occurrent id: RO:0002488 name: existence starts during def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002583 BFO:0000050 is_a: RO:0002490 ! existence overlaps is_a: RO:0002496 ! existence starts during or after @@ -3677,7 +3680,7 @@ transitive_over: BFO:0000050 ! part of id: RO:0002489 name: existence starts with def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002488 ! existence starts during [Typedef] @@ -3685,7 +3688,7 @@ id: RO:0002490 name: existence overlaps def: "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002487 ! relation between physical entity and a process or stage [Typedef] @@ -3694,7 +3697,7 @@ name: existence starts and ends during def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. synonym: "exists during" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002488 ! existence starts during is_a: RO:0002492 ! existence ends during @@ -3703,7 +3706,7 @@ id: RO:0002492 name: existence ends during def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002593 BFO:0000050 is_a: RO:0002490 ! existence overlaps is_a: RO:0002497 ! existence ends during or before @@ -3714,14 +3717,14 @@ id: RO:0002493 name: existence ends with def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002492 ! existence ends during [Typedef] id: RO:0002494 name: transformation of def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002202 ! develops from @@ -3729,7 +3732,7 @@ is_a: RO:0002202 ! develops from id: RO:0002495 name: immediate transformation of def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002494 is_a: RO:0002207 ! directly develops from is_a: RO:0002494 ! transformation of @@ -3739,7 +3742,7 @@ id: RO:0002496 name: existence starts during or after def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000050 RO:0002496 holds_over_chain: RO:0002258 RO:0002496 is_a: RO:0002487 ! relation between physical entity and a process or stage @@ -3752,7 +3755,7 @@ id: RO:0002497 name: existence ends during or before def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000050 RO:0002497 holds_over_chain: RO:0002286 RO:0002497 is_a: RO:0002487 ! relation between physical entity and a process or stage @@ -3772,7 +3775,7 @@ inverse_of: RO:0002608 ! process has causal agent id: RO:0002501 name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 ! occurrent @@ -3782,7 +3785,7 @@ is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002502 name: depends on -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso BFO:0000169 [Typedef] @@ -3790,7 +3793,7 @@ id: RO:0002503 name: towards def: "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" [] property_value: IAO:0000116 "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 is_a: RO:0002502 ! depends on @@ -3800,7 +3803,7 @@ name: has intermediate def: "p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c" [] subset: ro-eco property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string is_a: RO:0000057 ! has participant @@ -3808,7 +3811,7 @@ is_a: RO:0000057 ! has participant id: RO:0002506 name: causal relation between entities property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000002 ! continuant @@ -3820,11 +3823,11 @@ id: RO:0002507 name: determined by def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] subset: ro-eco -property_value: http://purl.org/dc/terms/creator "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/creator "Pier Buttigieg" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-4366-3088 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "A coral reef environment is determined by a particular coral reef" xsd:string property_value: IAO:0000116 "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602 property_value: IAO:0000589 "determined by (system to material entity)" xsd:string domain: RO:0002577 ! system @@ -3840,7 +3843,7 @@ name: determines def: "inverse of determined by" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "determines (material entity to system)" xsd:string is_a: RO:0002566 ! causally influences @@ -3849,7 +3852,7 @@ id: RO:0002509 name: determined by part of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 ! system range: BFO:0000040 ! material entity holds_over_chain: RO:0002507 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} @@ -3860,7 +3863,7 @@ is_a: RO:0002506 ! causal relation between entities id: RO:0002510 name: transcribed from def: "x is transcribed from y if and only if x is synthesized from template y" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to inverse_of: RO:0002511 ! transcribed to @@ -3870,7 +3873,7 @@ id: RO:0002511 name: transcribed to def: "inverse of transcribed from" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to @@ -3878,7 +3881,7 @@ is_a: RO:0002330 ! genomically related to id: RO:0002512 name: ribosomal translation of def: "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to inverse_of: RO:0002513 ! ribosomally translates to @@ -3887,7 +3890,7 @@ inverse_of: RO:0002513 ! ribosomally translates to id: RO:0002513 name: ribosomally translates to def: "inverse of ribosomal translation of" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to @@ -3896,7 +3899,7 @@ id: RO:0002514 name: sequentially related to def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string @@ -3911,7 +3914,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcript" xsd:string property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002527 ! does not overlap sequence of @@ -3921,7 +3924,7 @@ name: has start sequence def: "x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3934,7 +3937,7 @@ name: is start sequence of def: "inverse of has start sequence" [] subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3946,7 +3949,7 @@ name: has end sequence def: "x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3959,7 +3962,7 @@ name: is end sequence of def: "inverse of has end sequence" [] subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3971,7 +3974,7 @@ name: is consecutive sequence of def: "x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002524 ! has subsequence @@ -3981,7 +3984,7 @@ name: is sequentially aligned with def: "x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: RO:0002514 ! sequentially related to @@ -3991,7 +3994,7 @@ name: bounds sequence of def: "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002514 ! sequentially related to inverse_of: RO:0002523 ! is bound by sequence of @@ -4002,16 +4005,16 @@ name: is bound by sequence of def: "inverse of bounds sequence of" [] subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002514 ! sequentially related to [Typedef] id: RO:0002524 name: has subsequence -def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -4026,7 +4029,7 @@ name: is subsequence of def: "inverse of has subsequence" [] subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: BFO:0000050 ! part of @@ -4036,9 +4039,9 @@ is_a: RO:0002526 ! overlaps sequence of [Typedef] id: RO:0002526 name: overlaps sequence of -def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002524 RO:0002525 is_symmetric: true is_a: RO:0002131 ! overlaps @@ -4047,9 +4050,9 @@ is_a: RO:0002514 ! sequentially related to [Typedef] id: RO:0002527 name: does not overlap sequence of -def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "disconnected from" xsd:string is_symmetric: true is_a: RO:0002514 ! sequentially related to @@ -4059,7 +4062,7 @@ id: RO:0002528 name: is upstream of sequence of def: "inverse of downstream of sequence of" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002527 ! does not overlap sequence of @@ -4068,7 +4071,7 @@ id: RO:0002529 name: is downstream of sequence of def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002527 ! does not overlap sequence of inverse_of: RO:0002529 ! is downstream of sequence of @@ -4079,7 +4082,7 @@ name: is immediately downstream of sequence of def: "x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002529 is_a: RO:0002515 ! sequentially adjacent to is_a: RO:0002529 ! is downstream of sequence of @@ -4090,7 +4093,7 @@ name: is immediately upstream of sequence of def: "inverse of immediately downstream of" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002515 ! sequentially adjacent to is_a: RO:0002528 ! is upstream of sequence of @@ -4099,7 +4102,7 @@ id: RO:0002551 name: has skeleton def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 @@ -4112,7 +4115,7 @@ is_asymmetric: true id: RO:0002552 name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -4124,7 +4127,7 @@ subset: ro-eco synonym: "epiparasite of" RELATED [] synonym: "hyperparasitoid of" NARROW [] property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string holds_over_chain: RO:0002444 RO:0002444 @@ -4140,7 +4143,7 @@ subset: RO:0002259 synonym: "has epiparasite" RELATED [] synonym: "has hyperparasite" RELATED [] synonym: "hyperparasitoidized by" RELATED [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002445 RO:0002445 is_a: RO:0002453 ! host of @@ -4148,7 +4151,7 @@ is_a: RO:0002453 ! host of id: RO:0002555 name: allelopath of subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string @@ -4158,7 +4161,7 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with id: RO:0002556 name: pathogen of subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002454 ! has host inverse_of: RO:0002557 ! has pathogen @@ -4166,7 +4169,7 @@ inverse_of: RO:0002557 ! has pathogen id: RO:0002557 name: has pathogen subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002453 ! host of [Typedef] @@ -4176,14 +4179,14 @@ def: "inverse of is evidence for" [] comment: x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/25052702 is_a: RO:0002616 ! related via evidence or inference to [Typedef] id: RO:0002559 name: causally influenced by -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: RO:0002506 ! causal relation between entities @@ -4192,7 +4195,7 @@ inverse_of: RO:0002566 ! causally influences [Typedef] id: RO:0002563 name: interaction relation helper property -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI is_a: RO:0002464 ! helper property (not for use in curation) @@ -4200,7 +4203,7 @@ is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 name: molecular interaction relation helper property -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002563 ! interaction relation helper property [Typedef] @@ -4210,7 +4213,7 @@ def: "Holds between p and c when p is locomotion process and the outcome of this subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "" xsd:string is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -4218,8 +4221,8 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure id: RO:0002566 name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 ! continuant @@ -4230,7 +4233,7 @@ is_a: RO:0002506 ! causal relation between entities id: RO:0002567 name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: CARO:0000003 range: CARO:0000003 @@ -4240,7 +4243,7 @@ is_a: RO:0002328 ! functionally related to id: RO:0002568 name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string is_a: RO:0002567 ! biomechanically related to @@ -4250,7 +4253,7 @@ name: has branching part def: "inverse of branching part of" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: BFO:0000051 ! has part is_a: RO:0002375 ! in branching relationship with @@ -4260,7 +4263,7 @@ id: RO:0002570 name: conduit for def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 UBERON:cjm xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 ! material entity @@ -4272,7 +4275,7 @@ id: RO:0002571 name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:cjm xsd:string range: BFO:0000040 ! material entity is_a: BFO:0000050 ! part of @@ -4282,7 +4285,7 @@ id: RO:0002572 name: luminal space of def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000141 ! immaterial entity is_a: RO:0002571 ! lumen of @@ -4291,7 +4294,7 @@ id: RO:0002573 name: has modifier def: "A relation that holds between an attribute or a qualifier and another attribute." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." xsd:string domain: BFO:0000020 ! specifically dependent continuant @@ -4301,7 +4304,7 @@ range: BFO:0000020 ! specifically dependent continuant id: RO:0002574 name: participates in a biotic-biotic interaction with subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 domain: CARO:0001010 range: CARO:0001010 @@ -4312,7 +4315,7 @@ id: RO:0002576 name: skeleton of def: "inverse of has skeleton" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 is_a: BFO:0000050 ! part of @@ -4324,7 +4327,7 @@ def: "p directly regulates q iff p is immediately causally upstream of q and p r subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string property_value: RO:0002575 RO:0002211 @@ -4342,7 +4345,7 @@ id: RO:0002584 name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000051 RO:0002215 is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process @@ -4409,7 +4412,7 @@ id: RO:0002595 name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 ! material entity range: BFO:0000015 ! process @@ -4677,7 +4680,7 @@ def: "a produces b if some process that occurs_in a has_output b, where a and b comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity inverse_of: RO:0003001 ! produced by @@ -4688,7 +4691,7 @@ name: produced by def: "a produced_by b iff some process that occurs_in b has_output a." [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -4696,7 +4699,7 @@ range: BFO:0000040 ! material entity id: RO:0003002 name: represses expression of def: "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002449 ! directly negatively regulates activity of @@ -4705,7 +4708,7 @@ is_a: RO:0002449 ! directly negatively regulates activity of id: RO:0003003 name: increases expression of def: "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002450 ! directly positively regulates activity of @@ -4715,7 +4718,7 @@ id: RO:0003301 name: has role in modeling def: "A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." [] comment: The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate. -property_value: IAO:0000117 "Matthew Brush" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-1048-5019 property_value: IAO:0000118 "is used to study" xsd:string is_asymmetric: true @@ -4793,7 +4796,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: BFO:0000017 ! realizable entity is_a: RO:0002410 ! causally related to inverse_of: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:38:20Z [Typedef] @@ -4803,7 +4806,7 @@ property_value: seeAlso Orphanet:410295 property_value: seeAlso Orphanet:410296 is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004011 ! is causal gain of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:20Z [Typedef] @@ -4811,7 +4814,7 @@ id: RO:0004002 name: has material basis in loss of function germline mutation in is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004012 ! is causal loss of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:37Z [Typedef] @@ -4820,7 +4823,7 @@ name: has material basis in germline mutation in property_value: seeAlso Orphanet:317343 is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004013 ! is causal germline mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:54Z [Typedef] @@ -4829,7 +4832,7 @@ name: has material basis in somatic mutation in property_value: seeAlso Orphanet:317344 is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004014 ! is causal somatic mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z [Typedef] @@ -4837,7 +4840,7 @@ id: RO:0004005 name: has major susceptibility factor is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004015 ! is causal susceptibility factor for -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:26Z [Typedef] @@ -4845,7 +4848,7 @@ id: RO:0004006 name: has partial material basis in germline mutation in is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004016 ! is causal germline mutation partially giving rise to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:57Z [Typedef] @@ -4854,7 +4857,7 @@ name: has primary input or output def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology is_a: RO:0000057 ! has participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -4864,7 +4867,7 @@ def: "p has primary output c if (a) p has output c and (b) the goal of process i subset: http://purl.obolibrary.org/obo/valid_for_go_ontology is_a: RO:0002234 ! has output is_a: RO:0004007 ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -4874,7 +4877,7 @@ def: "p has primary input c if (a) p has input c and (b) the goal of process is subset: http://purl.obolibrary.org/obo/valid_for_go_ontology is_a: RO:0002233 ! has input is_a: RO:0004007 ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -4883,7 +4886,7 @@ name: is genetic basis for condition property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string range: BFO:0000017 ! realizable entity is_a: RO:0004018 ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:53:08Z [Typedef] @@ -4892,7 +4895,7 @@ name: is causal gain of function germline mutation of in def: "Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." [] property_value: seeAlso Orphanet:410296 is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:55:51Z [Typedef] @@ -4901,7 +4904,7 @@ name: is causal loss of function germline mutation of in def: "Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." [] property_value: seeAlso Orphanet:410295 is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:06Z [Typedef] @@ -4911,7 +4914,7 @@ def: "Relates a gene to condition, such that a mutation in this gene is sufficie property_value: seeAlso Orphanet:317343 is_a: RO:0003303 ! causes condition is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:40Z [Typedef] @@ -4921,7 +4924,7 @@ def: "Relates a gene to condition, such that a mutation in this gene is sufficie property_value: seeAlso Orphanet:317344 is_a: RO:0003303 ! causes condition is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:07Z [Typedef] @@ -4930,7 +4933,7 @@ name: is causal susceptibility factor for def: "Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]." [] property_value: seeAlso Orphanet:317345 is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:43Z [Typedef] @@ -4940,7 +4943,7 @@ def: "Relates a gene to condition, such that a mutation in this gene partially c property_value: seeAlso Orphanet:317346 is_a: RO:0003304 ! contributes to condition is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:58:43Z [Typedef] @@ -4948,14 +4951,14 @@ id: RO:0004017 name: realizable has basis in is_a: RO:0002410 ! causally related to inverse_of: RO:0004018 ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:01Z [Typedef] id: RO:0004018 name: is basis for realizable is_a: RO:0002410 ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:29Z [Typedef] @@ -4964,7 +4967,7 @@ name: disease has basis in domain: OGMS:0000031 is_a: RO:0004017 ! realizable has basis in is_a: RO:0004023 ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:26:47Z [Typedef] @@ -4974,7 +4977,7 @@ def: "A relation that holds between the disease and a material entity where the property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string range: CARO:0000006 is_a: RO:0004019 ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z [Typedef] @@ -4984,7 +4987,7 @@ def: "A relation that holds between the disease and a process where the physical property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 ! process is_a: RO:0004019 ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:37:52Z [Typedef] @@ -4994,7 +4997,7 @@ def: "A relation that holds between the disease and a feature (a phenotype or ot domain: OGMS:0000031 is_a: RO:0002200 ! has phenotype is_a: RO:0004019 ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:46:07Z [Typedef] @@ -5004,7 +5007,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: OGMS:0000031 is_a: RO:0002410 ! causally related to is_a: RO:0040035 ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:50:54Z [Typedef] @@ -5017,7 +5020,7 @@ range: BFO:0000015 ! process holds_over_chain: RO:0004025 RO:0002215 is_a: RO:0004023 ! causal relationship with disease as subject transitive_over: BFO:0000050 ! part of -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:51:09Z [Typedef] @@ -5028,7 +5031,7 @@ domain: OGMS:0000031 range: CARO:0000006 is_a: RO:0004023 ! causal relationship with disease as subject transitive_over: BFO:0000050 ! part of -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z [Typedef] @@ -5040,7 +5043,7 @@ property_value: IAO:0000232 "This relation is intentionally very general, and co domain: OGMS:0000031 range: BFO:0000004 ! independent continuant is_a: RO:0040035 ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T04:06:02Z [Typedef] @@ -5050,7 +5053,7 @@ def: "A relationship between a disease and an anatomical entity where the diseas domain: OGMS:0000031 range: BFO:0000004 ! independent continuant is_a: RO:0004026 ! disease has location -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:37:31Z [Typedef] @@ -5061,7 +5064,7 @@ domain: BFO:0000017 ! realizable entity range: BFO:0000040 ! material entity holds_over_chain: RO:0009501 RO:0002233 is_a: RO:0002410 ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:45:49Z [Typedef] @@ -5070,7 +5073,7 @@ name: disease has feature def: "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." [] domain: OGMS:0000031 is_a: RO:0040035 ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:50:53Z [Typedef] @@ -5079,7 +5082,7 @@ name: disease arises from alteration in structure def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." [] range: CARO:0000003 is_a: RO:0004019 ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z [Typedef] @@ -5088,7 +5091,7 @@ name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] holds_over_chain: RO:0002327 BFO:0000051 is_a: RO:0002328 ! functionally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z [Typedef] @@ -5099,7 +5102,7 @@ property_value: RO:0004049 RO:0002264 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z [Typedef] @@ -5109,7 +5112,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002264 holds_over_chain: RO:0002327 RO:0004046 is_a: RO:0002264 ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z [Typedef] @@ -5122,7 +5125,7 @@ property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of, holds_over_chain: RO:0002327 RO:0002304 is_a: RO:0002263 ! acts upstream of is_a: RO:0004032 ! acts upstream of or within, positive effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:14Z [Typedef] @@ -5135,7 +5138,7 @@ property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of, holds_over_chain: RO:0002327 RO:0002305 is_a: RO:0002263 ! acts upstream of is_a: RO:0004033 ! acts upstream of or within, negative effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:22Z [Typedef] @@ -5143,7 +5146,7 @@ id: RO:0004046 name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 is_a: RO:0002418 ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -5151,7 +5154,7 @@ id: RO:0004047 name: causally upstream of or within, positive effect property_value: RO:0004049 RO:0002418 is_a: RO:0002418 ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -5247,7 +5250,7 @@ def: "\"has substance added\" is a relation existing between a (physical) entity property_value: IAO:0000112 "muffin 'has substance added' some 'baking soda'" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." xsd:string -property_value: IAO:0000117 "Damion Dooley" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -5257,7 +5260,7 @@ name: has substance removed def: "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." [] property_value: IAO:0000112 "'egg white' 'has substance removed' some 'egg yolk'" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Damion Dooley" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -5267,7 +5270,7 @@ name: immersed in def: "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." [] property_value: IAO:0000112 "sardines 'immersed in' some 'oil and mustard'" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Damion Dooley" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -5277,7 +5280,7 @@ name: has consumer def: "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect." [] property_value: IAO:0000112 "sardine has consumer some homo sapiens" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Damion Dooley" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 domain: BFO:0000040 ! material entity range: CARO:0001010 @@ -5287,7 +5290,7 @@ name: has primary substance added def: "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." [] property_value: IAO:0000112 "bread 'has primary substance added' some 'flour'" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Damion Dooley" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 is_a: RO:0009001 ! has substance added [Typedef] @@ -5295,10 +5298,10 @@ id: RO:0009501 name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] synonym: "triggered by process" EXACT [RO:cjm] -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "David Osumi-Sutherland" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string @@ -5340,7 +5343,7 @@ holds_over_chain: RO:0000059 RO:0000053 id: RO:0011002 name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences @@ -5349,7 +5352,7 @@ is_a: RO:0002566 ! causally influences id: RO:0011003 name: regulates quantity of def: "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences @@ -5358,7 +5361,7 @@ is_a: RO:0002566 ! causally influences id: RO:0011004 name: indirectly regulates activity of def: "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0011002 ! regulates activity of @@ -5367,7 +5370,7 @@ is_a: RO:0011002 ! regulates activity of id: RO:0011007 name: decreases by repression quantity of def: "The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0011023 ! indirectly negatively regulates quantity of @@ -5376,7 +5379,7 @@ is_a: RO:0011023 ! indirectly negatively regulates quantity of id: RO:0011008 name: increases by expression quantity of def: "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0011024 ! indirectly positively regulates quantity of @@ -5385,7 +5388,7 @@ is_a: RO:0011024 ! indirectly positively regulates quantity of id: RO:0011009 name: directly positively regulates quantity of def: "The entity A has an activity that directly positively regulates the quantity of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0011021 ! directly regulates quantity of @@ -5394,7 +5397,7 @@ is_a: RO:0011021 ! directly regulates quantity of id: RO:0011010 name: directly negatively regulates quantity of def: "The entity A has an activity that directly negatively regulates the quantity of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0011021 ! directly regulates quantity of @@ -5403,7 +5406,7 @@ is_a: RO:0011021 ! directly regulates quantity of id: RO:0011013 name: indirectly positively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly activates" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -5414,7 +5417,7 @@ id: RO:0011014 name: destabilizes quantity of def: "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." [] property_value: IAO:0000112 "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0011010 ! directly negatively regulates quantity of @@ -5424,7 +5427,7 @@ id: RO:0011015 name: stabilizes quantity of def: "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." [] property_value: IAO:0000112 "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0011009 ! directly positively regulates quantity of @@ -5433,7 +5436,7 @@ is_a: RO:0011009 ! directly positively regulates quantity of id: RO:0011016 name: indirectly negatively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly inhibits" xsd:string is_a: RO:0011004 ! indirectly regulates activity of @@ -5441,28 +5444,28 @@ is_a: RO:0011004 ! indirectly regulates activity of id: RO:0011021 name: directly regulates quantity of def: "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011003 ! regulates quantity of [Typedef] id: RO:0011022 name: indirectly regulates quantity of def: "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011003 ! regulates quantity of [Typedef] id: RO:0011023 name: indirectly negatively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011022 ! indirectly regulates quantity of [Typedef] id: RO:0011024 name: indirectly positively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011022 ! indirectly regulates quantity of [Typedef] @@ -5684,7 +5687,7 @@ name: has exemplar data def: "A relation between a material entity and some data in which the data is taken as exemplifying the material entity." [] property_value: IAO:0000112 "transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data])" xsd:string property_value: IAO:0000116 "C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C." xsd:string -property_value: IAO:0000117 "Patrick Ray" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-5260-9315 property_value: IAO:0000232 "This relation is not meant to capture the relation between occurrents and data." xsd:string inverse_of: RO:0015002 ! exemplar data of transitive_over: RO:0015003 ! subcluster of @@ -5692,14 +5695,14 @@ transitive_over: RO:0015003 ! subcluster of [Typedef] id: RO:0015002 name: exemplar data of -property_value: IAO:0000117 "Patrick Ray" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-5260-9315 [Typedef] id: RO:0015003 name: subcluster of def: "A relation between a group and another group it is part of but does not fully constitute." [] property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." xsd:string -property_value: IAO:0000117 "Shawn Tan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true is_a: BFO:0000050 ! part of @@ -5795,7 +5798,7 @@ property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:s id: RO:0016002 name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string is_a: RO:0016001 ! has phenotype or disease @@ -5815,8 +5818,8 @@ name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 +property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string holds_over_chain: RO:0002215 RO:0002233 @@ -5910,7 +5913,7 @@ id: RO:0040035 name: disease relationship def: "This relation groups relations between diseases and any other kind of entity." [] property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z [Typedef] @@ -5918,7 +5921,7 @@ id: RO:0040036 name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] is_a: RO:0000057 ! has participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] diff --git a/ro-base.owl b/ro-base.owl index beb8d499..13478aaf 100644 --- a/ro-base.owl +++ b/ro-base.owl @@ -18,7 +18,7 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. OBO Relations Ontology @@ -166,7 +166,7 @@ tooth SubClassOf 'never in taxon' value 'Aves' x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. - Chris Mungall + Class: ?X DisjointWith: RO_0002162 some ?Y @@ -261,7 +261,7 @@ WHERE { S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. - https://orcid.org/0000-0002-6601-2165 + This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost dubious for taxon @@ -275,7 +275,7 @@ WHERE { S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S - https://orcid.org/0000-0002-6601-2165 + PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> @@ -650,7 +650,7 @@ Where we have an annotation assertion "directly P" "is direct form of" "P" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' - Chris Mungall + is direct form of @@ -662,7 +662,7 @@ Where we have an annotation assertion relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y - Chris Mungall + is indirect form of @@ -810,7 +810,7 @@ Where we have an annotation assertion true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation. - cjm + nominally disjoint with @@ -821,7 +821,7 @@ Where we have an annotation assertion Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" - cjm + 2018-03-13T23:59:29Z is directional form of @@ -832,7 +832,7 @@ Where we have an annotation assertion - cjm + 2018-03-14T00:03:16Z is positive form of @@ -843,7 +843,7 @@ Where we have an annotation assertion - cjm + 2018-03-14T00:03:24Z is negative form of @@ -856,7 +856,7 @@ Where we have an annotation assertion part-of is homeomorphic for independent continuants. R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. - cjm + 2018-10-21T19:46:34Z R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. is homeomorphic for @@ -1601,7 +1601,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. - David Osumi-Sutherland + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). @@ -1617,7 +1617,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first. - David Osumi-Sutherland + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). @@ -1633,7 +1633,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first. - David Osumi-Sutherland + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). @@ -1859,7 +1859,7 @@ range: spatial region or site (immaterial continuant) May be obsoleted, see https://github.com/oborel/obo-relations/issues/260 - David Osumi-Sutherland + aligned with @@ -1876,7 +1876,7 @@ range: spatial region or site (immaterial continuant) a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - David Osumi-Sutherland + has boundary has_2D_boundary @@ -1890,7 +1890,7 @@ range: spatial region or site (immaterial continuant) A relation that holds between two neurons that are electrically coupled via gap junctions. - David Osumi-Sutherland + electrically_synapsed_to @@ -1904,7 +1904,7 @@ range: spatial region or site (immaterial continuant) The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). - David Osumi-Sutherland + tracheates @@ -1916,7 +1916,7 @@ range: spatial region or site (immaterial continuant) - David Osumi-Sutherland + http://www.ncbi.nlm.nih.gov/pubmed/22402613 innervated_by @@ -1928,7 +1928,7 @@ range: spatial region or site (immaterial continuant) - David Osumi-Sutherland + has synaptic terminal of @@ -1960,7 +1960,7 @@ range: spatial region or site (immaterial continuant) has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland + A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. bounding layer of @@ -1996,7 +1996,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. Note from NCEAS meeting: consider changing primary label - David Osumi-Sutherland + Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. coincident with @@ -2010,7 +2010,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g. - David Osumi-Sutherland + x 'cell expresses' y iff: cell(x) AND gene(y) @@ -2029,7 +2029,7 @@ AND t has_input y x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - David Osumi-Sutherland + regulates in other organism @@ -2043,7 +2043,7 @@ AND t has_input y A relationship that holds between a process that regulates a transport process and the entity transported by that process. - David Osumi-Sutherland + regulates transport of @@ -2308,6 +2308,7 @@ Examples include: the relationship between two channels collected simultaneously + David Osumi-Sutherland t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) @@ -2348,7 +2349,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + di Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. encompasses @@ -2427,6 +2428,7 @@ Examples include: the relationship between two channels collected simultaneously + David Osumi-Sutherland ends_at_start_of meets @@ -2498,7 +2500,7 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure that its soma is part of. - David Osumi-Sutherland + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -2517,7 +2519,7 @@ Examples include: the relationship between two channels collected simultaneously relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - David Osumi-Sutherland + fasciculates with (forall (?x ?y) (iff @@ -2557,9 +2559,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure its axon forms (chemical) synapses in. - Chris Mungall - David Osumi-Sutherland - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -2589,8 +2590,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -2608,9 +2609,9 @@ Examples include: the relationship between two channels collected simultaneously Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - Alexander Diehl - Chris Mungall - Lindsay Cowell + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) @@ -2626,8 +2627,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -2644,8 +2645,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -2662,8 +2663,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) @@ -2678,8 +2679,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -2696,8 +2697,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -2719,8 +2720,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - Chris Mungall - David Osumi-Sutherland + + synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( @@ -2750,8 +2751,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -2829,8 +2830,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -2859,8 +2860,8 @@ N1 SubclassOf ( Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -2883,7 +2884,7 @@ N1 SubclassOf ( A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - David Osumi-Sutherland + has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) @@ -2953,7 +2954,7 @@ N1 SubclassOf ( The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - David Osumi-Sutherland + has fasciculating component (forall (?x ?y) (iff @@ -2997,7 +2998,7 @@ N1 SubclassOf ( Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - David Osumi-Sutherland + <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -3015,7 +3016,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. X continuous_with Y if and only if X and Y share a fiat boundary. - David Osumi-Sutherland + connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) @@ -3116,7 +3117,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria - Chris Mungall + only in taxon @@ -3168,8 +3169,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - Chris Mungall - Jennifer Deegan + + @@ -3187,7 +3188,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - Chris Mungall + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) @@ -3337,7 +3338,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - Chris Mungall + has phenotype @@ -3350,7 +3351,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of has phenotype - Chris Mungall + phenotype of @@ -3368,10 +3369,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - Terry Meehan + + + + This is the transitive form of the develops from relation develops from @@ -3387,9 +3388,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of develops from - Chris Mungall - David Osumi-Sutherland - Terry Meehan + + + develops into @@ -3426,7 +3427,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x" We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g. - Chris Mungall + gene product of @@ -3446,7 +3447,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y - Chris Mungall + has gene product @@ -3474,7 +3475,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.'neural crest cell' SubClassOf expresses some 'Wnt1 gene' x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process - Chris Mungall + expressed in @@ -3503,11 +3504,11 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - Chris Mungall - David Osumi-Sutherland - has developmental precursor + + FBbt + has developmental precursor TODO - add child relations from DOS directly develops from @@ -3570,9 +3571,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - Chris Mungall - David Hill - Tanya Berardini + + + GO Regulation precludes parthood; the regulatory process may not be within the regulated process. @@ -3597,7 +3598,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - Chris Mungall + negatively regulates (process to process) @@ -3625,7 +3626,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - Chris Mungall + positively regulates (process to process) @@ -3655,7 +3656,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) TODO: add homeomorphy axiom This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. - Chris Mungall + has prototype @@ -3670,7 +3671,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - Chris Mungall + has function realized in @@ -3691,7 +3692,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - Chris Mungall + has function in capable of part of @@ -3712,7 +3713,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role - Chris Mungall + agent in Obsoleted as the inverse property was obsoleted. @@ -3726,7 +3727,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. OBSOLETE x has participant y if and only if x realizes some active role that inheres in y - Chris Mungall + has agent obsolete has active participant @@ -3742,7 +3743,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - Chris Mungall + surrounded by @@ -3762,7 +3763,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - Chris Mungall + @@ -3784,7 +3785,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of surrounded by - Chris Mungall + surrounds @@ -3798,7 +3799,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 @@ -3817,6 +3818,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of starts with + Chris Mungall Allen @@ -3834,6 +3836,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall started by @@ -3852,7 +3855,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - Chris Mungall + develops from part of @@ -3869,7 +3872,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x develops_in y if x is located in y whilst x is developing - Chris Mungall + EHDAA2 Jonathan Bard, EHDAA2 develops in @@ -3905,6 +3908,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of ends with + Chris Mungall ends @@ -3920,6 +3924,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall finished by @@ -3940,7 +3945,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - Chris Mungall + starts with process that occurs in has start location @@ -3960,7 +3965,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - Chris Mungall + ends with process that occurs in has end location @@ -3980,7 +3985,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + consumes @@ -4002,7 +4007,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - Chris Mungall + produces @@ -4048,7 +4053,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - Bill Duncan (https://orcid.org/0000-0001-9625-1899) + This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. @@ -4201,7 +4206,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y - Chris Mungall + has developmental contribution from @@ -4218,7 +4223,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho inverse of has developmental contribution from - Chris Mungall + developmentally contributes to @@ -4234,9 +4239,9 @@ If you need an axiom that says 'has_participant min 2 object', you sho t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - Chris Mungall - David Osumi-Sutherland - Melissa Haendel + + + induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) @@ -4254,7 +4259,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally induced by - Chris Mungall + developmentally induces @@ -4270,7 +4275,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - Chris Mungall + In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by @@ -4350,7 +4355,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - Chris Mungall + replaces developmentally replaces @@ -4363,7 +4368,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally preceded by - Chris Mungall + developmentally succeeded by @@ -4379,7 +4384,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - Chris Mungall + part of developmental precursor of @@ -4393,7 +4398,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part. - Chris Mungall + ubiquitously expressed in @@ -4405,7 +4410,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of 'expressed in' - Chris Mungall + expresses @@ -4417,7 +4422,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho inverse of ubiquiotously expressed in - Chris Mungall + ubiquitously expresses @@ -4433,7 +4438,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - Chris Mungall + results in developmental progression of @@ -4448,7 +4453,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - Chris Mungall + http://www.geneontology.org/GO.doc.development.shtml @@ -4467,7 +4472,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - Chris Mungall + GOC:mtg_berkeley_2013 @@ -4486,7 +4491,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - Chris Mungall + GOC:mtg_berkeley_2013 @@ -4505,7 +4510,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - Chris Mungall + GOC:mtg_berkeley_2013 @@ -4521,7 +4526,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho foramen ovale closure SubClassOf results in disappearance of foramen ovale - Chris Mungall + May be merged into parent relation results in disappearance of @@ -4534,7 +4539,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) - Chris Mungall + May be merged into parent relation results in developmental regression of @@ -4547,7 +4552,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of 'is substance that treats' - cjm + is treated by substance @@ -4565,7 +4570,7 @@ where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. - Pier Buttigieg + adapted for living in A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. @@ -4581,7 +4586,7 @@ where p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - cjm + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y @@ -4597,7 +4602,7 @@ where p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - cjm + causally upstream of, negative effect @@ -4610,10 +4615,10 @@ where A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. - Austin Meier - Chris Mungall - Marie Angelique Laporte - cjm + + + + 2017-06-05T17:35:04Z has exposure stimulus @@ -4624,7 +4629,7 @@ where - Chris Mungall + evolutionary variant of @@ -4636,7 +4641,7 @@ where Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. - Chris Mungall + regulates localization of @@ -4660,7 +4665,7 @@ where q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of - Chris Mungall + inheres in part of @@ -4687,7 +4692,7 @@ where an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - Chris Mungall + GOC:mtg_berkeley_2013 @@ -4701,7 +4706,7 @@ where A relationship that holds via some environmental process - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to @@ -4713,7 +4718,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions ecologically related to @@ -4727,7 +4732,7 @@ where An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. - Chris Mungall + adapted for confers advantage in @@ -4739,7 +4744,7 @@ where A mereological relationship or a topological relationship - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to @@ -4751,7 +4756,7 @@ where A relationship that holds between entities participating in some developmental process (GO:0032502) - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to @@ -4766,9 +4771,8 @@ where Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. - Chris Mungall + In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - Gene Ontology Consortium colocalizes with @@ -4794,7 +4798,7 @@ then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. - Chris Mungall + In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. contributes to @@ -4817,7 +4821,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - Chris Mungall + catalyzes executes has @@ -4834,7 +4838,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to @@ -4850,7 +4854,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati this relation holds between c and p when c is part of some c', and c' is capable of p. - Chris Mungall + false part of structure that is capable of @@ -4872,7 +4876,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism genomically related to @@ -4893,7 +4897,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati c involved_in p if and only if c enables some process p', and p' is part of p - Chris Mungall + actively involved in enables part of involved in @@ -4910,7 +4914,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - Chris Mungall + regulates levels of (process to entity) regulates levels of @@ -4924,7 +4928,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables - Chris Mungall + enabled by @@ -4939,7 +4943,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of regulates - Chris Mungall + regulated by (processual) regulated by @@ -4952,7 +4956,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of negatively regulates - Chris Mungall + negatively regulated by @@ -4964,7 +4968,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of positively regulates - Chris Mungall + positively regulated by @@ -4977,7 +4981,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds via some process of localization - Chris Mungall + Do not use this relation directly. It is a grouping relation. related via localization to @@ -4993,7 +4997,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - Chris Mungall + @@ -5011,7 +5015,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - Chris Mungall + @@ -5025,7 +5029,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. - Chris Mungall + imports @@ -5037,7 +5041,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - Chris Mungall + results in transport along @@ -5049,7 +5053,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - Chris Mungall + results in transport across @@ -5062,7 +5066,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'pollen tube growth' results_in growth_of some 'pollen tube' - Chris Mungall + results in growth of @@ -5073,7 +5077,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - Chris Mungall + results in transport to from or in @@ -5084,7 +5088,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. - Chris Mungall + exports @@ -5098,7 +5102,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - Chris Mungall + @@ -5113,7 +5117,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - Chris Mungall + @@ -5157,7 +5161,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has input - Chris Mungall + input of @@ -5171,7 +5175,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has output - Chris Mungall + output of @@ -5183,7 +5187,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + formed as result of @@ -5195,7 +5199,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. - Chris Mungall + results in structural organization of @@ -5207,7 +5211,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - Chris Mungall + @@ -5221,7 +5225,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. - Chris Mungall + results in developmental induction of @@ -5231,7 +5235,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + http://neurolex.org/wiki/Property:DendriteLocation has dendrite location @@ -5245,7 +5249,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - Chris Mungall + attached to (anatomical structure to anatomical structure) attached to @@ -5260,7 +5264,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - Chris Mungall + Wikipedia:Insertion_(anatomy) has muscle origin @@ -5281,7 +5285,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - Chris Mungall + Wikipedia:Insertion_(anatomy) has muscle insertion @@ -5302,8 +5306,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati false x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat - Chris Mungall - Chris Mungall + has fused element A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. @@ -5320,7 +5323,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) @@ -5340,7 +5343,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - Chris Mungall + drains into drains to tributary channel of @@ -5363,7 +5366,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Deschutes River distributary_of Little Lava Lake x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - Chris Mungall + branch of distributary channel of http://en.wikipedia.org/wiki/Distributary @@ -5387,7 +5390,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. - Chris Mungall + anastomoses with anabranch of @@ -5407,7 +5410,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - Chris Mungall + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with @@ -5432,7 +5435,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - Chris Mungall + branching part of @@ -5449,7 +5452,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. - Chris Mungall + main stem of @@ -5463,7 +5466,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_distributary_of y iff x distributary_of y and x does not flow back into y - Chris Mungall + proper distributary of @@ -5476,7 +5479,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_tributary_of y iff x tributary_of y and x does not originate from y - Chris Mungall + proper tributary of @@ -5491,7 +5494,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - Chris Mungall + has developmental potential involving @@ -5503,7 +5506,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - Chris Mungall + has potential to developmentally contribute to @@ -5515,7 +5518,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - Chris Mungall + has potential to developmentally induce @@ -5527,7 +5530,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has the potential to develop into y iff x develops into y or if x is capable of developing into y - Chris Mungall + has potential to develop into @@ -5539,7 +5542,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - Chris Mungall + has potential to directly develop into @@ -5556,7 +5559,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' has direct input @@ -5568,7 +5571,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit obsolete has indirect input @@ -5583,7 +5586,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ translation SubClassOf has_direct_output some protein p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. - Chris Mungall + directly produces obsolete has direct output true @@ -5599,7 +5602,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - Chris Mungall + Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit obsolete has indirect output @@ -5616,7 +5619,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ inverse of upstream of - Chris Mungall + causally downstream of @@ -5629,7 +5632,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - Chris Mungall + immediately causally downstream of @@ -5669,7 +5672,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - Chris Mungall + indirectly activates indirectly positively regulates @@ -5707,7 +5710,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - Chris Mungall + indirectly inhibits indirectly negatively regulates @@ -5734,7 +5737,7 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to @@ -5754,7 +5757,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - Chris Mungall + causally upstream of @@ -5768,7 +5771,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - Chris Mungall + immediately causally upstream of @@ -5786,7 +5789,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit - Chris Mungall + directly provides input for directly provides input for (process to process) @@ -5804,7 +5807,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different transitive form of directly_provides_input_for - Chris Mungall + This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. transitively provides input for (process to process) transitively provides input for @@ -5820,7 +5823,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall + influences (processual) affects causally upstream of or within @@ -5832,7 +5835,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different false - Chris Mungall + This is an exploratory relation differs in https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions @@ -5852,7 +5855,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + differs in attribute of @@ -5863,7 +5866,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + differs in attribute @@ -5875,7 +5878,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - Chris Mungall + causally downstream of or within @@ -5897,7 +5900,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - Chris Mungall + involved in regulation of @@ -5916,7 +5919,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - Chris Mungall + involved in positive regulation of @@ -5936,7 +5939,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - Chris Mungall + involved in negative regulation of @@ -5951,7 +5954,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - Chris Mungall + involved in or reguates involved in or involved in regulation of @@ -5969,7 +5972,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall + executes activity in enables activity in @@ -5999,7 +6002,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - Chris Mungall + contributes to morphology of @@ -6014,7 +6017,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. - Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with @@ -6031,7 +6034,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) - Chris Mungall + genetically interacts with http://purl.obolibrary.org/obo/MI_0208 @@ -6045,7 +6048,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - Chris Mungall + binds molecularly binds with molecularly interacts with @@ -6064,7 +6067,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - Chris Mungall + interacts with on organism level biotically interacts with @@ -6079,7 +6082,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the partners are related via a feeding relationship. - Chris Mungall + trophically interacts with @@ -6095,9 +6098,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] Baleen whale preys on krill An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - Chris Mungall - Jorrit Poelen - Katja Shulz + + + is subject of predation interaction with preys upon @@ -6121,7 +6124,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A biotic interaction in which the two organisms live together in more or less intimate association. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism @@ -6142,7 +6145,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 commensually interacts with @@ -6162,7 +6165,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 mutualistically interacts with @@ -6182,7 +6185,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 This relation groups a pair of inverse relations, parasite of and parasitized by @@ -6205,7 +6208,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human - Chris Mungall + parasitizes direct parasite of @@ -6220,7 +6223,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + has parasite parasitised by directly parasitized by @@ -6237,7 +6240,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - Chris Mungall + semibiotically interacts with participates in a abiotic-biotic interaction with @@ -6256,7 +6259,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates @@ -6278,8 +6281,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - Chris Mungall - Vasundra Touré + + molecularly controls directly regulates activity of @@ -6299,8 +6302,8 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly inhibits molecularly decreases activity of directly negatively regulates activity of @@ -6321,8 +6324,8 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly activates molecularly increases activity of directly positively regulates activity of @@ -6337,7 +6340,7 @@ For example, A and B may be gene products and binding of B by A positively regul all dengue disease transmitted by some mosquito A relationship that holds between a disease and organism Add domain and range constraints - Chris Mungall + transmitted by @@ -6349,7 +6352,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between a disease or an organism and a phenotype - Chris Mungall + has symptom @@ -6359,7 +6362,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) host of @@ -6372,7 +6375,7 @@ For example, A and B may be gene products and binding of B by A positively regul X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y - Chris Mungall + has host http://eol.org/schema/terms/hasHost @@ -6387,7 +6390,7 @@ For example, A and B may be gene products and binding of B by A positively regul Bees pollinate Flowers This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - Chris Mungall + is subject of pollination interaction with pollinates @@ -6400,7 +6403,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + has polinator is target of pollination interaction with @@ -6415,7 +6418,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. acquires nutrients from @@ -6428,7 +6431,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of preys on - Chris Mungall + has predator is target of predation interaction with @@ -6446,7 +6449,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anopheles is a vector for Plasmodium - Chris Mungall + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism is vector for @@ -6458,7 +6461,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + has vector @@ -6469,7 +6472,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target partner in @@ -6480,7 +6483,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. subject participant in @@ -6491,7 +6494,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. target participant in @@ -6501,7 +6504,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) @@ -6512,7 +6515,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is symbiosis @@ -6522,7 +6525,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is commensalism @@ -6532,7 +6535,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is mutualism @@ -6542,7 +6545,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is parasitism @@ -6552,7 +6555,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + provides nutrients for @@ -6563,7 +6566,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is subject of eating interaction with eats @@ -6575,7 +6578,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + eaten by is target of eating interaction with @@ -6591,7 +6594,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and the a supports either the existence of b, or the truth value of b. - Chris Mungall + is evidence for @@ -6606,7 +6609,7 @@ the a supports either the existence of b, or the truth value of b. 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - Chris Mungall + @@ -6623,7 +6626,7 @@ the a supports either the existence of b, or the truth value of b. ABal nucleus child nucleus of ABa nucleus (in C elegans) c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d - Chris Mungall + This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. child nucleus of @@ -6635,7 +6638,7 @@ the a supports either the existence of b, or the truth value of b. A child nucleus relationship in which the cells are part of a hermaphroditic organism - Chris Mungall + child nucleus of in hermaphrodite @@ -6646,7 +6649,7 @@ the a supports either the existence of b, or the truth value of b. A child nucleus relationship in which the cells are part of a male organism - Chris Mungall + child nucleus of in male @@ -6662,7 +6665,7 @@ the a supports either the existence of b, or the truth value of b. p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall + has part that occurs in @@ -6689,7 +6692,7 @@ the a supports either the existence of b, or the truth value of b. An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y Axiomatization to GO to be added later - Chris Mungall + ubiquitinates @@ -6699,7 +6702,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + is kinase activity @@ -6709,7 +6712,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + is ubiquitination @@ -6721,7 +6724,7 @@ the a supports either the existence of b, or the truth value of b. See notes for inverse relation - Chris Mungall + receives input from @@ -6732,7 +6735,7 @@ the a supports either the existence of b, or the truth value of b. This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - Chris Mungall + sends output to @@ -6743,7 +6746,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. relation between physical entity and a process or stage @@ -6764,7 +6767,7 @@ the a supports either the existence of b, or the truth value of b. x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). - Chris Mungall + existence starts during @@ -6775,7 +6778,7 @@ the a supports either the existence of b, or the truth value of b. x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). - Chris Mungall + existence starts with @@ -6786,7 +6789,7 @@ the a supports either the existence of b, or the truth value of b. x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) - Chris Mungall + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps @@ -6799,7 +6802,7 @@ the a supports either the existence of b, or the truth value of b. x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) - Chris Mungall + exists during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts and ends during @@ -6821,7 +6824,7 @@ the a supports either the existence of b, or the truth value of b. x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). - Chris Mungall + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during @@ -6833,7 +6836,7 @@ the a supports either the existence of b, or the truth value of b. x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). - Chris Mungall + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with @@ -6846,7 +6849,7 @@ the a supports either the existence of b, or the truth value of b. x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - Chris Mungall + transformation of @@ -6858,7 +6861,7 @@ the a supports either the existence of b, or the truth value of b. x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - Chris Mungall + immediate transformation of @@ -6897,7 +6900,7 @@ the a supports either the existence of b, or the truth value of b. x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). - Chris Mungall + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after @@ -6936,7 +6939,7 @@ the a supports either the existence of b, or the truth value of b. x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. - Chris Mungall + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before @@ -6962,7 +6965,7 @@ the a supports either the existence of b, or the truth value of b. p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes @@ -6973,7 +6976,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + depends on @@ -6986,7 +6989,7 @@ the a supports either the existence of b, or the truth value of b. q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. - Chris Mungall + towards @@ -6999,7 +7002,7 @@ the a supports either the existence of b, or the truth value of b. 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c - Chris Mungall + has intermediate product has intermediate @@ -7014,7 +7017,7 @@ the a supports either the existence of b, or the truth value of b. The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities @@ -7034,11 +7037,11 @@ the a supports either the existence of b, or the truth value of b.A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future - Chris Mungall + determined by (system to material entity) - Chris Mungall - Pier Buttigieg + + determined by @@ -7050,7 +7053,7 @@ the a supports either the existence of b, or the truth value of b. inverse of determined by - Chris Mungall + determines (material entity to system) @@ -7071,7 +7074,7 @@ the a supports either the existence of b, or the truth value of b. s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. - Chris Mungall + determined by part of @@ -7109,7 +7112,7 @@ the a supports either the existence of b, or the truth value of b. x is transcribed from y if and only if x is synthesized from template y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 transcribed from @@ -7121,7 +7124,7 @@ the a supports either the existence of b, or the truth value of b. inverse of transcribed from - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 transcribed to @@ -7151,7 +7154,7 @@ the a supports either the existence of b, or the truth value of b. x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 ribosomal translation of @@ -7179,7 +7182,7 @@ the a supports either the existence of b, or the truth value of b. inverse of ribosomal translation of - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 ribosomally translates to @@ -7192,7 +7195,7 @@ the a supports either the existence of b, or the truth value of b. A relation that holds between two entities that have the property of being sequences or having sequences. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. @@ -7210,7 +7213,7 @@ the a supports either the existence of b, or the truth value of b.Two consecutive DNA residues are sequentially adjacent Two exons on a processed transcript that were previously connected by an intron are adjacent x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 sequentially adjacent to @@ -7226,7 +7229,7 @@ the a supports either the existence of b, or the truth value of b. Every CDS has as a start sequence the start codon for that transcript x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence - Chris Mungall + started by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -7241,7 +7244,7 @@ the a supports either the existence of b, or the truth value of b. inverse of has start sequence - Chris Mungall + starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -7259,7 +7262,7 @@ the a supports either the existence of b, or the truth value of b. Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence - Chris Mungall + ended by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -7274,7 +7277,7 @@ the a supports either the existence of b, or the truth value of b. inverse of has end sequence - Chris Mungall + ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -7290,7 +7293,7 @@ the a supports either the existence of b, or the truth value of b. x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. In the SO paper, this was defined as an instance-type relation - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 is consecutive sequence of @@ -7305,7 +7308,7 @@ the a supports either the existence of b, or the truth value of b. Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering - Chris Mungall + is sequentially aligned with @@ -7320,7 +7323,7 @@ the a supports either the existence of b, or the truth value of b. The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y - Chris Mungall + bounds sequence of @@ -7333,7 +7336,7 @@ the a supports either the existence of b, or the truth value of b. inverse of bounds sequence of - Chris Mungall + is bound by sequence of @@ -7349,8 +7352,8 @@ the a supports either the existence of b, or the truth value of b. - x has subsequence y iff all of the sequence parts of x are sequence parts of y - Chris Mungall + x has subsequence y iff all of the sequence parts of y are sequence parts of x + contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -7367,7 +7370,7 @@ the a supports either the existence of b, or the truth value of b. inverse of has subsequence - Chris Mungall + contained by @@ -7386,8 +7389,8 @@ the a supports either the existence of b, or the truth value of b. - x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. - Chris Mungall + x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. + overlaps sequence of @@ -7399,8 +7402,8 @@ the a supports either the existence of b, or the truth value of b. - x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. - Chris Mungall + x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + disconnected from does not overlap sequence of @@ -7414,7 +7417,7 @@ the a supports either the existence of b, or the truth value of b. inverse of downstream of sequence of - Chris Mungall + is upstream of sequence of @@ -7428,7 +7431,7 @@ the a supports either the existence of b, or the truth value of b. x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. - Chris Mungall + is downstream of sequence of @@ -7442,7 +7445,7 @@ the a supports either the existence of b, or the truth value of b. A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y - Chris Mungall + is immediately downstream of sequence of @@ -7457,7 +7460,7 @@ the a supports either the existence of b, or the truth value of b. A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript inverse of immediately downstream of - Chris Mungall + is immediately upstream of sequence of @@ -7475,7 +7478,7 @@ the a supports either the existence of b, or the truth value of b. Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - Chris Mungall + has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). has skeleton @@ -7495,7 +7498,7 @@ the a supports either the existence of b, or the truth value of b. p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. - Chris Mungall + results in ending of @@ -7512,7 +7515,7 @@ the a supports either the existence of b, or the truth value of b. x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - Chris Mungall + http://eol.org/schema/terms/hyperparasitoidOf https://en.wikipedia.org/wiki/Hyperparasite hyperparasitoid of @@ -7532,7 +7535,7 @@ the a supports either the existence of b, or the truth value of b. inverse of hyperparasite of - Chris Mungall + has epiparasite has hyperparasite hyperparasitoidized by @@ -7547,7 +7550,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + http://en.wikipedia.org/wiki/Allelopathy allelopath of @@ -7562,7 +7565,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + pathogen of @@ -7573,7 +7576,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + has pathogen @@ -7585,7 +7588,7 @@ the a supports either the existence of b, or the truth value of b. inverse of is evidence for - Chris Mungall + @@ -7600,7 +7603,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + causally influenced by (entity-centric) causally influenced by @@ -7612,7 +7615,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ @@ -7624,7 +7627,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + molecular interaction relation helper property @@ -7635,7 +7638,7 @@ the a supports either the existence of b, or the truth value of b. Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - Chris Mungall + @@ -7662,8 +7665,8 @@ the a supports either the existence of b, or the truth value of b. The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - Chris Mungall - Vasundra Touré + + causally influences (entity-centric) causally influences @@ -7678,7 +7681,7 @@ the a supports either the existence of b, or the truth value of b. A relation that holds between elements of a musculoskeletal system or its analogs. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. biomechanically related to @@ -7690,7 +7693,7 @@ the a supports either the existence of b, or the truth value of b. m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - Chris Mungall + Wikipedia:Antagonist_(muscle) has muscle antagonist @@ -7704,7 +7707,7 @@ the a supports either the existence of b, or the truth value of b. inverse of branching part of - Chris Mungall + has branching part @@ -7719,7 +7722,7 @@ the a supports either the existence of b, or the truth value of b. x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - Chris Mungall + UBERON:cjm This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. @@ -7734,7 +7737,7 @@ the a supports either the existence of b, or the truth value of b. x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - Chris Mungall + GOC:cjm lumen of @@ -7748,7 +7751,7 @@ the a supports either the existence of b, or the truth value of b. s is luminal space of x iff s is lumen_of x and s is an immaterial entity - Chris Mungall + luminal space of @@ -7761,7 +7764,7 @@ the a supports either the existence of b, or the truth value of b. A relation that holds between an attribute or a qualifier and another attribute. - Chris Mungall + This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. @@ -7776,7 +7779,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + participates in a biotic-biotic interaction with @@ -7791,7 +7794,7 @@ the a supports either the existence of b, or the truth value of b. inverse of has skeleton - Chris Mungall + skeleton of @@ -7804,7 +7807,7 @@ the a supports either the existence of b, or the truth value of b. p directly regulates q iff p is immediately causally upstream of q and p regulates q. - Chris Mungall + directly regulates (processual) @@ -7837,7 +7840,7 @@ the a supports either the existence of b, or the truth value of b. gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - Chris Mungall + has part structure that is capable of @@ -7944,7 +7947,7 @@ the a supports either the existence of b, or the truth value of b. A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall + causal relation between material entity and a process @@ -8371,7 +8374,7 @@ the a supports either the existence of b, or the truth value of b. a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. - Melissa Haendel + Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces @@ -8386,7 +8389,7 @@ the a supports either the existence of b, or the truth value of b. a produced_by b iff some process that occurs_in b has_output a. - Melissa Haendel + produced by @@ -8400,7 +8403,7 @@ the a supports either the existence of b, or the truth value of b. Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. - Vasundra Touré + represses expression of @@ -8413,7 +8416,7 @@ the a supports either the existence of b, or the truth value of b. Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. - Vasundra Touré + increases expression of @@ -8425,7 +8428,7 @@ the a supports either the existence of b, or the truth value of b. A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. - Matthew Brush + is used to study The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate. has role in modeling @@ -8562,7 +8565,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:38:20Z condition has genetic basis in @@ -8574,7 +8577,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:20Z has material basis in gain of function germline mutation in @@ -8588,7 +8591,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:37Z has material basis in loss of function germline mutation in @@ -8600,7 +8603,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:54Z has material basis in germline mutation in @@ -8613,7 +8616,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:07Z has material basis in somatic mutation in @@ -8626,7 +8629,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:26Z has major susceptibility factor @@ -8638,7 +8641,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:57Z has partial material basis in germline mutation in @@ -8650,7 +8653,7 @@ Environmental exposures include those imposed by natural environments, experimen p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - cjm + 2018-12-13T11:26:17Z has primary input or output @@ -8664,7 +8667,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - cjm + 2018-12-13T11:26:32Z has primary output @@ -8688,7 +8691,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - cjm + 2018-12-13T11:26:56Z has primary input @@ -8712,7 +8715,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:53:08Z is genetic basis for condition @@ -8724,7 +8727,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:55:51Z is causal gain of function germline mutation of in @@ -8737,7 +8740,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:06Z is causal loss of function germline mutation of in @@ -8751,7 +8754,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:40Z is causal germline mutation in @@ -8765,7 +8768,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:57:07Z is causal somatic mutation in @@ -8778,7 +8781,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. - cjm + 2017-11-05T02:57:43Z is causal susceptibility factor for @@ -8792,7 +8795,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. - cjm + 2017-11-05T02:58:43Z is causal germline mutation partially giving rise to @@ -8805,7 +8808,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:01Z realizable has basis in @@ -8816,7 +8819,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:29Z is basis for realizable @@ -8829,7 +8832,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:26:47Z disease has basis in @@ -8843,7 +8846,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) - cjm + 2017-11-05T03:29:32Z disease has basis in dysfunction of @@ -8857,7 +8860,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. disease has basis in disruption of (disease to process) - cjm + 2017-11-05T03:37:52Z disease has basis in disruption of @@ -8879,7 +8882,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. - cjm + 2017-11-05T03:46:07Z disease has basis in feature @@ -8893,7 +8896,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. - cjm + 2017-11-05T03:50:54Z causal relationship with disease as subject @@ -8916,7 +8919,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and a process where the disease process disrupts the execution of the process. disease causes disruption of (disease to process) - cjm + 2017-11-05T03:51:09Z disease causes disruption of @@ -8934,7 +8937,7 @@ Environmental exposures include those imposed by natural environments, experimen disease causes dysfunction of (disease to anatomical entity) - cjm + 2017-11-05T03:58:20Z disease causes dysfunction of @@ -8958,7 +8961,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. - cjm + 2017-11-05T04:06:02Z disease has location @@ -8980,7 +8983,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity - cjm + 2017-12-26T19:37:31Z disease has inflammation site @@ -8998,7 +9001,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - cjm + 2017-12-26T19:45:49Z realized in response to stimulus @@ -9019,7 +9022,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. - cjm + 2017-12-26T19:50:53Z disease has feature @@ -9032,7 +9035,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. - cjm + 2017-12-26T19:58:44Z disease arises from alteration in structure @@ -9048,7 +9051,7 @@ Environmental exposures include those imposed by natural environments, experimen Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - cjm + 2018-01-25T23:20:13Z enables subfunction @@ -9064,7 +9067,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:30Z acts upstream of or within, positive effect @@ -9082,7 +9085,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:51Z acts upstream of or within, negative effect @@ -9101,7 +9104,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - cjm + 2018-01-26T23:53:14Z acts upstream of, positive effect @@ -9121,7 +9124,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - cjm + 2018-01-26T23:53:22Z acts upstream of, negative effect @@ -9135,7 +9138,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:05Z causally upstream of or within, negative effect @@ -9147,7 +9150,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:19Z causally upstream of or within, positive effect @@ -9298,7 +9301,7 @@ Environmental exposures include those imposed by natural environments, experimen "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. - Damion Dooley + has substance added @@ -9313,7 +9316,7 @@ Environmental exposures include those imposed by natural environments, experimen 'egg white' 'has substance removed' some 'egg yolk' "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. - Damion Dooley + has substance removed @@ -9328,7 +9331,7 @@ Environmental exposures include those imposed by natural environments, experimen sardines 'immersed in' some 'oil and mustard' "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. - Damion Dooley + immersed in @@ -9342,7 +9345,7 @@ Environmental exposures include those imposed by natural environments, experimen sardine has consumer some homo sapiens 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. - Damion Dooley + has consumer @@ -9356,7 +9359,7 @@ Environmental exposures include those imposed by natural environments, experimen bread 'has primary substance added' some 'flour' 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance. - Damion Dooley + has primary substance added @@ -9376,10 +9379,10 @@ Environmental exposures include those imposed by natural environments, experimen An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - Austin Meier - Chris Mungall - David Osumi-Sutherland - Marie Angelique Laporte + + + + triggered by process realized in response to https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit @@ -9442,7 +9445,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - Vasundra Touré + regulates activity of @@ -9455,7 +9458,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. - Vasundra Touré + regulates quantity of @@ -9468,7 +9471,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. - Vasundra Touré + indirectly regulates activity of @@ -9483,7 +9486,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + decreases by repression quantity of @@ -9498,7 +9501,7 @@ For example, protein A (transcription factor) indirectly decreases by repression The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + increases by expression quantity of @@ -9511,7 +9514,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly positively regulates the quantity of B. - Vasundra Touré + directly positively regulates quantity of @@ -9524,7 +9527,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly negatively regulates the quantity of B. - Vasundra Touré + directly negatively regulates quantity of @@ -9537,7 +9540,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. - Vasundra Touré + indirectly activates indirectly positively regulates activity of @@ -9552,7 +9555,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. - Vasundra Touré + destabilizes quantity of @@ -9566,7 +9569,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. - Vasundra Touré + stabilizes quantity of @@ -9577,7 +9580,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. - Vasundra Touré + indirectly inhibits indirectly negatively regulates activity of @@ -9589,7 +9592,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. - Vasundra Touré + directly regulates quantity of @@ -9600,7 +9603,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. - Vasundra Touré + indirectly regulates quantity of @@ -9611,7 +9614,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. - Vasundra Touré + indirectly negatively regulates quantity of @@ -9622,7 +9625,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. - Vasundra Touré + indirectly positively regulates quantity of @@ -9957,7 +9960,7 @@ For example, protein A (transcription factor) indirectly increases by expression transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data]) A relation between a material entity and some data in which the data is taken as exemplifying the material entity. C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C. - Patrick Ray + This relation is not meant to capture the relation between occurrents and data. has exemplar data @@ -9968,7 +9971,7 @@ For example, protein A (transcription factor) indirectly increases by expression - Patrick Ray + exemplar data of @@ -9981,7 +9984,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relation between a group and another group it is part of but does not fully constitute. X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. - Shawn Tan + This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. subcluster of @@ -10172,7 +10175,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - http://orcid.org/0000-0002-7463-6306 + 2021-11-05T17:30:44Z has disease https://github.com/oborel/obo-relations/issues/478 @@ -10202,8 +10205,8 @@ For example, protein A (transcription factor) indirectly increases by expression A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - https://orcid.org/0000-0001-9625-1899 - https://orcid.org/0000-0003-2620-0345 + + A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z @@ -10358,7 +10361,7 @@ For example, protein A (transcription factor) indirectly increases by expression This relation groups relations between diseases and any other kind of entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. - cjm + 2018-09-26T00:00:32Z disease relationship @@ -10370,7 +10373,7 @@ For example, protein A (transcription factor) indirectly increases by expression p has anatomical participant c iff p has participant c, and c is an anatomical entity - cjm + 2018-09-26T01:08:58Z results in changes to anatomical or cellular structure @@ -12445,8 +12448,8 @@ For example, protein A (transcription factor) indirectly increases by expression An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes. A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism. This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions. - Chris Mungall - cjm + + 2017-06-05T17:55:39Z exposure event or process https://github.com/oborel/obo-relations/pull/173 @@ -12464,7 +12467,7 @@ For example, protein A (transcription factor) indirectly increases by expression Any entity that is ordered in discrete units along a linear axis. - Chris Mungall + sequentially ordered entity @@ -12475,7 +12478,7 @@ For example, protein A (transcription factor) indirectly increases by expression Any individual unit of a collection of like units arranged in a linear order - Chris Mungall + An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair. sequence atomic unit @@ -12487,7 +12490,7 @@ For example, protein A (transcription factor) indirectly increases by expression Any entity that can be divided into parts such that each part is an atomical unit of a sequence - Chris Mungall + Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence. sequence bearer @@ -12500,7 +12503,7 @@ For example, protein A (transcription factor) indirectly increases by expression A material entity consisting of multiple components that are causally integrated. May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 - Chris Mungall + http://www.jbiomedsem.com/content/4/1/43 system diff --git a/ro.json b/ro.json index 5a8d6e2f..eec07263 100644 --- a/ro.json +++ b/ro.json @@ -12,7 +12,7 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part." @@ -29,7 +29,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -42,9 +42,6 @@ "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { @@ -56,6 +53,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -69,11 +69,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." @@ -97,7 +97,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -124,7 +124,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -147,7 +147,7 @@ "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -165,7 +165,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" @@ -214,7 +214,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -227,7 +227,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -248,15 +248,15 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "replaces" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -381,12 +381,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/date", "val" : "2021-11-05T17:30:44Z" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/oborel/obo-relations/issues/478" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "http://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/478" } ] }, "type" : "PROPERTY", @@ -747,11 +747,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -765,6 +765,9 @@ }, "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "false" }, { @@ -773,9 +776,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -839,7 +839,7 @@ "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -856,7 +856,7 @@ "val" : "http://purl.obolibrary.org/obo/RO_0002494" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -871,7 +871,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" } ] }, "type" : "PROPERTY", @@ -911,7 +911,7 @@ "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -931,11 +931,26 @@ "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", "lbl" : "has developmental contribution from" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002497", + "meta" : { + "definition" : { + "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.", + "xrefs" : [ ] + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + }, + "type" : "PROPERTY", + "lbl" : "existence ends during or before" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002013", "meta" : { @@ -963,7 +978,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -971,21 +986,6 @@ }, "type" : "PROPERTY", "lbl" : "developmentally contributes to" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002497", - "meta" : { - "definition" : { - "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.", - "xrefs" : [ ] - }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "existence ends during or before" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002014", "meta" : { @@ -1013,10 +1013,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Melissa Haendel" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GO:0001759" @@ -1026,18 +1023,21 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "induced by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" } ] }, "type" : "PROPERTY", @@ -1057,7 +1057,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1072,7 +1072,7 @@ "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1087,11 +1087,25 @@ "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", "lbl" : "existence ends with" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + }, + "type" : "PROPERTY", + "lbl" : "transformation of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002252", "meta" : { @@ -1121,25 +1135,11 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" } ] }, "type" : "PROPERTY", "lbl" : "regulates in other organism" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002494", - "meta" : { - "definition" : { - "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "transformation of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002008", "meta" : { @@ -1151,7 +1151,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Note from NCEAS meeting: consider changing primary label" @@ -1171,7 +1171,7 @@ "val" : "x 'cell expresses' y iff:\ncell(x)\nAND gene(y)\nAND exists some 'transcription, DNA templated (GO_0006351)'(t)\nAND t occurs_in x\nAND t has_input y" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" } ] }, "type" : "PROPERTY", @@ -1185,7 +1185,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" } ] }, "type" : "PROPERTY", @@ -1199,7 +1199,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1222,7 +1222,7 @@ "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" } ] }, "type" : "PROPERTY", @@ -1236,7 +1236,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1272,7 +1272,7 @@ "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" } ] }, "type" : "PROPERTY", @@ -1288,7 +1288,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" } ] }, "type" : "PROPERTY", @@ -1366,6 +1366,19 @@ }, "type" : "PROPERTY", "lbl" : "curator guidance link" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" + } ] + }, + "type" : "PROPERTY", + "lbl" : "receives input from" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002001", "meta" : { @@ -1377,7 +1390,7 @@ "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -1385,19 +1398,6 @@ }, "type" : "PROPERTY", "lbl" : "aligned with" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002485", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "See notes for inverse relation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "receives input from" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002243", "meta" : { @@ -1420,6 +1420,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_2D_boundary" }, { @@ -1434,9 +1437,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has boundary" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." @@ -1448,11 +1448,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002486", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1479,7 +1479,7 @@ "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1492,11 +1492,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" } ] }, "type" : "PROPERTY", @@ -1519,11 +1519,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1533,7 +1533,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1557,7 +1557,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1665,7 +1665,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1679,7 +1679,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1704,7 +1704,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1728,7 +1728,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Bill Duncan (https://orcid.org/0000-0001-9625-1899)" + "val" : "https://orcid.org/0000-0001-9625-1899" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." @@ -1749,7 +1749,7 @@ "val" : "starts with process that occurs in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -1768,15 +1768,15 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -1819,12 +1819,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "ends with process that occurs in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -1848,14 +1848,14 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "consumes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -1889,14 +1889,14 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "produces" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -1911,12 +1911,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "ABal nucleus child nucleus of ABa nucleus (in C elegans)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -1952,11 +1952,11 @@ "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is subject of eating interaction with" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -1967,7 +1967,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "eaten by" @@ -1988,7 +1988,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2042,6 +2042,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "finished by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2070,6 +2073,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2094,6 +2100,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2103,7 +2112,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2117,7 +2126,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -2130,7 +2139,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2145,15 +2154,15 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Jonathan Bard, EHDAA2" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "EHDAA2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2163,7 +2172,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2174,7 +2183,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2256,15 +2265,15 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" @@ -2285,11 +2294,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002462", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2313,14 +2322,14 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2333,7 +2342,7 @@ "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2344,6 +2353,9 @@ "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" }, { @@ -2355,9 +2367,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -2370,7 +2379,7 @@ "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2384,6 +2393,9 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { @@ -2396,16 +2408,6 @@ }, "type" : "PROPERTY", "lbl" : "starts" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002465", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "is symbiosis" }, { "id" : "http://purl.obolibrary.org/obo/RO_0003311", "meta" : { @@ -2416,13 +2418,23 @@ }, "type" : "PROPERTY", "lbl" : "condition exacerbated by" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002465", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is symbiosis" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002460", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2431,11 +2443,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002461", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -2455,6 +2467,23 @@ }, "type" : "PROPERTY", "lbl" : "ameliorates condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002459", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Anopheles is a vector for Plasmodium" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is vector for" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002217", "meta" : { @@ -2464,11 +2493,11 @@ }, "comments" : [ "Obsoleted as the inverse property was obsoleted." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "agent in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "http://purl.obolibrary.org/obo/RO_0002608" @@ -2477,23 +2506,6 @@ }, "type" : "PROPERTY", "lbl" : "obsolete actively participates in" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002459", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Anopheles is a vector for Plasmodium" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "is vector for" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002218", "meta" : { @@ -2504,12 +2516,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has agent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "http://purl.obolibrary.org/obo/RO_0002500" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ], "deprecated" : true }, @@ -2529,16 +2541,6 @@ }, "type" : "PROPERTY", "lbl" : "contributes to frequency of condition" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003309", - "meta" : { - "definition" : { - "val" : "A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition.", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "exacerbates condition" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002219", "meta" : { @@ -2547,11 +2549,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" @@ -2559,6 +2561,16 @@ }, "type" : "PROPERTY", "lbl" : "surrounded by" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003309", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "exacerbates condition" }, { "id" : "http://purl.obolibrary.org/obo/RO_0003308", "meta" : { @@ -2580,12 +2592,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "positively regulates (process to process)" @@ -2609,7 +2621,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is subject of pollination interaction with" @@ -2633,15 +2645,15 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has polinator" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is target of pollination interaction with" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://eol.org/schema/terms/hasPollinator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2674,9 +2686,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))" @@ -2689,6 +2698,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO: add homeomorphy axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" @@ -2705,7 +2717,7 @@ "val" : "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2729,7 +2741,7 @@ "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has function realized in" @@ -2780,7 +2792,7 @@ "val" : "http://eol.org/schema/terms/HasPredator" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://polytraits.lifewatchgreece.eu/terms/PRED" @@ -2806,7 +2818,7 @@ "val" : "has function in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" @@ -2828,12 +2840,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "all dengue disease transmitted by some mosquito" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Add domain and range constraints" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2865,7 +2877,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2881,24 +2893,24 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GO" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Hill" + "val" : "https://orcid.org/0000-0001-7476-6306" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-3837-8864" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "false" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Tanya Berardini" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "regulates (processual)" @@ -2911,11 +2923,11 @@ "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2929,11 +2941,11 @@ }, "comments" : [ "The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate." ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-1048-5019" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is used to study" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Matthew Brush" } ] }, "type" : "PROPERTY", @@ -2955,7 +2967,7 @@ "val" : "http://eol.org/schema/terms/hasHost" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -2973,7 +2985,7 @@ "val" : "negatively regulates (process to process)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" @@ -2998,10 +3010,10 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0003-4639-4431" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "directly activates" @@ -3009,6 +3021,28 @@ }, "type" : "PROPERTY", "lbl" : "directly positively regulates activity of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002448", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.", + "xrefs" : [ ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + }, + "type" : "PROPERTY", + "lbl" : "directly regulates activity of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002206", "meta" : { @@ -3018,7 +3052,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" @@ -3030,27 +3064,37 @@ "type" : "PROPERTY", "lbl" : "expressed in" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002448", + "id" : "http://purl.obolibrary.org/obo/RO_0002207", "meta" : { "definition" : { - "val" : "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.", + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.", "xrefs" : [ ] }, + "comments" : [ "TODO - add child relations from DOS" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "molecularly controls", + "val" : "has developmental precursor", "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002202" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "FBbt" } ] }, "type" : "PROPERTY", - "lbl" : "directly regulates activity of" + "lbl" : "directly develops from" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002449", "meta" : { @@ -3065,47 +3109,17 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "directly inhibits" - } ] - }, - "type" : "PROPERTY", - "lbl" : "directly negatively regulates activity of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002207", - "meta" : { - "definition" : { - "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.", - "xrefs" : [ ] - }, - "comments" : [ "TODO - add child relations from DOS" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "has developmental precursor" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002202" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "FBbt" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", - "lbl" : "directly develops from" + "lbl" : "directly negatively regulates activity of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002208", "meta" : { @@ -3127,33 +3141,6 @@ }, "type" : "PROPERTY", "lbl" : "has parasitoid" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002202", - "meta" : { - "definition" : { - "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y", - "xrefs" : [ ] - }, - "comments" : [ "This is the transitive form of the develops from relation" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Terry Meehan" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Melissa Haendel" - } ] - }, - "type" : "PROPERTY", - "lbl" : "develops from" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002444", "meta" : { @@ -3174,11 +3161,38 @@ "val" : "http://eol.org/schema/terms/parasitizes" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", "lbl" : "parasite of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y", + "xrefs" : [ ] + }, + "comments" : [ "This is the transitive form of the develops from relation" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + }, + "type" : "PROPERTY", + "lbl" : "develops from" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002203", "meta" : { @@ -3192,13 +3206,13 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0003-1980-3228" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Terry Meehan" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -3213,6 +3227,9 @@ "xrefs" : [ ] } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has parasite" }, { @@ -3221,13 +3238,30 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "parasitised by" + } ] + }, + "type" : "PROPERTY", + "lbl" : "parasitized by" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002204", + "meta" : { + "definition" : { + "val" : "definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\"", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] }, "type" : "PROPERTY", - "lbl" : "parasitized by" + "lbl" : "gene product of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002446", "meta" : { @@ -3243,7 +3277,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" @@ -3254,26 +3288,6 @@ }, "type" : "PROPERTY", "lbl" : "participates in a abiotic-biotic interaction with" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002204", - "meta" : { - "definition" : { - "val" : "definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\"", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, - "type" : "PROPERTY", - "lbl" : "gene product of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002205", "meta" : { @@ -3282,14 +3296,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "every HOTAIR lncRNA is the gene product of some HOXC gene" @@ -3303,12 +3317,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Axiomatization to GO to be added later" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -3435,11 +3449,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" @@ -3456,11 +3470,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -3478,7 +3492,7 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -3496,50 +3510,50 @@ "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", "lbl" : "mutualistically interacts with" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002443", + "id" : "http://purl.obolibrary.org/obo/RO_0002201", "meta" : { "definition" : { - "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO).", + "val" : "inverse of has phenotype", "xrefs" : [ ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation groups a pair of inverse relations, parasite of and parasitized by" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] }, "type" : "PROPERTY", - "lbl" : "interacts with via parasite-host interaction" + "lbl" : "phenotype of" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "id" : "http://purl.obolibrary.org/obo/RO_0002443", "meta" : { "definition" : { - "val" : "inverse of has phenotype", + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO).", "xrefs" : [ ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation groups a pair of inverse relations, parasite of and parasitized by" } ] }, "type" : "PROPERTY", - "lbl" : "phenotype of" + "lbl" : "interacts with via parasite-host interaction" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002437", "meta" : { @@ -3556,7 +3570,7 @@ "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "interacts with on organism level" @@ -3577,7 +3591,7 @@ "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -3599,24 +3613,24 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preys upon" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is subject of predation interaction with" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Jorrit Poelen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0001-7134-3324" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-3138-4118" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.inaturalist.org/observations/2942824" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Katja Shulz" } ] }, "type" : "PROPERTY", @@ -3630,7 +3644,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -3651,15 +3665,15 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", "val" : "http://purl.obolibrary.org/obo/MI_0914" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." @@ -3684,7 +3698,7 @@ "val" : "http://purl.obolibrary.org/obo/ECO_0000316" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -3697,6 +3711,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "molecularly binds with" }, { @@ -3708,9 +3725,6 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ECO_0000353" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -3744,7 +3758,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002428" @@ -3760,11 +3774,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "involved in or reguates" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "OWL does not allow defining object properties via a Union" @@ -3788,12 +3802,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "executes activity in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A protein that enables activity in a cytosol." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -3803,7 +3817,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -3817,11 +3831,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -3835,7 +3849,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -3856,7 +3870,7 @@ "val" : "http://purl.obolibrary.org/obo/RO_0002428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -3880,14 +3894,14 @@ "meta" : { "comments" : [ "This is an exploratory relation" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "false" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -3897,7 +3911,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -4014,7 +4028,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" @@ -4035,7 +4049,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -4048,11 +4062,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002575", "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -4070,15 +4084,15 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "directly provides input for (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "directly provides input for" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -4093,12 +4107,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "transitively provides input for (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" @@ -4124,14 +4138,14 @@ "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -4148,7 +4162,7 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -4158,7 +4172,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" @@ -4186,14 +4200,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002579", "val" : "http://purl.obolibrary.org/obo/RO_0002213" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "indirectly activates" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -4206,14 +4220,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" @@ -4233,7 +4247,7 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ], "deprecated" : true }, @@ -4251,7 +4265,7 @@ "val" : "directly produces" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "translation SubClassOf has_direct_output some protein" @@ -4268,11 +4282,11 @@ "meta" : { "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ], "deprecated" : true }, @@ -4298,11 +4312,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002579", "val" : "http://purl.obolibrary.org/obo/RO_0002212" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "indirectly inhibits" @@ -4779,12 +4793,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -4824,15 +4838,15 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" } ], "deprecated" : true }, @@ -4883,7 +4897,7 @@ "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -7031,7 +7045,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-14T00:03:24Z" @@ -7053,28 +7067,28 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "Marie Angelique Laporte" + "val" : "https://orcid.org/0000-0001-6996-0040" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-8461-9745" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "Austin Meier" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7073-9172" } ] }, "type" : "PROPERTY", @@ -7088,7 +7102,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:19Z" @@ -7103,11 +7117,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004046", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:05Z" @@ -7119,11 +7133,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004049", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-14T00:03:16Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7140,7 +7154,7 @@ "val" : "2018-03-13T23:59:29Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7178,6 +7192,23 @@ }, "type" : "PROPERTY", "lbl" : "happens during" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004030", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:58:44Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "disease arises from alteration in structure" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002093", "meta" : { @@ -7196,23 +7227,6 @@ }, "type" : "PROPERTY", "lbl" : "ends during" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004030", - "meta" : { - "definition" : { - "val" : "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-12-26T19:58:44Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - } ] - }, - "type" : "PROPERTY", - "lbl" : "disease arises from alteration in structure" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002090", "meta" : { @@ -7227,6 +7241,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002575", "val" : "http://purl.obolibrary.org/obo/BFO_0000063" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" @@ -7243,7 +7260,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7257,11 +7274,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-01-26T23:53:22Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002263" @@ -7278,7 +7295,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" @@ -7304,7 +7321,7 @@ "val" : "2018-01-25T23:20:13Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7322,7 +7339,7 @@ "val" : "http://purl.obolibrary.org/obo/RO_0002263" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" @@ -7342,7 +7359,7 @@ "val" : "http://purl.obolibrary.org/obo/RO_0002264" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-01-26T23:49:51Z" @@ -7350,10 +7367,6 @@ }, "type" : "PROPERTY", "lbl" : "acts upstream of or within, negative effect" - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0016301", - "type" : "CLASS", - "lbl" : "kinase activity" }, { "id" : "http://purl.obolibrary.org/obo/RO_0004029", "meta" : { @@ -7363,7 +7376,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-26T19:50:53Z" @@ -7371,6 +7384,10 @@ }, "type" : "PROPERTY", "lbl" : "disease has feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0016301", + "type" : "CLASS", + "lbl" : "kinase activity" }, { "id" : "http://purl.obolibrary.org/obo/RO_0004028", "meta" : { @@ -7380,7 +7397,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-26T19:45:49Z" @@ -7425,6 +7442,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" } ] }, "type" : "PROPERTY", @@ -7445,11 +7465,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004025", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "disease causes dysfunction of (disease to anatomical entity)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:58:20Z" @@ -7481,7 +7501,7 @@ "val" : "2017-11-05T03:51:09Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "disease causes disruption of (disease to process)" @@ -7512,7 +7532,7 @@ "val" : "2017-12-26T19:37:31Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7527,12 +7547,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T04:06:02Z" @@ -7550,12 +7570,12 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:37:52Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "disease has basis in disruption of (disease to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7578,7 +7598,7 @@ "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "di" @@ -7601,7 +7621,7 @@ "val" : "2017-11-05T03:29:32Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7611,7 +7631,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." @@ -7657,7 +7677,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:46:07Z" @@ -7673,7 +7693,7 @@ "val" : "2017-11-05T03:20:29Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7682,11 +7702,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004017", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:20:01Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" } ] }, "type" : "PROPERTY", @@ -7699,7 +7719,7 @@ "val" : "2017-11-05T03:26:47Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7736,14 +7756,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.orpha.net/ORDO/Orphanet_317344" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:57:07Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" } ] }, "type" : "PROPERTY", @@ -7756,11 +7776,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:56:40Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.orpha.net/ORDO/Orphanet_317343" @@ -7780,7 +7800,7 @@ "val" : "2017-11-05T02:58:43Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.orpha.net/ORDO/Orphanet_317346" @@ -7798,12 +7818,12 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:57:43Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.orpha.net/ORDO/Orphanet_317345" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" } ] }, "type" : "PROPERTY", @@ -7814,12 +7834,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a more specific relations" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:53:08Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7839,7 +7859,7 @@ "val" : "2017-11-05T02:56:06Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7853,7 +7873,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:55:51Z" @@ -7877,7 +7897,7 @@ "val" : "2018-12-13T11:26:17Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7890,11 +7910,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004006", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:46:57Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7908,11 +7928,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:56Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7930,7 +7950,7 @@ "val" : "2018-12-13T11:26:32Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7939,11 +7959,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004003", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.orpha.net/ORDO/Orphanet_317343" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:45:54Z" @@ -7959,7 +7979,7 @@ "val" : "2017-11-05T02:45:37Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -7968,11 +7988,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004005", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:46:26Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" } ] }, "type" : "PROPERTY", @@ -7981,11 +8001,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004004", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:46:07Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.orpha.net/ORDO/Orphanet_317344" @@ -7997,11 +8017,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004001", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:45:20Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.orpha.net/ORDO/Orphanet_410296" @@ -8016,11 +8036,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004000", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:38:20Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a more specific relations" @@ -8356,6 +8376,9 @@ "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" @@ -8371,9 +8394,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -8405,7 +8425,7 @@ "val" : "tooth SubClassOf 'never in taxon' value 'Aves'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -8424,13 +8444,13 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Jennifer Deegan" + "val" : "https://orcid.org/0000-0001-9227-417X" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" @@ -8461,6 +8481,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" @@ -8470,9 +8493,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -8514,7 +8534,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -8532,7 +8552,7 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Melissa Haendel" + "val" : "https://orcid.org/0000-0001-9114-8737" } ] }, "type" : "PROPERTY", @@ -8566,7 +8586,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -8602,15 +8622,15 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "connected to" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "FMA:85972" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" } ] }, "type" : "PROPERTY", @@ -8653,7 +8673,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Melissa Haendel" + "val" : "https://orcid.org/0000-0001-9114-8737" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -8686,15 +8706,15 @@ "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "FMA:85994" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2212" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -8718,7 +8738,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" @@ -8734,11 +8754,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -8755,7 +8775,7 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -8779,7 +8799,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" @@ -8796,9 +8816,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2212" }, { @@ -8807,6 +8824,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -8821,7 +8841,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" @@ -8838,11 +8858,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -8859,7 +8879,7 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -8884,7 +8904,7 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -8897,14 +8917,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A lump of clay and a statue" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -8967,15 +8987,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "false" @@ -8991,14 +9008,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" @@ -9034,12 +9051,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004036", "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -9067,12 +9084,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.medindia.net/glossary/venous_tributary.htm" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Deschutes River tributary_of Columbia River" @@ -9102,15 +9119,15 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that ( some ( that some Y?)))" @@ -9129,7 +9146,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" @@ -9162,7 +9179,7 @@ "val" : "attached to (anatomical structure to anatomical structure)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -9182,7 +9199,7 @@ "val" : "Wikipedia:Insertion_(anatomy)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -9195,6 +9212,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { @@ -9203,9 +9223,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that some Y?)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" @@ -9249,7 +9266,7 @@ "val" : "http://dbpedia.org/property/insertion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Wikipedia:Insertion_(anatomy)" @@ -9283,23 +9300,23 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some (\n\t and some (\n\t http://purl.obolibrary.org/obo/GO_0042734 and some (\n\t and some ?Y)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" } ] }, "type" : "PROPERTY", @@ -9322,7 +9339,7 @@ "val" : "http://neurolex.org/wiki/Property:DendriteLocation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -9338,21 +9355,21 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that part_of some ( that some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -9367,7 +9384,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -9476,7 +9493,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -9525,6 +9542,9 @@ "xrefs" : [ ] } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-2620-0345" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" }, { @@ -9536,9 +9556,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A diagnostic testing device utilizes a specimen." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-2620-0345" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-11-08T12:00:00Z" @@ -9554,14 +9571,8 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" @@ -9571,6 +9582,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "synapsed in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" @@ -9608,7 +9625,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -9638,7 +9655,7 @@ "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." @@ -9656,7 +9673,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -9684,23 +9701,23 @@ }, "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Marta Costa" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" } ] }, "type" : "PROPERTY", @@ -9727,7 +9744,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -9791,7 +9808,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -9891,6 +9908,21 @@ }, "type" : "PROPERTY", "lbl" : "existence ends at start of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002349", + "meta" : { + "definition" : { + "val" : "p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment.", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + }, + "type" : "PROPERTY", + "lbl" : "results in determination of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002107", "meta" : { @@ -9901,13 +9933,13 @@ "comments" : [ "Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Marta Costa" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -9944,21 +9976,6 @@ }, "type" : "PROPERTY", "lbl" : "contained in" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002349", - "meta" : { - "definition" : { - "val" : "p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment.", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, - "type" : "PROPERTY", - "lbl" : "results in determination of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0001019", "meta" : { @@ -9982,6 +9999,9 @@ }, "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" }, { @@ -9992,13 +10012,10 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Marta Costa" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" } ] }, "type" : "PROPERTY", @@ -10025,10 +10042,10 @@ "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Marta Costa" + "val" : "https://orcid.org/0000-0001-5948-3092" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" } ] }, "type" : "PROPERTY", @@ -10050,18 +10067,18 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -10076,7 +10093,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -10100,29 +10117,29 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1617-8244" + }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9990-8331" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19243617" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alexander Diehl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Lindsay Cowell" } ] }, "type" : "PROPERTY", @@ -10175,23 +10192,23 @@ }, "comments" : [ "Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Marta Costa" } ] }, "type" : "PROPERTY", @@ -10209,7 +10226,7 @@ "val" : "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -10228,18 +10245,18 @@ }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Marta Costa" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" } ] }, "type" : "PROPERTY", @@ -10253,7 +10270,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -10280,7 +10297,7 @@ "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -10298,12 +10315,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some (\n and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" } ] }, "type" : "PROPERTY", @@ -10318,7 +10335,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -10344,7 +10361,7 @@ "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -10360,7 +10377,7 @@ "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -10385,19 +10402,6 @@ }, "type" : "PROPERTY", "lbl" : "results in breakdown of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002344", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" - } ] - }, - "type" : "PROPERTY", - "lbl" : "results in transport to from or in" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002102", "meta" : { @@ -10407,19 +10411,16 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some (\n and some (\n and some (\n and some ?Y)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" @@ -10430,6 +10431,19 @@ }, "type" : "PROPERTY", "lbl" : "axon synapses in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002344", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + }, + "type" : "PROPERTY", + "lbl" : "results in transport to from or in" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002580", "type" : "PROPERTY", @@ -10454,7 +10468,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -10479,7 +10493,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -10494,44 +10508,44 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", "lbl" : "has target end location" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002576", + "id" : "http://purl.obolibrary.org/obo/RO_0002334", "meta" : { "definition" : { - "val" : "inverse of has skeleton", + "val" : "inverse of regulates", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulated by (processual)" } ] }, "type" : "PROPERTY", - "lbl" : "skeleton of" + "lbl" : "regulated by" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002334", + "id" : "http://purl.obolibrary.org/obo/RO_0002576", "meta" : { "definition" : { - "val" : "inverse of regulates", + "val" : "inverse of has skeleton", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulated by (processual)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", - "lbl" : "regulated by" + "lbl" : "skeleton of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002335", "meta" : { @@ -10542,7 +10556,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -10562,7 +10576,7 @@ "val" : "http://www.jbiomedsem.com/content/4/1/43" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "CLASS", @@ -10576,6 +10590,9 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002575", "val" : "http://purl.obolibrary.org/obo/RO_0002211" }, { @@ -10584,9 +10601,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "directly regulates (processual)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -10601,7 +10615,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -10618,7 +10632,7 @@ "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" }, { "pred" : "http://purl.org/dc/terms/creator", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -10632,7 +10646,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is a grouping relation." @@ -10650,7 +10664,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -10667,7 +10681,7 @@ "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -10715,12 +10729,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "actively involved in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://wiki.geneontology.org/index.php/Involved_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -10735,7 +10749,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" @@ -10751,38 +10765,15 @@ "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" - } ] - }, - "type" : "PROPERTY", - "lbl" : "participates in a biotic-biotic interaction with" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002332", - "meta" : { - "definition" : { - "val" : "p regulates levels of c if p regulates some amount (PATO:0000070) of c", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates levels of (process to entity)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", - "lbl" : "regulates levels of" + "lbl" : "participates in a biotic-biotic interaction with" }, { "id" : "http://purl.obolibrary.org/obo/RO_0001001", "meta" : { @@ -10810,6 +10801,29 @@ }, "type" : "PROPERTY", "lbl" : "derives into" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002332", + "meta" : { + "definition" : { + "val" : "p regulates levels of c if p regulates some amount (PATO:0000070) of c", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates levels of (process to entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + }, + "type" : "PROPERTY", + "lbl" : "regulates levels of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002333", "meta" : { @@ -10820,7 +10834,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -10840,7 +10854,7 @@ "val" : "If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'" }, { "pred" : "http://purl.org/dc/terms/creator", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" @@ -10857,14 +10871,14 @@ }, "comments" : [ "R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C." ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-10-21T19:46:34Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/oborel/obo-relations/issues/164" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "part-of is homeomorphic for independent continuants." @@ -10881,11 +10895,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "UBERON:cjm" @@ -10906,7 +10920,7 @@ "val" : "GOC:cjm" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -10921,7 +10935,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -10937,6 +10951,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "executes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "catalyzes" @@ -10955,9 +10972,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -10971,7 +10985,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" @@ -10991,7 +11005,7 @@ "val" : "false" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -11006,12 +11020,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -11029,7 +11043,7 @@ "val" : "" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -11042,17 +11056,17 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "causally influences (entity-centric)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" } ] }, "type" : "PROPERTY", @@ -11066,7 +11080,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" @@ -11082,11 +11096,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -11100,14 +11114,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "Gene Ontology Consortium" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" @@ -11122,9 +11133,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." @@ -11137,6 +11145,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -11149,11 +11160,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Wikipedia:Antagonist_(muscle)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -11194,14 +11205,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-09-26T00:00:32Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" } ] }, "type" : "PROPERTY", @@ -11228,11 +11239,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -11260,7 +11271,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-09-26T01:08:58Z" @@ -11269,69 +11280,69 @@ "type" : "PROPERTY", "lbl" : "results in changes to anatomical or cellular structure" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002321", + "id" : "http://purl.obolibrary.org/obo/RO_0002563", "meta" : { - "definition" : { - "val" : "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" - } ] - }, - "type" : "PROPERTY", - "lbl" : "ecologically related to" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002563", - "meta" : { - "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", "lbl" : "interaction relation helper property" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002564", + "id" : "http://purl.obolibrary.org/obo/RO_0002321", "meta" : { + "definition" : { + "val" : "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" } ] }, "type" : "PROPERTY", - "lbl" : "molecular interaction relation helper property" + "lbl" : "ecologically related to" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002322", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "adapted for" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", "lbl" : "confers advantage in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002564", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + }, + "type" : "PROPERTY", + "lbl" : "molecular interaction relation helper property" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002560", "meta" : { @@ -11356,11 +11367,11 @@ "comments" : [ "x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x." ], "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/25052702" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -11370,7 +11381,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" @@ -11404,7 +11415,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -11414,7 +11425,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -11424,14 +11435,14 @@ "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://en.wikipedia.org/wiki/Allelopathy" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://eol.org/schema/terms/allelopathyYes" @@ -11449,7 +11460,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "regulates localization of" @@ -11473,15 +11484,15 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "inheres in part of" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -11492,7 +11503,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -11506,14 +11517,14 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GOC:mtg_berkeley_2013" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -11524,7 +11535,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -11547,6 +11558,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" }, { @@ -11555,9 +11569,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -11575,6 +11586,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-06-05T17:55:39Z" @@ -11584,12 +11598,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/oborel/obo-relations/pull/173" - }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "Chris Mungall" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "CLASS", @@ -11603,7 +11614,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -11633,7 +11644,7 @@ "val" : "http://eol.org/schema/terms/hyperparasitoidOf" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" @@ -11642,40 +11653,40 @@ "type" : "PROPERTY", "lbl" : "hyperparasite of" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002547", + "id" : "http://purl.obolibrary.org/obo/RO_0002305", "meta" : { "definition" : { - "val" : "Count of number of days intervening between the start of the stage and the time of coitum.", + "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.", "xrefs" : [ ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)" + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" } ] }, "type" : "PROPERTY", - "lbl" : "start, days post coitum" + "lbl" : "causally upstream of, negative effect" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002305", + "id" : "http://purl.obolibrary.org/obo/RO_0002547", "meta" : { "definition" : { - "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.", + "val" : "Count of number of days intervening between the start of the stage and the time of coitum.", "xrefs" : [ ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "cjm" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)" } ] }, "type" : "PROPERTY", - "lbl" : "causally upstream of, negative effect" + "lbl" : "start, days post coitum" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002548", "meta" : { @@ -11722,7 +11733,7 @@ "val" : "May be merged into parent relation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -11743,7 +11754,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/creator", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -11772,11 +11783,11 @@ "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y." ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-4366-3088" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Pier Buttigieg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "adapted for living in" @@ -11812,7 +11823,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/creator", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002411" @@ -11842,20 +11853,20 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "Chris Mungall" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-06-05T17:35:04Z" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "Marie Angelique Laporte" + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "Austin Meier" + "val" : "https://orcid.org/0000-0002-8461-9745" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -11906,14 +11917,14 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002300", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "May be merged into parent relation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "foramen ovale closure SubClassOf results in disappearance of foramen ovale" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -11996,7 +12007,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "CLASS", @@ -12010,7 +12021,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair." @@ -12027,7 +12038,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence." @@ -12101,7 +12112,7 @@ "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -12118,7 +12129,7 @@ "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" @@ -12137,12 +12148,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "contained by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -12151,15 +12162,15 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002526", "meta" : { "definition" : { - "val" : "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y.", + "val" : "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y.", "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -12168,18 +12179,18 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002527", "meta" : { "definition" : { - "val" : "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y.", + "val" : "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y.", "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "disconnected from" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -12192,11 +12203,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -12209,14 +12220,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -12229,11 +12240,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" @@ -12254,11 +12265,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -12267,15 +12278,15 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002524", "meta" : { "definition" : { - "val" : "x has subsequence y iff all of the sequence parts of x are sequence parts of y", + "val" : "x has subsequence y iff all of the sequence parts of y are sequence parts of x", "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" @@ -12298,7 +12309,7 @@ "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -12312,7 +12323,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" @@ -12334,6 +12345,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" }, { @@ -12345,9 +12359,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -12365,15 +12376,15 @@ }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Two consecutive DNA residues are sequentially adjacent" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Two exons on a processed transcript that were previously connected by an intron are adjacent" @@ -12394,15 +12405,15 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "started by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -12421,12 +12432,12 @@ }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "starts" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -12440,7 +12451,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" @@ -12461,28 +12472,11 @@ "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", "lbl" : "transcribed to" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002512", - "meta" : { - "definition" : { - "val" : "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" - } ] - }, - "type" : "PROPERTY", - "lbl" : "ribosomal translation of" }, { "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "meta" : { @@ -12498,7 +12492,24 @@ } ] }, "type" : "PROPERTY", - "lbl" : "valid_for_go_annotation_extension" + "lbl" : "valid_for_go_annotation_extension" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002512", + "meta" : { + "definition" : { + "val" : "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + } ] + }, + "type" : "PROPERTY", + "lbl" : "ribosomal translation of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002513", "meta" : { @@ -12507,11 +12518,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -12531,7 +12542,7 @@ "val" : "ended by" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" @@ -12551,11 +12562,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "ends" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" @@ -12574,14 +12585,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -12625,7 +12636,7 @@ "val" : "has intermediate product" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -12644,7 +12655,7 @@ "val" : "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -12673,12 +12684,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -12687,11 +12698,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002502", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/BFO_0000169" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", @@ -12705,26 +12716,26 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "determined by (system to material entity)" }, { "pred" : "http://purl.org/dc/terms/creator", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-4366-3088" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/24330602" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A coral reef environment is determined by a particular coral reef" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" - }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "Pier Buttigieg" } ] }, "type" : "PROPERTY", @@ -12739,7 +12750,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "determines (material entity to system)" @@ -12757,7 +12768,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] }, "type" : "PROPERTY", @@ -12789,14 +12800,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Damion Dooley" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'egg white' 'has substance removed' some 'egg yolk'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" } ] }, "type" : "PROPERTY", @@ -12810,7 +12821,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Damion Dooley" + "val" : "https://orcid.org/0000-0002-8844-9165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "muffin 'has substance added' some 'baking soda'" @@ -12836,7 +12847,7 @@ "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Damion Dooley" + "val" : "https://orcid.org/0000-0002-8844-9165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "bread 'has primary substance added' some 'flour'" @@ -12854,12 +12865,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "sardine has consumer some homo sapiens" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Damion Dooley" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" } ] }, "type" : "PROPERTY", @@ -12876,7 +12887,7 @@ "val" : "sardines 'immersed in' some 'oil and mustard'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Damion Dooley" + "val" : "https://orcid.org/0000-0002-8844-9165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" @@ -13059,7 +13070,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -13073,7 +13084,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -13087,7 +13098,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -13101,7 +13112,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -13115,7 +13126,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -13133,7 +13144,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -13161,7 +13172,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -13178,7 +13189,7 @@ "val" : "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -13195,7 +13206,7 @@ "val" : "indirectly inhibits" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -13212,7 +13223,7 @@ "val" : "indirectly activates" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -13229,7 +13240,7 @@ "val" : "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -13253,7 +13264,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -13267,7 +13278,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -13281,7 +13292,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -13312,7 +13323,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] }, "type" : "PROPERTY", @@ -14069,7 +14080,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Patrick Ray" + "val" : "https://orcid.org/0000-0002-5260-9315" } ] }, "type" : "PROPERTY", @@ -14083,7 +14094,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Shawn Tan" + "val" : "https://orcid.org/0000-0001-7258-9596" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." @@ -14165,7 +14176,7 @@ "val" : "C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Patrick Ray" + "val" : "https://orcid.org/0000-0002-5260-9315" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation is not meant to capture the relation between occurrents and data." @@ -14285,14 +14296,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002505", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002578", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002211" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002555", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002574" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002578", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002211" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002375", "pred" : "subPropertyOf", @@ -14341,14 +14352,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002083", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002081" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0011013", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0011004" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002083", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002081" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004007", "pred" : "subPropertyOf", @@ -14489,14 +14500,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004047", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002016", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002017" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004005", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0004000" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002016", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002017" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002411", "pred" : "subPropertyOf", @@ -14661,14 +14672,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004028", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002410" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002381", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002488", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002490" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002381", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0001023", "pred" : "subPropertyOf", @@ -14989,14 +15000,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012006", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012004" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002230", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000022", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002230", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002590", "pred" : "subPropertyOf", @@ -15233,6 +15244,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002315", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0040036" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002455", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002442" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002466", "pred" : "subPropertyOf", @@ -15241,10 +15256,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002252", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002375" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002455", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002442" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002263", "pred" : "subPropertyOf", @@ -15469,14 +15480,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002203", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002388" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000037", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000034", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000037" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000037", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002203", "pred" : "subPropertyOf", @@ -15585,14 +15596,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002533", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/RO_0002532" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002260", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000087" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002022", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002334" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002260", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000087" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000012", "pred" : "subPropertyOf", @@ -15893,14 +15904,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002229", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0042734", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044456" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004002", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0004012" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0042734", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0044456" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002384", "pred" : "subPropertyOf", @@ -16033,14 +16044,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002245", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002206" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002231", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002479" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002180", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002231", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002479" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013005", "pred" : "subPropertyOf", @@ -16101,14 +16112,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002085", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002092" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002087", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002090" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002084", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002093" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002087", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002090" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0011004", "pred" : "subPropertyOf", @@ -16129,26 +16140,26 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002004", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0001018" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002476", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002258" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002458", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002476", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002258" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002233", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0001020", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0001022" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002006", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002130" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0001020", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0001022" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002622", "pred" : "inverseOf", @@ -16229,14 +16240,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002216", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002328" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002024", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002022" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002622", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002618" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002024", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002022" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002387", "pred" : "subPropertyOf", @@ -16613,26 +16624,26 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0000079", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000085" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002090", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000063" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002159", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002320" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000045", + "sub" : "http://purl.obolibrary.org/obo/RO_0002090", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000063" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002618", + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000045", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002574" + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002585", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0040036" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002618", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002574" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002623", "pred" : "subPropertyOf", @@ -16841,14 +16852,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012009", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002304" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002177", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002323" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003305", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002177", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002323" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002551", "pred" : "inverseOf", @@ -16893,14 +16904,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004014", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003303" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002349", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002295" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000054", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000062" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002349", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002295" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002445", "pred" : "subPropertyOf", @@ -16969,14 +16980,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0013003", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0013001" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002286", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002384" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002026", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002323" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002286", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002384" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000050", "pred" : "inverseOf", @@ -17049,14 +17060,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0045202", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CARO_0000003" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000063", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002222" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002014", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002013" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000063", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002222" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002377", "pred" : "subPropertyOf", @@ -17421,14 +17432,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002641", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002635" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002091", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002222" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002326", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002329" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002091", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002222" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002512", "pred" : "inverseOf", @@ -17698,12 +17709,12 @@ "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 146 Logical Axioms: 45]" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-01-04" + "val" : "2023-02-19" }, { "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : " https://github.com/oborel/obo-relations/" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-01-04/ro.owl" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-02-19/ro.owl" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ ], @@ -17812,14 +17823,6 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000019", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -17828,10 +17831,18 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000031", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -17978,13 +17989,13 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_HOM0000000", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", - "pred" : "http://purl.obolibrary.org/obo/RO_HOM0000000", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", "pred" : "http://purl.obolibrary.org/obo/RO_HOM0000000", "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", + "pred" : "http://purl.obolibrary.org/obo/RO_HOM0000000", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002414", diff --git a/ro.obo b/ro.obo index b43a1292..1ce182cd 100644 --- a/ro.obo +++ b/ro.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2023-01-04 +data-version: releases/2023-02-19 subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -26,8 +26,8 @@ property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations O property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2023-01-04" xsd:string -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: (first order logic expression)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (nominally disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is homeomorphic for)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (located in)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf()))\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (gene product of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (transcribed from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (ribosomal translation of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (ribosomally translates to)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has inflammation site)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nSubClassOf( owl:Thing)\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nSubClassOf( owl:Thing)\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nSubClassOf( owl:Thing)\n\n# Class: (ubiquitin-protein ligase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( owl:Thing)\n\n# Class: (nucleus)\n\nSubClassOf( owl:Thing)\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( owl:Thing)\nSubClassOf( ObjectHasSelf())\n\n# Class: (cell projection)\n\nSubClassOf( owl:Thing)\n\n# Class: (synapse part)\n\nSubClassOf( owl:Thing)\n\n# Class: (sequentially ordered entity)\n\nSubClassOf( owl:Thing)\n\n# Class: owl:Nothing (owl:Nothing)\n\nSubClassOf(owl:Nothing owl:Nothing)\n\n# Class: ()\n\nSubClassOf( owl:Thing)\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) +property_value: owl:versionInfo "2023-02-19" xsd:string +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: (first order logic expression)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (nominally disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is homeomorphic for)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (located in)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf()))\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (gene product of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (transcribed from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (ribosomal translation of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (ribosomally translates to)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has inflammation site)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nSubClassOf( owl:Thing)\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nSubClassOf( owl:Thing)\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nSubClassOf( owl:Thing)\n\n# Class: (ubiquitin-protein ligase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( owl:Thing)\n\n# Class: (nucleus)\n\nSubClassOf( owl:Thing)\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( owl:Thing)\nSubClassOf( ObjectHasSelf())\n\n# Class: (cell projection)\n\nSubClassOf( owl:Thing)\n\n# Class: (synapse part)\n\nSubClassOf( owl:Thing)\n\n# Class: (sequentially ordered entity)\n\nSubClassOf( owl:Thing)\n\n# Class: owl:Nothing (owl:Nothing)\n\nSubClassOf(owl:Nothing owl:Nothing)\n\n# Class: ()\n\nSubClassOf( owl:Thing)\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\") Annotation(rdfs:label \"infer input from direct reg\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\") Annotation(rdfs:label \"involved in BP\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) [Term] id: BFO:0000002 @@ -386,12 +386,12 @@ id: RO:0002310 name: exposure event or process def: "A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." [] is_a: BFO:0000015 ! process -property_value: http://purl.org/dc/terms/creator "Chris Mungall" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," xsd:string property_value: IAO:0000112 "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes." xsd:anyURI property_value: IAO:0000116 "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions." xsd:string property_value: seeAlso https://github.com/oborel/obo-relations/pull/173 xsd:anyURI -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:55:39Z [Term] @@ -399,14 +399,14 @@ id: RO:0002532 name: sequentially ordered entity def: "Any entity that is ordered in discrete units along a linear axis." [] relationship: RO:0002524 RO:0002533 ! has subsequence sequence atomic unit -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 [Term] id: RO:0002533 name: sequence atomic unit def: "Any individual unit of a collection of like units arranged in a linear order" [] is_a: RO:0002532 ! sequentially ordered entity -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair." xsd:string [Term] @@ -414,7 +414,7 @@ id: RO:0002534 name: sequence bearer def: "Any entity that can be divided into parts such that each part is an atomical unit of a sequence" [] is_a: RO:0002532 ! sequentially ordered entity -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence." xsd:string [Term] @@ -423,7 +423,7 @@ name: system def: "A material entity consisting of multiple components that are causally integrated." [] is_a: BFO:0000040 ! material entity property_value: IAO:0000116 "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.jbiomedsem.com/content/4/1/43 xsd:string [Term] @@ -744,7 +744,7 @@ def: "OBSOLETE A relation that holds between two neurons connected directly via comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_transitive: true is_obsolete: true @@ -756,7 +756,7 @@ def: "OBSOLETE A relation that holds between a neuron that is synapsed_to anothe comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_transitive: true is_obsolete: true @@ -768,7 +768,7 @@ def: "OBSOLETE A relation that holds between a neuron that is synapsed_by anothe comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_transitive: true is_obsolete: true @@ -903,7 +903,7 @@ id: RO:0002001 name: aligned with property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "May be obsoleted, see https://github.com/oborel/obo-relations/issues/260" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_transitive: true @@ -914,7 +914,7 @@ def: "a relation between a material entity and a 2D immaterial entity (the bound property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has boundary" xsd:string property_value: IAO:0000118 "has_2D_boundary" xsd:string property_value: RO:0001900 RO:0001901 @@ -927,14 +927,14 @@ id: RO:0002003 name: electrically_synapsed_to def: "A relation that holds between two neurons that are electrically coupled via gap junctions." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0002170 ! connected to [Typedef] id: RO:0002004 name: tracheates def: "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to)." [] -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: CARO:0000003 ! connected anatomical structure range: CARO:0000003 ! connected anatomical structure is_a: RO:0001018 ! contained in @@ -943,7 +943,7 @@ is_a: RO:0001018 ! contained in id: RO:0002005 name: innervated_by property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: CARO:0000003 ! connected anatomical structure range: CARO:0001001 ! neuron projection bundle inverse_of: RO:0002134 ! innervates @@ -952,7 +952,7 @@ inverse_of: RO:0002134 ! innervates id: RO:0002006 name: has synaptic terminal of property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0002131 ! overlaps inverse_of: RO:0002130 ! has synaptic terminal in @@ -962,7 +962,7 @@ name: bounding layer of def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" [] comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 ! material entity is_a: BFO:0000050 ! part of @@ -973,7 +973,7 @@ def: "A relation that holds between two linear structures that are approximately comment: Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. subset: ro-eco property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0002323 ! mereotopologically related to [Typedef] @@ -981,7 +981,7 @@ id: RO:0002009 name: cell expresses def: "A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g." [] property_value: http://purl.org/dc/terms/description "x 'cell expresses' y iff:\ncell(x)\nAND gene(y)\nAND exists some 'transcription, DNA templated (GO_0006351)'(t)\nAND t occurs_in x\nAND t has_input y" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: CL:0000000 ! cell is_a: RO:0002292 ! expresses @@ -989,7 +989,7 @@ is_a: RO:0002292 ! expresses id: RO:0002010 name: regulates in other organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 ! process range: BFO:0000015 ! process is_a: RO:0002418 ! causally upstream of or within @@ -999,7 +999,7 @@ id: RO:0002011 name: regulates transport of def: "A relationship that holds between a process that regulates a transport process and the entity transported by that process." [] subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 holds_over_chain: RO:0002211 RO:0002313 [Typedef] @@ -1153,6 +1153,7 @@ name: simultaneous with comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_transitive: true is_a: RO:0002081 ! before or simultaneous with @@ -1178,7 +1179,7 @@ inverse_of: RO:0002093 ! ends during id: RO:0002085 name: encompasses comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "di" xsd:string is_transitive: true is_a: RO:0002088 ! during which starts @@ -1228,6 +1229,7 @@ name: immediately precedes comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "ends_at_start_of" xsd:string property_value: IAO:0000118 "meets" xsd:string property_value: RO:0002575 BFO:0000063 @@ -1275,7 +1277,7 @@ id: RO:0002100 name: has soma location def: "Relation between a neuron and an anatomical structure that its soma is part of." [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron range: CARO:0000003 ! connected anatomical structure @@ -1289,7 +1291,7 @@ name: fasciculates with def: "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 @@ -1304,9 +1306,8 @@ name: axon synapses in def: "Relation between a neuron and some structure its axon forms (chemical) synapses in." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002113 ! has presynaptic terminal in @@ -1319,8 +1320,8 @@ name: synapsed by def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002485 ! receives input from inverse_of: RO:0002120 ! synapsed to @@ -1332,9 +1333,9 @@ name: has plasma membrane part def: "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." [] property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Alexander Diehl" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 ! material anatomical entity @@ -1349,8 +1350,8 @@ def: "A relation between a motor neuron and a muscle that it synapses to via a t comment: Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002120 ! synapsed to inverse_of: RO:0002109 ! synapsed_by_via_type_Ib_bouton @@ -1363,8 +1364,8 @@ def: "A relation between a motor neuron and a muscle that it synapses to via a t comment: Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002120 ! synapsed to inverse_of: RO:0002112 ! synapsed_by_via_type_Is_bouton @@ -1376,8 +1377,8 @@ name: synapsed_via_type_II_bouton_to def: "A relation between a motor neuron and a muscle that it synapses to via a type II bouton." [] comment: Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002120 ! synapsed to inverse_of: RO:0002108 ! synapsed_by_via_type_II_bouton @@ -1390,8 +1391,8 @@ def: "Relation between a muscle and a motor neuron that synapses to it via a typ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002103 ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" [] @@ -1403,8 +1404,8 @@ def: "Relation between a muscle and a motor neuron that synapses to it via a typ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002103 ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -1415,8 +1416,8 @@ name: has postsynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "synapsed in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron @@ -1440,8 +1441,8 @@ def: "Relation between a muscle and a motor neuron that synapses to it via a typ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002103 ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -1487,8 +1488,8 @@ def: " Relation between a neuron and an anatomical structure (including cells) t comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n ‘synapse ; GO:0045202’ that has_part some (\n ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002486 ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -1499,8 +1500,8 @@ name: dendrite synapsed in def: "Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.\n\n " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002110 ! has postsynaptic terminal in @@ -1513,7 +1514,7 @@ name: has synaptic terminal in def: "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has synapse in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron @@ -1544,7 +1545,7 @@ name: has fasciculating neuron projection def: "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 @@ -1557,7 +1558,7 @@ name: innervates def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CARO:0001001 ! neuron projection bundle transitive_over: BFO:0000050 ! part of @@ -1568,7 +1569,7 @@ id: RO:0002150 name: continuous with def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 @@ -1637,7 +1638,7 @@ def: "x only in taxon y if and only if x is in taxon y, and there is no other or property_value: IAO:0000112 "lactation SubClassOf 'only in taxon' some 'Mammalia'" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints @@ -1650,8 +1651,8 @@ def: "x is in taxon y if an only if y is an organism, and the relationship betwe comment: Connects a biological entity to its taxon of origin. subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Jennifer Deegan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints @@ -1674,7 +1675,7 @@ def: "A is spatially_disjoint_from B if and only if they have no parts in common subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 @@ -1749,7 +1750,7 @@ name: has phenotype def: "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: UPHENO:0001001 ! phenotype is_a: RO:0016001 ! has phenotype or disease inverse_of: RO:0002201 ! phenotype of @@ -1761,7 +1762,7 @@ def: "inverse of has phenotype" [] subset: ro-eco subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_functional: true [Typedef] @@ -1770,10 +1771,10 @@ name: develops from def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] comment: This is the transitive form of the develops from relation property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_transitive: true @@ -1786,9 +1787,9 @@ name: develops into def: "inverse of develops from" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 is_transitive: true is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002387 ! has potential to develop into @@ -1800,7 +1801,7 @@ name: gene product of def: "definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\"" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000004 ! independent continuant range: BFO:0000002 ! continuant holds_over_chain: RO:0002512 RO:0002510 @@ -1814,7 +1815,7 @@ def: "x has gene product y if and only if x is a gene (SO:0000704) that particip property_value: IAO:0000112 "every HOTAIR lncRNA is the gene product of some HOXC gene" xsd:string property_value: IAO:0000112 "every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000002 ! continuant range: BFO:0000004 ! independent continuant holds_over_chain: RO:0002511 RO:0002513 @@ -1826,7 +1827,7 @@ name: expressed in def: "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" [] property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000002 ! continuant range: CARO:0000006 ! material anatomical entity is_a: RO:0002330 ! genomically related to @@ -1838,10 +1839,10 @@ id: RO:0002207 name: directly develops from def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "has developmental precursor" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000119 "FBbt" xsd:string property_value: RO:0002575 RO:0002202 is_a: RO:0002202 ! develops from @@ -1877,9 +1878,9 @@ def: "p regulates q iff p is causally upstream of q, the execution of p is not c subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Hill" xsd:string -property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 +property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string @@ -1901,7 +1902,7 @@ def: "p negatively regulates q iff p regulates q, and p decreases the rate or ma subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 @@ -1917,7 +1918,7 @@ def: "p positively regulates q iff p regulates q, and p increases the rate or ma subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002211 @@ -1938,7 +1939,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" xsd:string property_value: IAO:0000116 "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants." xsd:string property_value: IAO:0000116 "TODO: add homeomorphy axiom" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 [Typedef] id: RO:0002215 @@ -1947,7 +1948,7 @@ def: "A relation between a material entity (such as a cell) and a process, in wh subset: ro-eco property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 @@ -1960,7 +1961,7 @@ is_a: RO:0002216 ! capable of part of id: RO:0002216 name: capable of part of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} @@ -1972,7 +1973,7 @@ id: RO:0002217 name: obsolete actively participates in def: "OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role" [] comment: Obsoleted as the inverse property was obsoleted. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "agent in" xsd:string is_obsolete: true replaced_by: RO:0002608 @@ -1981,7 +1982,7 @@ replaced_by: RO:0002608 id: RO:0002218 name: obsolete has active participant def: "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has agent" xsd:string is_obsolete: true replaced_by: RO:0002500 @@ -1991,7 +1992,7 @@ id: RO:0002219 name: surrounded by def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: RO:0002220 ! adjacent to inverse_of: RO:0002221 ! surrounds @@ -2009,7 +2010,7 @@ property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cy property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant @@ -2021,7 +2022,7 @@ name: surrounds def: "inverse of surrounded by" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: RO:0002220 ! adjacent to @@ -2032,7 +2033,7 @@ comment: A relation that holds between two occurrents. This is a grouping relati subset: ro-eco property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string domain: BFO:0000003 ! occurrent @@ -2045,6 +2046,7 @@ def: "inverse of starts with" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Allen" xsd:string is_a: BFO:0000050 ! part of is_a: RO:0002222 ! temporally related to @@ -2058,6 +2060,7 @@ subset: ro-eco property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string is_transitive: true is_a: BFO:0000051 ! has part @@ -2068,7 +2071,7 @@ id: RO:0002225 name: develops from part of def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002207 BFO:0000050 is_a: RO:0002202 ! develops from @@ -2077,7 +2080,7 @@ id: RO:0002226 name: develops in def: "x develops_in y if x is located in y whilst x is developing" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string domain: CARO:0000000 ! anatomical entity @@ -2103,6 +2106,7 @@ def: "inverse of ends with" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: BFO:0000050 ! part of is_a: RO:0002222 ! temporally related to inverse_of: RO:0002230 ! ends with @@ -2114,6 +2118,7 @@ def: "x ends with y if and only if x has part y and the time point at which x en subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "finished by" xsd:string is_transitive: true is_a: BFO:0000051 ! has part @@ -2125,7 +2130,7 @@ name: has start location def: "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant @@ -2138,7 +2143,7 @@ name: has end location def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant @@ -2154,7 +2159,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 ! process holds_over_chain: RO:0002224 RO:0002233 @@ -2170,7 +2175,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string holds_over_chain: RO:0002230 RO:0002234 is_a: RO:0000057 ! has participant @@ -2198,7 +2203,7 @@ is_a: RO:0002444 ! parasite of id: RO:0002238 name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] -property_value: IAO:0000117 "Bill Duncan (https://orcid.org/0000-0001-9625-1899)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: RO:0000057 ! has participant @@ -2294,7 +2299,7 @@ name: has developmental contribution from def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 ! anatomical entity range: CARO:0000000 ! anatomical entity holds_over_chain: BFO:0000051 RO:0002202 @@ -2307,7 +2312,7 @@ name: developmentally contributes to def: "inverse of has developmental contribution from" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002203 BFO:0000050 is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002385 ! has potential to developmentally contribute to @@ -2317,9 +2322,9 @@ id: RO:0002256 name: developmentally induced by def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string property_value: IAO:0000119 GO:0001759 xsd:string @@ -2335,7 +2340,7 @@ id: RO:0002257 name: developmentally induces def: "Inverse of developmentally induced by" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002386 ! has potential to developmentally induce @@ -2346,7 +2351,7 @@ def: "Candidate definition: x developmentally related to y if and only if there comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant @@ -2398,7 +2403,7 @@ name: developmentally replaces def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "replaces" xsd:string is_a: RO:0002258 ! developmentally preceded by @@ -2407,7 +2412,7 @@ id: RO:0002286 name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] @@ -2415,7 +2420,7 @@ id: RO:0002287 name: part of developmental precursor of property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000050 RO:0002210 is_a: RO:0002286 ! developmentally succeeded by @@ -2425,7 +2430,7 @@ name: ubiquitously expressed in def: "x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002206 ! expressed in inverse_of: RO:0002293 ! ubiquitously expresses @@ -2434,7 +2439,7 @@ id: RO:0002292 name: expresses def: "Inverse of 'expressed in'" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002330 ! genomically related to [Typedef] @@ -2443,7 +2448,7 @@ name: ubiquitously expresses def: "inverse of ubiquiotously expressed in" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002292 ! expresses [Typedef] @@ -2452,7 +2457,7 @@ name: results in developmental progression of def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 ! biological_process range: CARO:0000000 ! anatomical entity @@ -2467,7 +2472,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2481,7 +2486,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: RO:0002234 ! has output is_a: RO:0002295 ! results in developmental progression of @@ -2497,7 +2502,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2512,7 +2517,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2522,7 +2527,7 @@ id: RO:0002300 name: results in disappearance of property_value: IAO:0000112 "foramen ovale closure SubClassOf results in disappearance of foramen ovale" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: RO:0002552 ! results in ending of @@ -2531,7 +2536,7 @@ id: RO:0002301 name: results in developmental regression of property_value: IAO:0000112 "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: RO:0002552 ! results in ending of @@ -2540,7 +2545,7 @@ id: RO:0002302 name: is treated by substance def: "Inverse of 'is substance that treats'" [] subset: RO:0002259 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 is_a: RO:0002410 ! causally related to inverse_of: RO:0002606 ! is substance that treats @@ -2552,7 +2557,7 @@ comment: A population of xs will possess adaptations (either evolved naturally o subset: ro-eco property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Pier Buttigieg" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string domain: CARO:0001010 ! organism or virus or viroid range: ENVO:01000254 ! environmental system @@ -2565,7 +2570,7 @@ def: "p is causally upstream of, positive effect q iff p is casually upstream of comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 is_a: RO:0002411 ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -2576,7 +2581,7 @@ name: causally upstream of, negative effect def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 is_a: RO:0002411 ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect @@ -2585,17 +2590,17 @@ is_a: RO:0004046 ! causally upstream of or within, negative effect id: RO:0002309 name: has exposure stimulus def: "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." [] -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 is_a: RO:0002244 ! related via exposure to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:35:04Z [Typedef] id: RO:0002312 name: evolutionary variant of -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002320 ! evolutionarily related to [Typedef] @@ -2605,7 +2610,7 @@ def: "Holds between p and c when p is a localization process (localization cover subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "regulates localization of" xsd:string is_a: RO:0002337 ! related via localization to is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2615,7 +2620,7 @@ id: RO:0002314 name: characteristic of part of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 @@ -2632,7 +2637,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string range: CARO:0000003 ! connected anatomical structure is_a: RO:0002295 ! results in developmental progression of @@ -2642,7 +2647,7 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure id: RO:0002320 name: evolutionarily related to def: "A relationship that holds via some environmental process" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." xsd:string [Typedef] @@ -2651,7 +2656,7 @@ name: ecologically related to def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] subset: ro-eco property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string [Typedef] @@ -2659,7 +2664,7 @@ id: RO:0002322 name: confers advantage in subset: ro-eco property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "adapted for" xsd:string range: ENVO:01000254 ! environmental system is_a: RO:0002321 ! ecologically related to @@ -2668,7 +2673,7 @@ is_a: RO:0002321 ! ecologically related to id: RO:0002323 name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string property_value: RO:0001900 RO:0001901 @@ -2676,7 +2681,7 @@ property_value: RO:0001900 RO:0001901 id: RO:0002324 name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] @@ -2684,9 +2689,8 @@ id: RO:0002325 name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -2700,7 +2704,7 @@ property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a het property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string is_a: RO:0002216 ! capable of part of is_a: RO:0002329 ! part of structure that is capable of @@ -2711,7 +2715,7 @@ name: enables def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string property_value: IAO:0000118 "has" xsd:string @@ -2727,14 +2731,14 @@ transitive_over: RO:0002017 ! has component activity id: RO:0002328 name: functionally related to def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string [Typedef] id: RO:0002329 name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} is_a: RO:0002328 ! functionally related to @@ -2743,7 +2747,7 @@ is_a: RO:0002328 ! functionally related to id: RO:0002330 name: genomically related to def: "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant @@ -2752,7 +2756,7 @@ range: BFO:0000002 ! continuant id: RO:0002331 name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in @@ -2766,7 +2770,7 @@ id: RO:0002332 name: regulates levels of def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 ! process @@ -2778,7 +2782,7 @@ id: RO:0002333 name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0000057 ! has participant is_a: RO:0002328 ! functionally related to @@ -2787,7 +2791,7 @@ id: RO:0002334 name: regulated by def: "inverse of regulates" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 ! process range: BFO:0000015 ! process @@ -2799,7 +2803,7 @@ id: RO:0002335 name: negatively regulated by def: "inverse of negatively regulates" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002334 ! regulated by [Typedef] @@ -2807,14 +2811,14 @@ id: RO:0002336 name: positively regulated by def: "inverse of positively regulates" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002334 ! regulated by [Typedef] id: RO:0002337 name: related via localization to def: "A relationship that holds via some process of localization" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 ! process range: BFO:0000002 ! continuant @@ -2826,7 +2830,7 @@ def: "This relationship holds between p and l when p is a transport or localizat subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002344 ! results in transport to from or in transitive_over: BFO:0000050 ! part of @@ -2837,7 +2841,7 @@ def: "This relationship holds between p and l when p is a transport or localizat subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002344 ! results in transport to from or in transitive_over: BFO:0000050 ! part of @@ -2846,14 +2850,14 @@ id: RO:0002340 name: imports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002020 ! transports [Typedef] id: RO:0002341 name: results in transport along def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to [Typedef] @@ -2861,7 +2865,7 @@ id: RO:0002342 name: results in transport across def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002021 ! occurs across is_a: RO:0002344 ! results in transport to from or in @@ -2869,7 +2873,7 @@ is_a: RO:0002344 ! results in transport to from or in id: RO:0002343 name: results in growth of property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2877,7 +2881,7 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure id: RO:0002344 name: results in transport to from or in property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to [Typedef] @@ -2885,7 +2889,7 @@ id: RO:0002345 name: exports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002020 ! transports [Typedef] @@ -2896,7 +2900,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 ! cell is_a: RO:0002295 ! results in developmental progression of @@ -2907,7 +2911,7 @@ def: "p 'results in determination of' c if and only if p is a developmental proc subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 ! cell is_a: RO:0002295 ! results in developmental progression of @@ -2937,7 +2941,7 @@ name: input of def: "inverse of has input" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0000056 ! participates in is_a: RO:0002328 ! functionally related to @@ -2947,21 +2951,21 @@ name: output of def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0000056 ! participates in is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002354 name: formed as result of -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002353 ! output of [Typedef] id: RO:0002355 name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2972,7 +2976,7 @@ def: "The relationship linking a cell and its participation in a process that re subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 ! cell is_a: RO:0002295 ! results in developmental progression of @@ -2980,14 +2984,14 @@ is_a: RO:0002295 ! results in developmental progression of id: RO:0002357 name: results in developmental induction of def: "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of [Typedef] id: RO:0002360 name: has dendrite location property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002131 ! overlaps [Typedef] @@ -2995,7 +2999,7 @@ id: RO:0002371 name: attached to def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: RO:0002170 ! connected to @@ -3005,7 +3009,7 @@ is_a: RO:0002177 ! attached to part of id: RO:0002372 name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! connected anatomical structure @@ -3016,7 +3020,7 @@ is_a: RO:0002567 ! biomechanically related to id: RO:0002373 name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! connected anatomical structure @@ -3031,8 +3035,7 @@ comment: A has_fused_element B does not imply that A has_part some B: rather tha synonym: "has fused element" BROAD [] property_value: IAO:0000112 "false" xsd:boolean property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 is_a: RO:0002156 ! derived by descent from @@ -3041,7 +3044,7 @@ id: RO:0002375 name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 @@ -3059,7 +3062,7 @@ subset: ro-eco property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string @@ -3079,7 +3082,7 @@ comment: This is both a mereotopological relationship and a relationship defined subset: ro-eco property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string @@ -3092,7 +3095,7 @@ name: anabranch of def: "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." [] subset: ro-eco property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "anastomoses with" xsd:string is_a: RO:0002377 ! distributary of disjoint_from: RO:0002382 ! proper distributary of @@ -3103,7 +3106,7 @@ id: RO:0002379 name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: RO:0002131 ! overlaps @@ -3113,7 +3116,7 @@ name: branching part of def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] subset: ro-eco property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso FMA:85994 xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 holds_over_chain: RO:0002377 RO:0002381 @@ -3128,7 +3131,7 @@ def: "x main_stem_of y if y is a branching structure and x is a channel that tra subset: ro-eco property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: BFO:0000050 ! part of is_a: RO:0002375 ! in branching relationship with @@ -3139,7 +3142,7 @@ name: proper distributary of def: "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" [] subset: ro-eco property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002377 ! distributary of [Typedef] @@ -3148,7 +3151,7 @@ name: proper tributary of def: "x proper_tributary_of y iff x tributary_of y and x does not originate from y" [] subset: ro-eco property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002376 ! tributary of [Typedef] @@ -3156,7 +3159,7 @@ id: RO:0002384 name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 ! anatomical entity range: CARO:0000000 ! anatomical entity is_a: RO:0002324 ! developmentally related to @@ -3166,7 +3169,7 @@ id: RO:0002385 name: has potential to developmentally contribute to def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] @@ -3174,7 +3177,7 @@ id: RO:0002386 name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] @@ -3182,7 +3185,7 @@ id: RO:0002387 name: has potential to develop into def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] @@ -3190,7 +3193,7 @@ id: RO:0002388 name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002387 ! has potential to develop into [Typedef] @@ -3199,7 +3202,7 @@ name: has direct input def: "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] property_value: IAO:0000112 "'protein catabolic process' SubClassOf has_direct_input some protein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly consumes" xsd:string property_value: IAO:0000232 "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" xsd:string holds_over_chain: RO:0002224 RO:0002400 @@ -3210,7 +3213,7 @@ id: RO:0002401 name: obsolete has indirect input comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_obsolete: true [Typedef] @@ -3219,7 +3222,7 @@ name: obsolete has direct output def: "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. " [] property_value: IAO:0000112 "translation SubClassOf has_direct_output some protein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly produces" xsd:string is_obsolete: true @@ -3228,7 +3231,7 @@ id: RO:0002403 name: obsolete has indirect output comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002411 RO:0002402 is_obsolete: true @@ -3237,7 +3240,7 @@ id: RO:0002404 name: causally downstream of def: "inverse of upstream of" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: BFO:0000062 ! preceded by is_a: RO:0002427 ! causally downstream of or within inverse_of: RO:0002411 ! causally upstream of @@ -3246,7 +3249,7 @@ inverse_of: RO:0002411 ! causally upstream of id: RO:0002405 name: immediately causally downstream of property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002087 ! immediately preceded by is_a: RO:0002404 ! causally downstream of inverse_of: RO:0002412 ! immediately causally upstream of @@ -3262,7 +3265,7 @@ replaced_by: RO:0002629 id: RO:0002407 name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 holds_over_chain: RO:0002409 RO:0002409 @@ -3284,7 +3287,7 @@ replaced_by: RO:0002630 id: RO:0002409 name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 holds_over_chain: RO:0002630 RO:0002409 @@ -3299,7 +3302,7 @@ id: RO:0002410 name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] @@ -3308,7 +3311,7 @@ name: causally upstream of def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: BFO:0000063 ! precedes is_a: RO:0002418 ! causally upstream of or within @@ -3317,7 +3320,7 @@ is_a: RO:0002418 ! causally upstream of or within id: RO:0002412 name: immediately causally upstream of def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: RO:0002090 ! immediately precedes is_a: RO:0002411 ! causally upstream of @@ -3327,7 +3330,7 @@ id: RO:0002413 name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string @@ -3340,7 +3343,7 @@ id: RO:0002414 name: transitively provides input for def: "transitive form of directly_provides_input_for" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." xsd:string property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string domain: BFO:0000015 ! process @@ -3354,7 +3357,7 @@ name: causally upstream of or within def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true is_a: RO:0002501 ! causal relation between processes @@ -3365,19 +3368,19 @@ id: RO:0002424 name: differs in comment: This is an exploratory relation property_value: IAO:0000116 "false" xsd:boolean -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions xsd:anyURI [Typedef] id: RO:0002425 name: differs in attribute of -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002424 ! differs in [Typedef] id: RO:0002426 name: differs in attribute -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: BFO:0000020 ! specifically dependent continuant is_a: RO:0002424 ! differs in @@ -3386,7 +3389,7 @@ id: RO:0002427 name: causally downstream of or within def: "inverse of causally upstream of or within" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: RO:0002501 ! causal relation between processes @@ -3395,7 +3398,7 @@ is_a: RO:0002501 ! causal relation between processes id: RO:0002428 name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002327 RO:0002211 holds_over_chain: RO:0002331 RO:0002211 is_a: RO:0002263 ! acts upstream of @@ -3405,7 +3408,7 @@ is_a: RO:0002431 ! involved in or involved in regulation of id: RO:0002429 name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002428 holds_over_chain: RO:0002327 RO:0002213 holds_over_chain: RO:0002331 RO:0002213 @@ -3415,7 +3418,7 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002430 name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 holds_over_chain: RO:0002327 RO:0002212 holds_over_chain: RO:0002331 RO:0002212 @@ -3426,7 +3429,7 @@ id: RO:0002431 name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: RO:0002264 ! acts upstream of or within is_a: RO:0002328 ! functionally related to @@ -3438,7 +3441,7 @@ name: is active in def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] synonym: "enables activity in" EXACT [] property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} is_a: RO:0002131 ! overlaps @@ -3448,7 +3451,7 @@ is_a: RO:0002328 ! functionally related to id: RO:0002433 name: contributes to morphology of def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002131 ! overlaps [Typedef] @@ -3460,7 +3463,7 @@ synonym: "in pairwise interaction with" EXACT [] property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI domain: BFO:0000040 ! material entity @@ -3472,7 +3475,7 @@ id: RO:0002435 name: genetically interacts with property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: RO:0002434 ! interacts with @@ -3482,7 +3485,7 @@ id: RO:0002436 name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 @@ -3494,7 +3497,7 @@ id: RO:0002437 name: biotically interacts with def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string @@ -3509,7 +3512,7 @@ id: RO:0002438 name: trophically interacts with def: "An interaction relationship in which the partners are related via a feeding relationship." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: RO:0002574 ! participates in a biotic-biotic interaction with @@ -3520,9 +3523,9 @@ def: "An interaction relationship involving a predation process, where the subje subset: ro-eco property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Jorrit Poelen" xsd:string -property_value: IAO:0000117 "Katja Shulz" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7134-3324 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string @@ -3535,7 +3538,7 @@ id: RO:0002440 name: symbiotically interacts with def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true @@ -3546,7 +3549,7 @@ id: RO:0002441 name: commensually interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: RO:0002440 ! symbiotically interacts with @@ -3555,7 +3558,7 @@ id: RO:0002442 name: mutualistically interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: RO:0002440 ! symbiotically interacts with @@ -3564,7 +3567,7 @@ id: RO:0002443 name: interacts with via parasite-host interaction def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: RO:0002440 ! symbiotically interacts with @@ -3575,7 +3578,7 @@ name: parasite of subset: ro-eco synonym: "direct parasite of" EXACT [] property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string is_a: RO:0002443 ! interacts with via parasite-host interaction @@ -3587,7 +3590,7 @@ id: RO:0002445 name: parasitized by subset: ro-eco synonym: "directly parasitized by" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string @@ -3601,7 +3604,7 @@ def: "A biotic interaction relationship in which one partner is an organism and subset: ro-eco synonym: "semibiotically interacts with" RELATED [] property_value: IAO:0000112 "Porifiera attaches to substrate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: RO:0002437 ! biotically interacts with @@ -3609,7 +3612,7 @@ is_a: RO:0002437 ! biotically interacts with id: RO:0002447 name: phosphorylates property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: RO:0002436 ! molecularly interacts with @@ -3618,8 +3621,8 @@ id: RO:0002448 name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002436 ! molecularly interacts with @@ -3630,8 +3633,8 @@ id: RO:0002449 name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -3642,8 +3645,8 @@ id: RO:0002450 name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -3655,14 +3658,14 @@ name: transmitted by def: "A relationship that holds between a disease and organism" [] property_value: IAO:0000112 "all dengue disease transmitted by some mosquito" xsd:string property_value: IAO:0000116 "Add domain and range constraints" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0002452 name: has symptom def: "A relation that holds between a disease or an organism and a phenotype" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: OGMS:0000031 ! disease is_a: RO:0002200 ! has phenotype @@ -3670,7 +3673,7 @@ is_a: RO:0002200 ! has phenotype id: RO:0002453 name: host of subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string is_a: RO:0002440 ! symbiotically interacts with @@ -3679,7 +3682,7 @@ id: RO:0002454 name: has host def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string is_a: RO:0002440 ! symbiotically interacts with @@ -3689,7 +3692,7 @@ name: pollinates subset: ro-eco property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string is_a: RO:0002442 ! mutualistically interacts with @@ -3699,7 +3702,7 @@ inverse_of: RO:0002456 ! pollinated by id: RO:0002456 name: pollinated by subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string @@ -3709,7 +3712,7 @@ is_a: RO:0002442 ! mutualistically interacts with id: RO:0002457 name: acquires nutrients from subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string is_a: RO:0002438 ! trophically interacts with inverse_of: RO:0002469 ! provides nutrients for @@ -3720,7 +3723,7 @@ name: preyed upon by def: "inverse of preys on" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string @@ -3732,7 +3735,7 @@ id: RO:0002459 name: is vector for subset: ro-eco property_value: IAO:0000112 "Anopheles is a vector for Plasmodium" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" xsd:string is_a: RO:0002574 ! participates in a biotic-biotic interaction with inverse_of: RO:0002460 ! has vector @@ -3741,72 +3744,72 @@ inverse_of: RO:0002460 ! has vector id: RO:0002460 name: has vector subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002461 name: partner in -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string is_a: RO:0000056 ! participates in [Typedef] id: RO:0002462 name: subject participant in -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: RO:0002461 ! partner in [Typedef] id: RO:0002463 name: target participant in -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: RO:0002461 ! partner in [Typedef] id: RO:0002464 name: helper property (not for use in curation) -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string [Typedef] id: RO:0002465 name: is symbiosis -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002563 ! interaction relation helper property [Typedef] id: RO:0002466 name: is commensalism -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002465 ! is symbiosis [Typedef] id: RO:0002467 name: is mutualism -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002465 ! is symbiosis [Typedef] id: RO:0002468 name: is parasitism -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002465 ! is symbiosis [Typedef] id: RO:0002469 name: provides nutrients for subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002438 ! trophically interacts with [Typedef] id: RO:0002470 name: eats subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: RO:0002438 ! trophically interacts with @@ -3814,7 +3817,7 @@ is_a: RO:0002438 ! trophically interacts with id: RO:0002471 name: is eaten by subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string is_a: RO:0002438 ! trophically interacts with @@ -3824,7 +3827,7 @@ id: RO:0002472 name: is evidence for def: "A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and \nthe a supports either the existence of b, or the truth value of b." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002616 ! related via evidence or inference to inverse_of: RO:0002558 ! has evidence @@ -3834,7 +3837,7 @@ name: composed primarily of def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] subset: ro-eco property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 ! material entity @@ -3846,7 +3849,7 @@ id: RO:0002476 name: child nucleus of def: "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" [] property_value: IAO:0000112 "ABal nucleus child nucleus of ABa nucleus (in C elegans)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." xsd:string domain: GO:0005634 ! nucleus range: GO:0005634 ! nucleus @@ -3856,14 +3859,14 @@ is_a: RO:0002258 ! developmentally preceded by id: RO:0002477 name: child nucleus of in hermaphrodite def: "A child nucleus relationship in which the cells are part of a hermaphroditic organism" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002476 ! child nucleus of [Typedef] id: RO:0002478 name: child nucleus of in male def: "A child nucleus relationship in which the cells are part of a male organism" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002476 ! child nucleus of [Typedef] @@ -3871,7 +3874,7 @@ id: RO:0002479 name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} @@ -3881,26 +3884,26 @@ id: RO:0002480 name: ubiquitinates def: "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" [] property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002436 ! molecularly interacts with [Typedef] id: RO:0002481 name: is kinase activity -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002482 name: is ubiquitination -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002485 name: receives input from property_value: IAO:0000116 "See notes for inverse relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002170 ! connected to inverse_of: RO:0002486 ! sends output to @@ -3908,13 +3911,13 @@ inverse_of: RO:0002486 ! sends output to id: RO:0002486 name: sends output to property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002170 ! connected to [Typedef] id: RO:0002487 name: relation between physical entity and a process or stage -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000003 ! occurrent @@ -3923,7 +3926,7 @@ range: BFO:0000003 ! occurrent id: RO:0002488 name: existence starts during def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002583 BFO:0000050 is_a: RO:0002490 ! existence overlaps is_a: RO:0002496 ! existence starts during or after @@ -3933,7 +3936,7 @@ transitive_over: BFO:0000050 ! part of id: RO:0002489 name: existence starts with def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002488 ! existence starts during [Typedef] @@ -3941,7 +3944,7 @@ id: RO:0002490 name: existence overlaps def: "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002487 ! relation between physical entity and a process or stage [Typedef] @@ -3950,7 +3953,7 @@ name: existence starts and ends during def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. synonym: "exists during" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002488 ! existence starts during is_a: RO:0002492 ! existence ends during @@ -3959,7 +3962,7 @@ id: RO:0002492 name: existence ends during def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002593 BFO:0000050 is_a: RO:0002490 ! existence overlaps is_a: RO:0002497 ! existence ends during or before @@ -3970,14 +3973,14 @@ id: RO:0002493 name: existence ends with def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002492 ! existence ends during [Typedef] id: RO:0002494 name: transformation of def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002202 ! develops from @@ -3985,7 +3988,7 @@ is_a: RO:0002202 ! develops from id: RO:0002495 name: immediate transformation of def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002494 is_a: RO:0002207 ! directly develops from is_a: RO:0002494 ! transformation of @@ -3995,7 +3998,7 @@ id: RO:0002496 name: existence starts during or after def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000050 RO:0002496 holds_over_chain: RO:0002258 RO:0002496 is_a: RO:0002487 ! relation between physical entity and a process or stage @@ -4008,7 +4011,7 @@ id: RO:0002497 name: existence ends during or before def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000050 RO:0002497 holds_over_chain: RO:0002286 RO:0002497 is_a: RO:0002487 ! relation between physical entity and a process or stage @@ -4028,7 +4031,7 @@ inverse_of: RO:0002608 ! process has causal agent id: RO:0002501 name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 ! occurrent @@ -4038,7 +4041,7 @@ is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002502 name: depends on -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso BFO:0000169 [Typedef] @@ -4046,7 +4049,7 @@ id: RO:0002503 name: towards def: "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" [] property_value: IAO:0000116 "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 is_a: RO:0002502 ! depends on @@ -4056,7 +4059,7 @@ name: has intermediate def: "p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c" [] subset: ro-eco property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string is_a: RO:0000057 ! has participant @@ -4064,7 +4067,7 @@ is_a: RO:0000057 ! has participant id: RO:0002506 name: causal relation between entities property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000002 ! continuant @@ -4076,11 +4079,11 @@ id: RO:0002507 name: determined by def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] subset: ro-eco -property_value: http://purl.org/dc/terms/creator "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/creator "Pier Buttigieg" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-4366-3088 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "A coral reef environment is determined by a particular coral reef" xsd:string property_value: IAO:0000116 "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602 property_value: IAO:0000589 "determined by (system to material entity)" xsd:string domain: RO:0002577 ! system @@ -4096,7 +4099,7 @@ name: determines def: "inverse of determined by" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "determines (material entity to system)" xsd:string is_a: RO:0002566 ! causally influences @@ -4105,7 +4108,7 @@ id: RO:0002509 name: determined by part of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 ! system range: BFO:0000040 ! material entity holds_over_chain: RO:0002507 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} @@ -4116,7 +4119,7 @@ is_a: RO:0002506 ! causal relation between entities id: RO:0002510 name: transcribed from def: "x is transcribed from y if and only if x is synthesized from template y" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to inverse_of: RO:0002511 ! transcribed to @@ -4126,7 +4129,7 @@ id: RO:0002511 name: transcribed to def: "inverse of transcribed from" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to @@ -4134,7 +4137,7 @@ is_a: RO:0002330 ! genomically related to id: RO:0002512 name: ribosomal translation of def: "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to inverse_of: RO:0002513 ! ribosomally translates to @@ -4143,7 +4146,7 @@ inverse_of: RO:0002513 ! ribosomally translates to id: RO:0002513 name: ribosomally translates to def: "inverse of ribosomal translation of" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to @@ -4152,7 +4155,7 @@ id: RO:0002514 name: sequentially related to def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string @@ -4167,7 +4170,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcript" xsd:string property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002527 ! does not overlap sequence of @@ -4177,7 +4180,7 @@ name: has start sequence def: "x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -4190,7 +4193,7 @@ name: is start sequence of def: "inverse of has start sequence" [] subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -4202,7 +4205,7 @@ name: has end sequence def: "x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -4215,7 +4218,7 @@ name: is end sequence of def: "inverse of has end sequence" [] subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -4227,7 +4230,7 @@ name: is consecutive sequence of def: "x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002524 ! has subsequence @@ -4237,7 +4240,7 @@ name: is sequentially aligned with def: "x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: RO:0002514 ! sequentially related to @@ -4247,7 +4250,7 @@ name: bounds sequence of def: "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002514 ! sequentially related to inverse_of: RO:0002523 ! is bound by sequence of @@ -4258,16 +4261,16 @@ name: is bound by sequence of def: "inverse of bounds sequence of" [] subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002514 ! sequentially related to [Typedef] id: RO:0002524 name: has subsequence -def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -4282,7 +4285,7 @@ name: is subsequence of def: "inverse of has subsequence" [] subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: BFO:0000050 ! part of @@ -4292,9 +4295,9 @@ is_a: RO:0002526 ! overlaps sequence of [Typedef] id: RO:0002526 name: overlaps sequence of -def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002524 RO:0002525 is_symmetric: true is_a: RO:0002131 ! overlaps @@ -4303,9 +4306,9 @@ is_a: RO:0002514 ! sequentially related to [Typedef] id: RO:0002527 name: does not overlap sequence of -def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "disconnected from" xsd:string is_symmetric: true is_a: RO:0002514 ! sequentially related to @@ -4315,7 +4318,7 @@ id: RO:0002528 name: is upstream of sequence of def: "inverse of downstream of sequence of" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002527 ! does not overlap sequence of @@ -4324,7 +4327,7 @@ id: RO:0002529 name: is downstream of sequence of def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002527 ! does not overlap sequence of inverse_of: RO:0002529 ! is downstream of sequence of @@ -4335,7 +4338,7 @@ name: is immediately downstream of sequence of def: "x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002529 is_a: RO:0002515 ! sequentially adjacent to is_a: RO:0002529 ! is downstream of sequence of @@ -4346,7 +4349,7 @@ name: is immediately upstream of sequence of def: "inverse of immediately downstream of" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002515 ! sequentially adjacent to is_a: RO:0002528 ! is upstream of sequence of @@ -4355,7 +4358,7 @@ id: RO:0002551 name: has skeleton def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 ! connected anatomical structure @@ -4368,7 +4371,7 @@ is_asymmetric: true id: RO:0002552 name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -4380,7 +4383,7 @@ subset: ro-eco synonym: "epiparasite of" RELATED [] synonym: "hyperparasitoid of" NARROW [] property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string holds_over_chain: RO:0002444 RO:0002444 @@ -4396,7 +4399,7 @@ subset: RO:0002259 synonym: "has epiparasite" RELATED [] synonym: "has hyperparasite" RELATED [] synonym: "hyperparasitoidized by" RELATED [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002445 RO:0002445 is_a: RO:0002453 ! host of @@ -4404,7 +4407,7 @@ is_a: RO:0002453 ! host of id: RO:0002555 name: allelopath of subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string @@ -4414,7 +4417,7 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with id: RO:0002556 name: pathogen of subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002454 ! has host inverse_of: RO:0002557 ! has pathogen @@ -4422,7 +4425,7 @@ inverse_of: RO:0002557 ! has pathogen id: RO:0002557 name: has pathogen subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002453 ! host of [Typedef] @@ -4432,14 +4435,14 @@ def: "inverse of is evidence for" [] comment: x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/25052702 is_a: RO:0002616 ! related via evidence or inference to [Typedef] id: RO:0002559 name: causally influenced by -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: RO:0002506 ! causal relation between entities @@ -4448,7 +4451,7 @@ inverse_of: RO:0002566 ! causally influences [Typedef] id: RO:0002563 name: interaction relation helper property -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI is_a: RO:0002464 ! helper property (not for use in curation) @@ -4456,7 +4459,7 @@ is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 name: molecular interaction relation helper property -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002563 ! interaction relation helper property [Typedef] @@ -4466,7 +4469,7 @@ def: "Holds between p and c when p is locomotion process and the outcome of this subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "" xsd:string is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -4474,8 +4477,8 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure id: RO:0002566 name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 ! continuant @@ -4486,7 +4489,7 @@ is_a: RO:0002506 ! causal relation between entities id: RO:0002567 name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: CARO:0000003 ! connected anatomical structure range: CARO:0000003 ! connected anatomical structure @@ -4496,7 +4499,7 @@ is_a: RO:0002328 ! functionally related to id: RO:0002568 name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string is_a: RO:0002567 ! biomechanically related to @@ -4506,7 +4509,7 @@ name: has branching part def: "inverse of branching part of" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: BFO:0000051 ! has part is_a: RO:0002375 ! in branching relationship with @@ -4516,7 +4519,7 @@ id: RO:0002570 name: conduit for def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 UBERON:cjm xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 ! material entity @@ -4528,7 +4531,7 @@ id: RO:0002571 name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:cjm xsd:string range: BFO:0000040 ! material entity is_a: BFO:0000050 ! part of @@ -4538,7 +4541,7 @@ id: RO:0002572 name: luminal space of def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000141 ! immaterial entity is_a: RO:0002571 ! lumen of @@ -4547,7 +4550,7 @@ id: RO:0002573 name: has modifier def: "A relation that holds between an attribute or a qualifier and another attribute." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." xsd:string domain: BFO:0000020 ! specifically dependent continuant @@ -4557,7 +4560,7 @@ range: BFO:0000020 ! specifically dependent continuant id: RO:0002574 name: participates in a biotic-biotic interaction with subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 domain: CARO:0001010 ! organism or virus or viroid range: CARO:0001010 ! organism or virus or viroid @@ -4568,7 +4571,7 @@ id: RO:0002576 name: skeleton of def: "inverse of has skeleton" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 ! connected anatomical structure range: CARO:0000003 ! connected anatomical structure is_a: BFO:0000050 ! part of @@ -4580,7 +4583,7 @@ def: "p directly regulates q iff p is immediately causally upstream of q and p r subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string property_value: RO:0002575 RO:0002211 @@ -4598,7 +4601,7 @@ id: RO:0002584 name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000051 RO:0002215 is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process @@ -4665,7 +4668,7 @@ id: RO:0002595 name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 ! material entity range: BFO:0000015 ! process @@ -4933,7 +4936,7 @@ def: "a produces b if some process that occurs_in a has_output b, where a and b comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity inverse_of: RO:0003001 ! produced by @@ -4944,7 +4947,7 @@ name: produced by def: "a produced_by b iff some process that occurs_in b has_output a." [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -4952,7 +4955,7 @@ range: BFO:0000040 ! material entity id: RO:0003002 name: represses expression of def: "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002449 ! directly negatively regulates activity of @@ -4961,7 +4964,7 @@ is_a: RO:0002449 ! directly negatively regulates activity of id: RO:0003003 name: increases expression of def: "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002450 ! directly positively regulates activity of @@ -4971,7 +4974,7 @@ id: RO:0003301 name: has role in modeling def: "A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." [] comment: The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate. -property_value: IAO:0000117 "Matthew Brush" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-1048-5019 property_value: IAO:0000118 "is used to study" xsd:string is_asymmetric: true @@ -5049,7 +5052,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: BFO:0000017 ! realizable entity is_a: RO:0002410 ! causally related to inverse_of: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:38:20Z [Typedef] @@ -5059,7 +5062,7 @@ property_value: seeAlso Orphanet:410295 property_value: seeAlso Orphanet:410296 is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004011 ! is causal gain of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:20Z [Typedef] @@ -5067,7 +5070,7 @@ id: RO:0004002 name: has material basis in loss of function germline mutation in is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004012 ! is causal loss of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:37Z [Typedef] @@ -5076,7 +5079,7 @@ name: has material basis in germline mutation in property_value: seeAlso Orphanet:317343 is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004013 ! is causal germline mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:54Z [Typedef] @@ -5085,7 +5088,7 @@ name: has material basis in somatic mutation in property_value: seeAlso Orphanet:317344 is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004014 ! is causal somatic mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z [Typedef] @@ -5093,7 +5096,7 @@ id: RO:0004005 name: has major susceptibility factor is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004015 ! is causal susceptibility factor for -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:26Z [Typedef] @@ -5101,7 +5104,7 @@ id: RO:0004006 name: has partial material basis in germline mutation in is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004016 ! is causal germline mutation partially giving rise to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:57Z [Typedef] @@ -5110,7 +5113,7 @@ name: has primary input or output def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology is_a: RO:0000057 ! has participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -5120,7 +5123,7 @@ def: "p has primary output c if (a) p has output c and (b) the goal of process i subset: http://purl.obolibrary.org/obo/valid_for_go_ontology is_a: RO:0002234 ! has output is_a: RO:0004007 ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -5130,7 +5133,7 @@ def: "p has primary input c if (a) p has input c and (b) the goal of process is subset: http://purl.obolibrary.org/obo/valid_for_go_ontology is_a: RO:0002233 ! has input is_a: RO:0004007 ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -5139,7 +5142,7 @@ name: is genetic basis for condition property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string range: BFO:0000017 ! realizable entity is_a: RO:0004018 ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:53:08Z [Typedef] @@ -5148,7 +5151,7 @@ name: is causal gain of function germline mutation of in def: "Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." [] property_value: seeAlso Orphanet:410296 is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:55:51Z [Typedef] @@ -5157,7 +5160,7 @@ name: is causal loss of function germline mutation of in def: "Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." [] property_value: seeAlso Orphanet:410295 is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:06Z [Typedef] @@ -5167,7 +5170,7 @@ def: "Relates a gene to condition, such that a mutation in this gene is sufficie property_value: seeAlso Orphanet:317343 is_a: RO:0003303 ! causes condition is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:40Z [Typedef] @@ -5177,7 +5180,7 @@ def: "Relates a gene to condition, such that a mutation in this gene is sufficie property_value: seeAlso Orphanet:317344 is_a: RO:0003303 ! causes condition is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:07Z [Typedef] @@ -5186,7 +5189,7 @@ name: is causal susceptibility factor for def: "Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]." [] property_value: seeAlso Orphanet:317345 is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:43Z [Typedef] @@ -5196,7 +5199,7 @@ def: "Relates a gene to condition, such that a mutation in this gene partially c property_value: seeAlso Orphanet:317346 is_a: RO:0003304 ! contributes to condition is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:58:43Z [Typedef] @@ -5204,14 +5207,14 @@ id: RO:0004017 name: realizable has basis in is_a: RO:0002410 ! causally related to inverse_of: RO:0004018 ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:01Z [Typedef] id: RO:0004018 name: is basis for realizable is_a: RO:0002410 ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:29Z [Typedef] @@ -5220,7 +5223,7 @@ name: disease has basis in domain: OGMS:0000031 ! disease is_a: RO:0004017 ! realizable has basis in is_a: RO:0004023 ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:26:47Z [Typedef] @@ -5230,7 +5233,7 @@ def: "A relation that holds between the disease and a material entity where the property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string range: CARO:0000006 ! material anatomical entity is_a: RO:0004019 ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z [Typedef] @@ -5240,7 +5243,7 @@ def: "A relation that holds between the disease and a process where the physical property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 ! process is_a: RO:0004019 ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:37:52Z [Typedef] @@ -5250,7 +5253,7 @@ def: "A relation that holds between the disease and a feature (a phenotype or ot domain: OGMS:0000031 ! disease is_a: RO:0002200 ! has phenotype is_a: RO:0004019 ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:46:07Z [Typedef] @@ -5260,7 +5263,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: OGMS:0000031 ! disease is_a: RO:0002410 ! causally related to is_a: RO:0040035 ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:50:54Z [Typedef] @@ -5273,7 +5276,7 @@ range: BFO:0000015 ! process holds_over_chain: RO:0004025 RO:0002215 is_a: RO:0004023 ! causal relationship with disease as subject transitive_over: BFO:0000050 ! part of -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:51:09Z [Typedef] @@ -5284,7 +5287,7 @@ domain: OGMS:0000031 ! disease range: CARO:0000006 ! material anatomical entity is_a: RO:0004023 ! causal relationship with disease as subject transitive_over: BFO:0000050 ! part of -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z [Typedef] @@ -5296,7 +5299,7 @@ property_value: IAO:0000232 "This relation is intentionally very general, and co domain: OGMS:0000031 ! disease range: BFO:0000004 ! independent continuant is_a: RO:0040035 ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T04:06:02Z [Typedef] @@ -5306,7 +5309,7 @@ def: "A relationship between a disease and an anatomical entity where the diseas domain: OGMS:0000031 ! disease range: BFO:0000004 ! independent continuant is_a: RO:0004026 ! disease has location -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:37:31Z [Typedef] @@ -5317,7 +5320,7 @@ domain: BFO:0000017 ! realizable entity range: BFO:0000040 ! material entity holds_over_chain: RO:0009501 RO:0002233 is_a: RO:0002410 ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:45:49Z [Typedef] @@ -5326,7 +5329,7 @@ name: disease has feature def: "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." [] domain: OGMS:0000031 ! disease is_a: RO:0040035 ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:50:53Z [Typedef] @@ -5335,7 +5338,7 @@ name: disease arises from alteration in structure def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." [] range: CARO:0000003 ! connected anatomical structure is_a: RO:0004019 ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z [Typedef] @@ -5344,7 +5347,7 @@ name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] holds_over_chain: RO:0002327 BFO:0000051 is_a: RO:0002328 ! functionally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z [Typedef] @@ -5355,7 +5358,7 @@ property_value: RO:0004049 RO:0002264 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z [Typedef] @@ -5365,7 +5368,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002264 holds_over_chain: RO:0002327 RO:0004046 is_a: RO:0002264 ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z [Typedef] @@ -5378,7 +5381,7 @@ property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of, holds_over_chain: RO:0002327 RO:0002304 is_a: RO:0002263 ! acts upstream of is_a: RO:0004032 ! acts upstream of or within, positive effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:14Z [Typedef] @@ -5391,7 +5394,7 @@ property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of, holds_over_chain: RO:0002327 RO:0002305 is_a: RO:0002263 ! acts upstream of is_a: RO:0004033 ! acts upstream of or within, negative effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:22Z [Typedef] @@ -5399,7 +5402,7 @@ id: RO:0004046 name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 is_a: RO:0002418 ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -5407,7 +5410,7 @@ id: RO:0004047 name: causally upstream of or within, positive effect property_value: RO:0004049 RO:0002418 is_a: RO:0002418 ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -5503,7 +5506,7 @@ def: "\"has substance added\" is a relation existing between a (physical) entity property_value: IAO:0000112 "muffin 'has substance added' some 'baking soda'" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." xsd:string -property_value: IAO:0000117 "Damion Dooley" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -5513,7 +5516,7 @@ name: has substance removed def: "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." [] property_value: IAO:0000112 "'egg white' 'has substance removed' some 'egg yolk'" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Damion Dooley" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -5523,7 +5526,7 @@ name: immersed in def: "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." [] property_value: IAO:0000112 "sardines 'immersed in' some 'oil and mustard'" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Damion Dooley" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -5533,7 +5536,7 @@ name: has consumer def: "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect." [] property_value: IAO:0000112 "sardine has consumer some homo sapiens" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Damion Dooley" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 domain: BFO:0000040 ! material entity range: CARO:0001010 ! organism or virus or viroid @@ -5543,7 +5546,7 @@ name: has primary substance added def: "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." [] property_value: IAO:0000112 "bread 'has primary substance added' some 'flour'" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Damion Dooley" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 is_a: RO:0009001 ! has substance added [Typedef] @@ -5551,10 +5554,10 @@ id: RO:0009501 name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] synonym: "triggered by process" EXACT [RO:cjm] -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "David Osumi-Sutherland" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string @@ -5596,7 +5599,7 @@ holds_over_chain: RO:0000059 RO:0000053 id: RO:0011002 name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences @@ -5605,7 +5608,7 @@ is_a: RO:0002566 ! causally influences id: RO:0011003 name: regulates quantity of def: "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences @@ -5614,7 +5617,7 @@ is_a: RO:0002566 ! causally influences id: RO:0011004 name: indirectly regulates activity of def: "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0011002 ! regulates activity of @@ -5623,7 +5626,7 @@ is_a: RO:0011002 ! regulates activity of id: RO:0011007 name: decreases by repression quantity of def: "The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0011023 ! indirectly negatively regulates quantity of @@ -5632,7 +5635,7 @@ is_a: RO:0011023 ! indirectly negatively regulates quantity of id: RO:0011008 name: increases by expression quantity of def: "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0011024 ! indirectly positively regulates quantity of @@ -5641,7 +5644,7 @@ is_a: RO:0011024 ! indirectly positively regulates quantity of id: RO:0011009 name: directly positively regulates quantity of def: "The entity A has an activity that directly positively regulates the quantity of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0011021 ! directly regulates quantity of @@ -5650,7 +5653,7 @@ is_a: RO:0011021 ! directly regulates quantity of id: RO:0011010 name: directly negatively regulates quantity of def: "The entity A has an activity that directly negatively regulates the quantity of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0011021 ! directly regulates quantity of @@ -5659,7 +5662,7 @@ is_a: RO:0011021 ! directly regulates quantity of id: RO:0011013 name: indirectly positively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly activates" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -5670,7 +5673,7 @@ id: RO:0011014 name: destabilizes quantity of def: "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." [] property_value: IAO:0000112 "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0011010 ! directly negatively regulates quantity of @@ -5680,7 +5683,7 @@ id: RO:0011015 name: stabilizes quantity of def: "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." [] property_value: IAO:0000112 "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0011009 ! directly positively regulates quantity of @@ -5689,7 +5692,7 @@ is_a: RO:0011009 ! directly positively regulates quantity of id: RO:0011016 name: indirectly negatively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly inhibits" xsd:string is_a: RO:0011004 ! indirectly regulates activity of @@ -5697,28 +5700,28 @@ is_a: RO:0011004 ! indirectly regulates activity of id: RO:0011021 name: directly regulates quantity of def: "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011003 ! regulates quantity of [Typedef] id: RO:0011022 name: indirectly regulates quantity of def: "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011003 ! regulates quantity of [Typedef] id: RO:0011023 name: indirectly negatively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011022 ! indirectly regulates quantity of [Typedef] id: RO:0011024 name: indirectly positively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011022 ! indirectly regulates quantity of [Typedef] @@ -5940,7 +5943,7 @@ name: has exemplar data def: "A relation between a material entity and some data in which the data is taken as exemplifying the material entity." [] property_value: IAO:0000112 "transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data])" xsd:string property_value: IAO:0000116 "C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C." xsd:string -property_value: IAO:0000117 "Patrick Ray" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-5260-9315 property_value: IAO:0000232 "This relation is not meant to capture the relation between occurrents and data." xsd:string inverse_of: RO:0015002 ! exemplar data of transitive_over: RO:0015003 ! subcluster of @@ -5948,14 +5951,14 @@ transitive_over: RO:0015003 ! subcluster of [Typedef] id: RO:0015002 name: exemplar data of -property_value: IAO:0000117 "Patrick Ray" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-5260-9315 [Typedef] id: RO:0015003 name: subcluster of def: "A relation between a group and another group it is part of but does not fully constitute." [] property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." xsd:string -property_value: IAO:0000117 "Shawn Tan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true is_a: BFO:0000050 ! part of @@ -6051,7 +6054,7 @@ property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:s id: RO:0016002 name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string is_a: RO:0016001 ! has phenotype or disease @@ -6071,8 +6074,8 @@ name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 +property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string holds_over_chain: RO:0002215 RO:0002233 @@ -6166,7 +6169,7 @@ id: RO:0040035 name: disease relationship def: "This relation groups relations between diseases and any other kind of entity." [] property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z [Typedef] @@ -6174,7 +6177,7 @@ id: RO:0040036 name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] is_a: RO:0000057 ! has participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] diff --git a/ro.owl b/ro.owl index 9cb67e03..e1982ee4 100644 --- a/ro.owl +++ b/ro.owl @@ -18,7 +18,7 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -35,7 +35,7 @@ The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. OBO Relations Ontology - 2023-01-04 + 2023-02-19 https://github.com/oborel/obo-relations/ @@ -106,11 +106,11 @@ tooth SubClassOf 'never in taxon' value 'Aves' x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. - Chris Mungall + Class: ?X DisjointWith: RO_0002162 some ?Y - PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> + PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161> @@ -133,7 +133,7 @@ CONSTRUCT { WHERE { ?x never_in_taxon: ?taxon . } - never in taxon + never in taxon @@ -148,7 +148,7 @@ WHERE { shares no parts with Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) - PREFIX owl: <http://www.w3.org/2002/07/owl#> + PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171> CONSTRUCT { @@ -201,7 +201,7 @@ WHERE { S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. - https://orcid.org/0000-0002-6601-2165 + This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost dubious for taxon @@ -215,9 +215,9 @@ WHERE { S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S - https://orcid.org/0000-0002-6601-2165 + - PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> + PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175> @@ -590,7 +590,7 @@ Where we have an annotation assertion "directly P" "is direct form of" "P" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' - Chris Mungall + is direct form of @@ -602,7 +602,7 @@ Where we have an annotation assertion relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y - Chris Mungall + is indirect form of @@ -750,7 +750,7 @@ Where we have an annotation assertion true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation. - cjm + nominally disjoint with @@ -761,7 +761,7 @@ Where we have an annotation assertion Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" - cjm + 2018-03-13T23:59:29Z is directional form of @@ -772,7 +772,7 @@ Where we have an annotation assertion - cjm + 2018-03-14T00:03:16Z is positive form of @@ -783,7 +783,7 @@ Where we have an annotation assertion - cjm + 2018-03-14T00:03:24Z is negative form of @@ -796,7 +796,7 @@ Where we have an annotation assertion part-of is homeomorphic for independent continuants. R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. - cjm + 2018-10-21T19:46:34Z R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. is homeomorphic for @@ -809,7 +809,7 @@ Where we have an annotation assertion - pg + pg 2020-09-22T11:05:29Z valid_for_go_annotation_extension @@ -821,7 +821,7 @@ Where we have an annotation assertion - pg + pg 2020-09-22T11:05:18Z valid_for_go_gp2term @@ -833,7 +833,7 @@ Where we have an annotation assertion - pg + pg 2020-09-22T11:04:12Z valid_for_go_ontology @@ -845,7 +845,7 @@ Where we have an annotation assertion - pg + pg 2020-09-22T11:05:45Z valid_for_gocam @@ -939,7 +939,7 @@ Where we have an annotation assertion - subset_property + subset_property @@ -965,7 +965,7 @@ Where we have an annotation assertion - has_narrow_synonym + has_narrow_synonym @@ -973,7 +973,7 @@ Where we have an annotation assertion - in_subset + in_subset @@ -1108,7 +1108,7 @@ Where we have an annotation assertion OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. - David Osumi-Sutherland + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). @@ -1124,7 +1124,7 @@ Where we have an annotation assertion OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first. - David Osumi-Sutherland + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). @@ -1140,7 +1140,7 @@ Where we have an annotation assertion OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first. - David Osumi-Sutherland + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). @@ -1261,7 +1261,7 @@ range: spatial region or site (immaterial continuant) May be obsoleted, see https://github.com/oborel/obo-relations/issues/260 - David Osumi-Sutherland + aligned with @@ -1272,7 +1272,7 @@ range: spatial region or site (immaterial continuant) - David Osumi-Sutherland + @@ -1282,9 +1282,9 @@ range: spatial region or site (immaterial continuant) A relation that holds between two neurons that are electrically coupled via gap junctions. - David Osumi-Sutherland + - electrically_synapsed_to + electrically_synapsed_to @@ -1295,8 +1295,8 @@ range: spatial region or site (immaterial continuant) - The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). - David Osumi-Sutherland + The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). + tracheates @@ -1308,7 +1308,7 @@ range: spatial region or site (immaterial continuant) - David Osumi-Sutherland + http://www.ncbi.nlm.nih.gov/pubmed/22402613 innervated_by @@ -1320,7 +1320,7 @@ range: spatial region or site (immaterial continuant) - David Osumi-Sutherland + has synaptic terminal of @@ -1352,7 +1352,7 @@ range: spatial region or site (immaterial continuant) has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland + A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. bounding layer of @@ -1386,9 +1386,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. + A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. Note from NCEAS meeting: consider changing primary label - David Osumi-Sutherland + Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. coincident with @@ -1402,7 +1402,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g. - David Osumi-Sutherland + x 'cell expresses' y iff: cell(x) AND gene(y) @@ -1421,7 +1421,7 @@ AND t has_input y x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - David Osumi-Sutherland + regulates in other organism @@ -1435,7 +1435,7 @@ AND t has_input y A relationship that holds between a process that regulates a transport process and the entity transported by that process. - David Osumi-Sutherland + regulates transport of @@ -1461,7 +1461,7 @@ AND t has_input y A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + dos 2017-05-24T09:30:46Z has regulatory component activity @@ -1474,7 +1474,7 @@ AND t has_input y A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + dos 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity @@ -1488,7 +1488,7 @@ AND t has_input y A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity @@ -1501,7 +1501,7 @@ AND t has_input y - dos + dos 2017-05-24T09:36:08Z A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. has necessary component activity @@ -1513,7 +1513,7 @@ AND t has_input y - dos + dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity @@ -1528,7 +1528,7 @@ AND t has_input y w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + dos 2017-05-24T09:49:21Z has component process @@ -1540,7 +1540,7 @@ AND t has_input y A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + dos 2017-07-19T17:30:36Z has ligand @@ -1552,7 +1552,7 @@ AND t has_input y Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + dos 2017-07-20T17:11:08Z transports @@ -1564,7 +1564,7 @@ AND t has_input y A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + dos 2017-07-20T17:19:37Z occurs across @@ -1576,7 +1576,7 @@ AND t has_input y - dos + dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by @@ -1585,7 +1585,7 @@ AND t has_input y Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + GOC:dos @@ -1596,7 +1596,7 @@ AND t has_input y Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + dos 2017-09-17T13:52:38Z directly negatively regulated by @@ -1604,7 +1604,7 @@ AND t has_input y Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + GOC:dos @@ -1615,7 +1615,7 @@ AND t has_input y Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + dos 2017-09-17T13:52:47Z directly positively regulated by @@ -1623,7 +1623,7 @@ AND t has_input y Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + GOC:dos @@ -1634,7 +1634,7 @@ AND t has_input y A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity @@ -1643,7 +1643,7 @@ AND t has_input y A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + GOC:dos @@ -1662,7 +1662,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + dos 2017-12-07T12:58:06Z in register with @@ -1677,7 +1677,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + GOC:dos @@ -1685,7 +1685,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + @@ -1697,7 +1697,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + di Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. encompasses @@ -1731,7 +1731,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + @@ -1770,7 +1770,7 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure that its soma is part of. - David Osumi-Sutherland + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -1789,9 +1789,9 @@ Examples include: the relationship between two channels collected simultaneously relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - David Osumi-Sutherland + fasciculates with - (forall (?x ?y) + (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) @@ -1829,9 +1829,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure its axon forms (chemical) synapses in. - Chris Mungall - David Osumi-Sutherland - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -1861,8 +1860,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -1880,9 +1879,9 @@ Examples include: the relationship between two channels collected simultaneously Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - Alexander Diehl - Chris Mungall - Lindsay Cowell + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) @@ -1898,8 +1897,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -1916,8 +1915,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -1934,8 +1933,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) @@ -1950,8 +1949,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1968,8 +1967,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1991,8 +1990,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - Chris Mungall - David Osumi-Sutherland + + synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( @@ -2022,8 +2021,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -2101,8 +2100,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -2131,8 +2130,8 @@ N1 SubclassOf ( Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -2155,7 +2154,7 @@ N1 SubclassOf ( A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - David Osumi-Sutherland + has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) @@ -2225,9 +2224,9 @@ N1 SubclassOf ( The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - David Osumi-Sutherland + has fasciculating component - (forall (?x ?y) + (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) @@ -2269,7 +2268,7 @@ N1 SubclassOf ( Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - David Osumi-Sutherland + <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -2286,8 +2285,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - X continuous_with Y if and only if X and Y share a fiat boundary. - David Osumi-Sutherland + X continuous_with Y if and only if X and Y share a fiat boundary. + connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) @@ -2304,8 +2303,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom - proper overlaps - (forall (?x ?y) + proper overlaps + (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and @@ -2326,10 +2325,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. - ancestral_stucture_of - evolutionarily_descended_from - derived by descent from + d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. + ancestral_stucture_of + evolutionarily_descended_from + derived by descent from @@ -2342,7 +2341,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of derived by descent from - has derived by descendant + has derived by descendant @@ -2358,10 +2357,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. + two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. Consider obsoleting and merging with child relation, 'in homology relationship with' - VBO calls this homologous_to - shares ancestor with + VBO calls this homologous_to + shares ancestor with @@ -2373,7 +2372,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - serially homologous to + serially homologous to @@ -2388,10 +2387,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria - Chris Mungall + - only in taxon + only in taxon @@ -2440,13 +2439,13 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - Chris Mungall - Jennifer Deegan + + - Connects a biological entity to its taxon of origin. - in taxon + Connects a biological entity to its taxon of origin. + in taxon @@ -2459,13 +2458,13 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - Chris Mungall + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) - spatially disjoint from + spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern @@ -2609,7 +2608,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - Chris Mungall + has phenotype @@ -2622,7 +2621,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of has phenotype - Chris Mungall + phenotype of @@ -2640,10 +2639,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - Terry Meehan + + + + This is the transitive form of the develops from relation develops from @@ -2659,9 +2658,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of develops from - Chris Mungall - David Osumi-Sutherland - Terry Meehan + + + develops into @@ -2698,7 +2697,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x" We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g. - Chris Mungall + gene product of @@ -2718,7 +2717,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y - Chris Mungall + has gene product @@ -2746,7 +2745,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.'neural crest cell' SubClassOf expresses some 'Wnt1 gene' x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process - Chris Mungall + expressed in @@ -2775,11 +2774,11 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - Chris Mungall - David Osumi-Sutherland - has developmental precursor + + FBbt + has developmental precursor TODO - add child relations from DOS directly develops from @@ -2842,9 +2841,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - Chris Mungall - David Hill - Tanya Berardini + + + GO Regulation precludes parthood; the regulatory process may not be within the regulated process. @@ -2869,7 +2868,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - Chris Mungall + negatively regulates (process to process) @@ -2897,7 +2896,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - Chris Mungall + positively regulates (process to process) @@ -2927,7 +2926,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) TODO: add homeomorphy axiom This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. - Chris Mungall + has prototype @@ -2942,7 +2941,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - Chris Mungall + has function realized in @@ -2963,7 +2962,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - Chris Mungall + has function in capable of part of @@ -2984,11 +2983,11 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role - Chris Mungall + agent in - Obsoleted as the inverse property was obsoleted. - obsolete actively participates in + Obsoleted as the inverse property was obsoleted. + obsolete actively participates in true @@ -2998,10 +2997,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. OBSOLETE x has participant y if and only if x realizes some active role that inheres in y - Chris Mungall + has agent - obsolete has active participant + obsolete has active participant true @@ -3014,7 +3013,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - Chris Mungall + surrounded by @@ -3034,7 +3033,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - Chris Mungall + @@ -3056,7 +3055,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of surrounded by - Chris Mungall + surrounds @@ -3067,7 +3066,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 @@ -3079,7 +3078,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Chris Mungall + @@ -3089,7 +3088,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Chris Mungall + @@ -3105,7 +3104,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - Chris Mungall + develops from part of @@ -3122,7 +3121,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x develops_in y if x is located in y whilst x is developing - Chris Mungall + EHDAA2 Jonathan Bard, EHDAA2 develops in @@ -3154,7 +3153,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Chris Mungall + @@ -3164,7 +3163,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Chris Mungall + @@ -3182,7 +3181,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - Chris Mungall + starts with process that occurs in has start location @@ -3202,7 +3201,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - Chris Mungall + ends with process that occurs in has end location @@ -3222,7 +3221,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + consumes @@ -3244,7 +3243,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - Chris Mungall + produces @@ -3290,7 +3289,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - Bill Duncan (https://orcid.org/0000-0001-9625-1899) + This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. @@ -3443,7 +3442,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y - Chris Mungall + has developmental contribution from @@ -3460,7 +3459,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho inverse of has developmental contribution from - Chris Mungall + developmentally contributes to @@ -3476,9 +3475,9 @@ If you need an axiom that says 'has_participant min 2 object', you sho t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - Chris Mungall - David Osumi-Sutherland - Melissa Haendel + + + induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) @@ -3496,7 +3495,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally induced by - Chris Mungall + developmentally induces @@ -3512,7 +3511,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - Chris Mungall + In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by @@ -3580,7 +3579,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - Chris Mungall + replaces developmentally replaces @@ -3593,7 +3592,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally preceded by - Chris Mungall + developmentally succeeded by @@ -3609,7 +3608,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - Chris Mungall + part of developmental precursor of @@ -3623,7 +3622,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part. - Chris Mungall + ubiquitously expressed in @@ -3635,7 +3634,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of 'expressed in' - Chris Mungall + expresses @@ -3647,7 +3646,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho inverse of ubiquiotously expressed in - Chris Mungall + ubiquitously expresses @@ -3663,7 +3662,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - Chris Mungall + results in developmental progression of @@ -3678,7 +3677,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - Chris Mungall + http://www.geneontology.org/GO.doc.development.shtml @@ -3697,7 +3696,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - Chris Mungall + GOC:mtg_berkeley_2013 @@ -3716,7 +3715,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - Chris Mungall + GOC:mtg_berkeley_2013 @@ -3735,7 +3734,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - Chris Mungall + GOC:mtg_berkeley_2013 @@ -3751,7 +3750,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho foramen ovale closure SubClassOf results in disappearance of foramen ovale - Chris Mungall + May be merged into parent relation results in disappearance of @@ -3764,7 +3763,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) - Chris Mungall + May be merged into parent relation results in developmental regression of @@ -3777,7 +3776,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of 'is substance that treats' - cjm + is treated by substance @@ -3795,7 +3794,7 @@ where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. - Pier Buttigieg + adapted for living in A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. @@ -3811,7 +3810,7 @@ where p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - cjm + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y @@ -3827,7 +3826,7 @@ where p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - cjm + causally upstream of, negative effect @@ -3840,10 +3839,10 @@ where A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. - Austin Meier - Chris Mungall - Marie Angelique Laporte - cjm + + + + 2017-06-05T17:35:04Z has exposure stimulus @@ -3854,7 +3853,7 @@ where - Chris Mungall + evolutionary variant of @@ -3866,7 +3865,7 @@ where Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. - Chris Mungall + regulates localization of @@ -3890,7 +3889,7 @@ where q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of - Chris Mungall + inheres in part of @@ -3917,7 +3916,7 @@ where an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - Chris Mungall + GOC:mtg_berkeley_2013 @@ -3931,7 +3930,7 @@ where A relationship that holds via some environmental process - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to @@ -3943,7 +3942,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions ecologically related to @@ -3957,7 +3956,7 @@ where An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. - Chris Mungall + adapted for confers advantage in @@ -3969,7 +3968,7 @@ where A mereological relationship or a topological relationship - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to @@ -3981,7 +3980,7 @@ where A relationship that holds between entities participating in some developmental process (GO:0032502) - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to @@ -3996,9 +3995,8 @@ where Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. - Chris Mungall + In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - Gene Ontology Consortium colocalizes with @@ -4024,7 +4022,7 @@ then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. - Chris Mungall + In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. contributes to @@ -4047,7 +4045,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - Chris Mungall + catalyzes executes has @@ -4064,7 +4062,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to @@ -4080,7 +4078,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati this relation holds between c and p when c is part of some c', and c' is capable of p. - Chris Mungall + false part of structure that is capable of @@ -4102,7 +4100,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism genomically related to @@ -4123,7 +4121,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati c involved_in p if and only if c enables some process p', and p' is part of p - Chris Mungall + actively involved in enables part of involved in @@ -4140,7 +4138,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - Chris Mungall + regulates levels of (process to entity) regulates levels of @@ -4154,7 +4152,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables - Chris Mungall + enabled by @@ -4169,7 +4167,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of regulates - Chris Mungall + regulated by (processual) regulated by @@ -4182,7 +4180,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of negatively regulates - Chris Mungall + negatively regulated by @@ -4194,7 +4192,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of positively regulates - Chris Mungall + positively regulated by @@ -4207,7 +4205,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds via some process of localization - Chris Mungall + Do not use this relation directly. It is a grouping relation. related via localization to @@ -4223,7 +4221,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - Chris Mungall + @@ -4241,7 +4239,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - Chris Mungall + @@ -4255,7 +4253,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. - Chris Mungall + imports @@ -4267,7 +4265,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - Chris Mungall + results in transport along @@ -4279,7 +4277,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - Chris Mungall + results in transport across @@ -4292,7 +4290,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'pollen tube growth' results_in growth_of some 'pollen tube' - Chris Mungall + results in growth of @@ -4303,7 +4301,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - Chris Mungall + results in transport to from or in @@ -4313,8 +4311,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. - Chris Mungall + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. + exports @@ -4328,7 +4326,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - Chris Mungall + @@ -4343,7 +4341,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - Chris Mungall + @@ -4358,7 +4356,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has input - Chris Mungall + input of @@ -4372,7 +4370,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has output - Chris Mungall + output of @@ -4384,7 +4382,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + formed as result of @@ -4396,7 +4394,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. - Chris Mungall + results in structural organization of @@ -4408,7 +4406,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - Chris Mungall + @@ -4422,7 +4420,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. - Chris Mungall + results in developmental induction of @@ -4432,7 +4430,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + http://neurolex.org/wiki/Property:DendriteLocation has dendrite location @@ -4446,7 +4444,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - Chris Mungall + attached to (anatomical structure to anatomical structure) attached to @@ -4461,7 +4459,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - Chris Mungall + Wikipedia:Insertion_(anatomy) has muscle origin @@ -4482,7 +4480,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - Chris Mungall + Wikipedia:Insertion_(anatomy) has muscle insertion @@ -4503,8 +4501,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati false x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat - Chris Mungall - Chris Mungall + has fused element A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. @@ -4521,7 +4518,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) @@ -4541,7 +4538,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - Chris Mungall + drains into drains to tributary channel of @@ -4564,7 +4561,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Deschutes River distributary_of Little Lava Lake x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - Chris Mungall + branch of distributary channel of http://en.wikipedia.org/wiki/Distributary @@ -4588,7 +4585,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. - Chris Mungall + anastomoses with anabranch of @@ -4608,7 +4605,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - Chris Mungall + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with @@ -4633,7 +4630,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - Chris Mungall + branching part of @@ -4650,7 +4647,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. - Chris Mungall + main stem of @@ -4664,7 +4661,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_distributary_of y iff x distributary_of y and x does not flow back into y - Chris Mungall + proper distributary of @@ -4677,7 +4674,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_tributary_of y iff x tributary_of y and x does not originate from y - Chris Mungall + proper tributary of @@ -4692,7 +4689,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - Chris Mungall + has developmental potential involving @@ -4704,7 +4701,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - Chris Mungall + has potential to developmentally contribute to @@ -4716,7 +4713,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - Chris Mungall + has potential to developmentally induce @@ -4728,7 +4725,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has the potential to develop into y iff x develops into y or if x is capable of developing into y - Chris Mungall + has potential to develop into @@ -4740,7 +4737,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - Chris Mungall + has potential to directly develop into @@ -4757,7 +4754,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' has direct input @@ -4769,10 +4766,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect input + obsolete has indirect input true @@ -4784,9 +4781,9 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ translation SubClassOf has_direct_output some protein p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. - Chris Mungall + directly produces - obsolete has direct output + obsolete has direct output true @@ -4800,10 +4797,10 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - Chris Mungall + Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect output + obsolete has indirect output true @@ -4817,7 +4814,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ inverse of upstream of - Chris Mungall + causally downstream of @@ -4830,7 +4827,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - Chris Mungall + immediately causally downstream of @@ -4840,7 +4837,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - This term was obsoleted because it has the same meaning as 'directly positively regulates'. + This term was obsoleted because it has the same meaning as 'directly positively regulates'. obsolete directly activates true @@ -4870,7 +4867,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - Chris Mungall + indirectly activates indirectly positively regulates @@ -4882,7 +4879,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - This term was obsoleted because it has the same meaning as 'directly negatively regulates'. + This term was obsoleted because it has the same meaning as 'directly negatively regulates'. obsolete directly inhibits true @@ -4908,7 +4905,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - Chris Mungall + indirectly inhibits indirectly negatively regulates @@ -4935,7 +4932,7 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to @@ -4955,7 +4952,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - Chris Mungall + causally upstream of @@ -4969,7 +4966,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - Chris Mungall + immediately causally upstream of @@ -4987,7 +4984,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit - Chris Mungall + directly provides input for directly provides input for (process to process) @@ -5005,7 +5002,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different transitive form of directly_provides_input_for - Chris Mungall + This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. transitively provides input for (process to process) transitively provides input for @@ -5021,7 +5018,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall + influences (processual) affects causally upstream of or within @@ -5033,7 +5030,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different false - Chris Mungall + This is an exploratory relation differs in https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions @@ -5053,7 +5050,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + differs in attribute of @@ -5064,7 +5061,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + differs in attribute @@ -5076,7 +5073,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - Chris Mungall + causally downstream of or within @@ -5098,7 +5095,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - Chris Mungall + involved in regulation of @@ -5117,7 +5114,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - Chris Mungall + involved in positive regulation of @@ -5137,7 +5134,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - Chris Mungall + involved in negative regulation of @@ -5152,7 +5149,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - Chris Mungall + involved in or reguates involved in or involved in regulation of @@ -5170,7 +5167,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall + executes activity in enables activity in @@ -5189,8 +5186,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + GOC:cjm + GOC:dos @@ -5200,7 +5197,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - Chris Mungall + contributes to morphology of @@ -5213,9 +5210,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. - Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. - Chris Mungall + Considering relabeling as 'pairwise interacts with' + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with @@ -5232,7 +5229,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) - Chris Mungall + genetically interacts with http://purl.obolibrary.org/obo/MI_0208 @@ -5246,7 +5243,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - Chris Mungall + binds molecularly binds with molecularly interacts with @@ -5265,7 +5262,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - Chris Mungall + interacts with on organism level biotically interacts with @@ -5280,7 +5277,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the partners are related via a feeding relationship. - Chris Mungall + trophically interacts with @@ -5296,9 +5293,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] Baleen whale preys on krill An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - Chris Mungall - Jorrit Poelen - Katja Shulz + + + is subject of predation interaction with preys upon @@ -5322,7 +5319,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A biotic interaction in which the two organisms live together in more or less intimate association. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism @@ -5343,7 +5340,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 commensually interacts with @@ -5363,7 +5360,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 mutualistically interacts with @@ -5383,7 +5380,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 This relation groups a pair of inverse relations, parasite of and parasitized by @@ -5406,7 +5403,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human - Chris Mungall + parasitizes direct parasite of @@ -5421,7 +5418,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + has parasite parasitised by directly parasitized by @@ -5438,7 +5435,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - Chris Mungall + semibiotically interacts with participates in a abiotic-biotic interaction with @@ -5457,7 +5454,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates @@ -5479,8 +5476,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - Chris Mungall - Vasundra Touré + + molecularly controls directly regulates activity of @@ -5500,8 +5497,8 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly inhibits molecularly decreases activity of directly negatively regulates activity of @@ -5522,8 +5519,8 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly activates molecularly increases activity of directly positively regulates activity of @@ -5538,7 +5535,7 @@ For example, A and B may be gene products and binding of B by A positively regul all dengue disease transmitted by some mosquito A relationship that holds between a disease and organism Add domain and range constraints - Chris Mungall + transmitted by @@ -5550,7 +5547,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between a disease or an organism and a phenotype - Chris Mungall + has symptom @@ -5560,7 +5557,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) host of @@ -5573,7 +5570,7 @@ For example, A and B may be gene products and binding of B by A positively regul X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y - Chris Mungall + has host http://eol.org/schema/terms/hasHost @@ -5588,7 +5585,7 @@ For example, A and B may be gene products and binding of B by A positively regul Bees pollinate Flowers This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - Chris Mungall + is subject of pollination interaction with pollinates @@ -5601,7 +5598,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + has polinator is target of pollination interaction with @@ -5616,7 +5613,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. acquires nutrients from @@ -5629,7 +5626,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of preys on - Chris Mungall + has predator is target of predation interaction with @@ -5647,7 +5644,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anopheles is a vector for Plasmodium - Chris Mungall + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism is vector for @@ -5659,7 +5656,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + has vector @@ -5670,7 +5667,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target partner in @@ -5681,7 +5678,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. subject participant in @@ -5692,7 +5689,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. target participant in @@ -5702,7 +5699,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) @@ -5713,7 +5710,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is symbiosis @@ -5723,7 +5720,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is commensalism @@ -5733,7 +5730,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is mutualism @@ -5743,7 +5740,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is parasitism @@ -5753,7 +5750,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + provides nutrients for @@ -5764,7 +5761,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is subject of eating interaction with eats @@ -5776,7 +5773,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + eaten by is target of eating interaction with @@ -5792,7 +5789,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and the a supports either the existence of b, or the truth value of b. - Chris Mungall + is evidence for @@ -5807,7 +5804,7 @@ the a supports either the existence of b, or the truth value of b. 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - Chris Mungall + @@ -5824,7 +5821,7 @@ the a supports either the existence of b, or the truth value of b. ABal nucleus child nucleus of ABa nucleus (in C elegans) c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d - Chris Mungall + This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. child nucleus of @@ -5836,7 +5833,7 @@ the a supports either the existence of b, or the truth value of b. A child nucleus relationship in which the cells are part of a hermaphroditic organism - Chris Mungall + child nucleus of in hermaphrodite @@ -5847,7 +5844,7 @@ the a supports either the existence of b, or the truth value of b. A child nucleus relationship in which the cells are part of a male organism - Chris Mungall + child nucleus of in male @@ -5863,7 +5860,7 @@ the a supports either the existence of b, or the truth value of b. p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall + has part that occurs in @@ -5890,7 +5887,7 @@ the a supports either the existence of b, or the truth value of b. An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y Axiomatization to GO to be added later - Chris Mungall + ubiquitinates @@ -5900,7 +5897,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + is kinase activity @@ -5910,7 +5907,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + is ubiquitination @@ -5922,7 +5919,7 @@ the a supports either the existence of b, or the truth value of b. See notes for inverse relation - Chris Mungall + receives input from @@ -5933,7 +5930,7 @@ the a supports either the existence of b, or the truth value of b. This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - Chris Mungall + sends output to @@ -5944,7 +5941,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. relation between physical entity and a process or stage @@ -5965,7 +5962,7 @@ the a supports either the existence of b, or the truth value of b. x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). - Chris Mungall + existence starts during @@ -5976,7 +5973,7 @@ the a supports either the existence of b, or the truth value of b. x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). - Chris Mungall + existence starts with @@ -5987,7 +5984,7 @@ the a supports either the existence of b, or the truth value of b. x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) - Chris Mungall + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps @@ -5999,9 +5996,9 @@ the a supports either the existence of b, or the truth value of b. - x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) - Chris Mungall - exists during + x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) + + exists during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts and ends during @@ -6022,7 +6019,7 @@ the a supports either the existence of b, or the truth value of b. x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). - Chris Mungall + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during @@ -6034,7 +6031,7 @@ the a supports either the existence of b, or the truth value of b. x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). - Chris Mungall + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with @@ -6047,7 +6044,7 @@ the a supports either the existence of b, or the truth value of b. x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - Chris Mungall + transformation of @@ -6059,7 +6056,7 @@ the a supports either the existence of b, or the truth value of b. x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - Chris Mungall + immediate transformation of @@ -6098,7 +6095,7 @@ the a supports either the existence of b, or the truth value of b. x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). - Chris Mungall + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after @@ -6137,7 +6134,7 @@ the a supports either the existence of b, or the truth value of b. x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. - Chris Mungall + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before @@ -6163,7 +6160,7 @@ the a supports either the existence of b, or the truth value of b. p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes @@ -6174,7 +6171,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + depends on @@ -6187,7 +6184,7 @@ the a supports either the existence of b, or the truth value of b. q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. - Chris Mungall + towards @@ -6200,7 +6197,7 @@ the a supports either the existence of b, or the truth value of b. 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c - Chris Mungall + has intermediate product has intermediate @@ -6215,7 +6212,7 @@ the a supports either the existence of b, or the truth value of b. The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities @@ -6235,11 +6232,11 @@ the a supports either the existence of b, or the truth value of b.A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future - Chris Mungall + determined by (system to material entity) - Chris Mungall - Pier Buttigieg + + determined by @@ -6251,7 +6248,7 @@ the a supports either the existence of b, or the truth value of b. inverse of determined by - Chris Mungall + determines (material entity to system) @@ -6272,7 +6269,7 @@ the a supports either the existence of b, or the truth value of b. s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. - Chris Mungall + determined by part of @@ -6310,7 +6307,7 @@ the a supports either the existence of b, or the truth value of b. x is transcribed from y if and only if x is synthesized from template y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 transcribed from @@ -6322,7 +6319,7 @@ the a supports either the existence of b, or the truth value of b. inverse of transcribed from - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 transcribed to @@ -6352,7 +6349,7 @@ the a supports either the existence of b, or the truth value of b. x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 ribosomal translation of @@ -6380,7 +6377,7 @@ the a supports either the existence of b, or the truth value of b. inverse of ribosomal translation of - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 ribosomally translates to @@ -6393,7 +6390,7 @@ the a supports either the existence of b, or the truth value of b. A relation that holds between two entities that have the property of being sequences or having sequences. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. @@ -6411,7 +6408,7 @@ the a supports either the existence of b, or the truth value of b.Two consecutive DNA residues are sequentially adjacent Two exons on a processed transcript that were previously connected by an intron are adjacent x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 sequentially adjacent to @@ -6427,7 +6424,7 @@ the a supports either the existence of b, or the truth value of b. Every CDS has as a start sequence the start codon for that transcript x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence - Chris Mungall + started by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6442,7 +6439,7 @@ the a supports either the existence of b, or the truth value of b. inverse of has start sequence - Chris Mungall + starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6460,7 +6457,7 @@ the a supports either the existence of b, or the truth value of b. Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence - Chris Mungall + ended by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6475,7 +6472,7 @@ the a supports either the existence of b, or the truth value of b. inverse of has end sequence - Chris Mungall + ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6491,7 +6488,7 @@ the a supports either the existence of b, or the truth value of b. x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. In the SO paper, this was defined as an instance-type relation - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 is consecutive sequence of @@ -6506,7 +6503,7 @@ the a supports either the existence of b, or the truth value of b. Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering - Chris Mungall + is sequentially aligned with @@ -6521,7 +6518,7 @@ the a supports either the existence of b, or the truth value of b. The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y - Chris Mungall + bounds sequence of @@ -6534,7 +6531,7 @@ the a supports either the existence of b, or the truth value of b. inverse of bounds sequence of - Chris Mungall + is bound by sequence of @@ -6550,8 +6547,8 @@ the a supports either the existence of b, or the truth value of b. - x has subsequence y iff all of the sequence parts of x are sequence parts of y - Chris Mungall + x has subsequence y iff all of the sequence parts of y are sequence parts of x + contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6568,7 +6565,7 @@ the a supports either the existence of b, or the truth value of b. inverse of has subsequence - Chris Mungall + contained by @@ -6587,8 +6584,8 @@ the a supports either the existence of b, or the truth value of b. - x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. - Chris Mungall + x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. + overlaps sequence of @@ -6600,8 +6597,8 @@ the a supports either the existence of b, or the truth value of b. - x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. - Chris Mungall + x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + disconnected from does not overlap sequence of @@ -6615,7 +6612,7 @@ the a supports either the existence of b, or the truth value of b. inverse of downstream of sequence of - Chris Mungall + is upstream of sequence of @@ -6629,7 +6626,7 @@ the a supports either the existence of b, or the truth value of b. x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. - Chris Mungall + is downstream of sequence of @@ -6643,7 +6640,7 @@ the a supports either the existence of b, or the truth value of b. A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y - Chris Mungall + is immediately downstream of sequence of @@ -6658,7 +6655,7 @@ the a supports either the existence of b, or the truth value of b. A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript inverse of immediately downstream of - Chris Mungall + is immediately upstream of sequence of @@ -6676,7 +6673,7 @@ the a supports either the existence of b, or the truth value of b. Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - Chris Mungall + has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). has skeleton @@ -6696,7 +6693,7 @@ the a supports either the existence of b, or the truth value of b. p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. - Chris Mungall + results in ending of @@ -6713,7 +6710,7 @@ the a supports either the existence of b, or the truth value of b. x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - Chris Mungall + http://eol.org/schema/terms/hyperparasitoidOf https://en.wikipedia.org/wiki/Hyperparasite hyperparasitoid of @@ -6733,7 +6730,7 @@ the a supports either the existence of b, or the truth value of b. inverse of hyperparasite of - Chris Mungall + has epiparasite has hyperparasite hyperparasitoidized by @@ -6748,7 +6745,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + http://en.wikipedia.org/wiki/Allelopathy allelopath of @@ -6763,7 +6760,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + pathogen of @@ -6774,7 +6771,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + has pathogen @@ -6786,7 +6783,7 @@ the a supports either the existence of b, or the truth value of b. inverse of is evidence for - Chris Mungall + @@ -6801,7 +6798,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + causally influenced by (entity-centric) causally influenced by @@ -6813,7 +6810,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ @@ -6825,7 +6822,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + molecular interaction relation helper property @@ -6836,7 +6833,7 @@ the a supports either the existence of b, or the truth value of b. Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - Chris Mungall + @@ -6863,8 +6860,8 @@ the a supports either the existence of b, or the truth value of b. The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - Chris Mungall - Vasundra Touré + + causally influences (entity-centric) causally influences @@ -6879,7 +6876,7 @@ the a supports either the existence of b, or the truth value of b. A relation that holds between elements of a musculoskeletal system or its analogs. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. biomechanically related to @@ -6891,7 +6888,7 @@ the a supports either the existence of b, or the truth value of b. m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - Chris Mungall + Wikipedia:Antagonist_(muscle) has muscle antagonist @@ -6905,7 +6902,7 @@ the a supports either the existence of b, or the truth value of b. inverse of branching part of - Chris Mungall + has branching part @@ -6920,7 +6917,7 @@ the a supports either the existence of b, or the truth value of b. x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - Chris Mungall + UBERON:cjm This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. @@ -6935,7 +6932,7 @@ the a supports either the existence of b, or the truth value of b. x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - Chris Mungall + GOC:cjm lumen of @@ -6949,7 +6946,7 @@ the a supports either the existence of b, or the truth value of b. s is luminal space of x iff s is lumen_of x and s is an immaterial entity - Chris Mungall + luminal space of @@ -6962,7 +6959,7 @@ the a supports either the existence of b, or the truth value of b. A relation that holds between an attribute or a qualifier and another attribute. - Chris Mungall + This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. @@ -6977,7 +6974,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + participates in a biotic-biotic interaction with @@ -6992,7 +6989,7 @@ the a supports either the existence of b, or the truth value of b. inverse of has skeleton - Chris Mungall + skeleton of @@ -7005,7 +7002,7 @@ the a supports either the existence of b, or the truth value of b. p directly regulates q iff p is immediately causally upstream of q and p regulates q. - Chris Mungall + directly regulates (processual) @@ -7038,7 +7035,7 @@ the a supports either the existence of b, or the truth value of b. gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - Chris Mungall + has part structure that is capable of @@ -7145,7 +7142,7 @@ the a supports either the existence of b, or the truth value of b. A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall + causal relation between material entity and a process @@ -7272,7 +7269,7 @@ the a supports either the existence of b, or the truth value of b. A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - obsolete related via dependence to + obsolete related via dependence to true @@ -7571,10 +7568,10 @@ the a supports either the existence of b, or the truth value of b. - a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. - Melissa Haendel + a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. + - Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. + Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces @@ -7587,7 +7584,7 @@ the a supports either the existence of b, or the truth value of b. a produced_by b iff some process that occurs_in b has_output a. - Melissa Haendel + produced by @@ -7601,7 +7598,7 @@ the a supports either the existence of b, or the truth value of b. Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. - Vasundra Touré + represses expression of @@ -7614,7 +7611,7 @@ the a supports either the existence of b, or the truth value of b. Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. - Vasundra Touré + increases expression of @@ -7626,7 +7623,7 @@ the a supports either the existence of b, or the truth value of b. A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. - Matthew Brush + is used to study The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate. has role in modeling @@ -7763,7 +7760,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:38:20Z condition has genetic basis in @@ -7775,7 +7772,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:20Z has material basis in gain of function germline mutation in @@ -7789,7 +7786,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:37Z has material basis in loss of function germline mutation in @@ -7801,7 +7798,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:54Z has material basis in germline mutation in @@ -7814,7 +7811,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:07Z has material basis in somatic mutation in @@ -7827,7 +7824,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:26Z has major susceptibility factor @@ -7839,7 +7836,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:57Z has partial material basis in germline mutation in @@ -7851,7 +7848,7 @@ Environmental exposures include those imposed by natural environments, experimen p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - cjm + 2018-12-13T11:26:17Z has primary input or output @@ -7865,7 +7862,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - cjm + 2018-12-13T11:26:32Z has primary output @@ -7874,10 +7871,10 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm - GOC:dph GOC:kva GOC:pt + GOC:cjm + GOC:dph PMID:27812932 @@ -7889,7 +7886,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - cjm + 2018-12-13T11:26:56Z has primary input @@ -7898,10 +7895,10 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm - GOC:dph GOC:kva GOC:pt + GOC:cjm + GOC:dph PMID:27812932 @@ -7913,7 +7910,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:53:08Z is genetic basis for condition @@ -7925,7 +7922,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:55:51Z is causal gain of function germline mutation of in @@ -7938,7 +7935,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:06Z is causal loss of function germline mutation of in @@ -7952,7 +7949,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:40Z is causal germline mutation in @@ -7966,7 +7963,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:57:07Z is causal somatic mutation in @@ -7979,7 +7976,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. - cjm + 2017-11-05T02:57:43Z is causal susceptibility factor for @@ -7993,7 +7990,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. - cjm + 2017-11-05T02:58:43Z is causal germline mutation partially giving rise to @@ -8006,7 +8003,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:01Z realizable has basis in @@ -8017,7 +8014,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:29Z is basis for realizable @@ -8030,7 +8027,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:26:47Z disease has basis in @@ -8044,7 +8041,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) - cjm + 2017-11-05T03:29:32Z disease has basis in dysfunction of @@ -8058,7 +8055,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. disease has basis in disruption of (disease to process) - cjm + 2017-11-05T03:37:52Z disease has basis in disruption of @@ -8080,7 +8077,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. - cjm + 2017-11-05T03:46:07Z disease has basis in feature @@ -8094,7 +8091,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. - cjm + 2017-11-05T03:50:54Z causal relationship with disease as subject @@ -8117,7 +8114,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and a process where the disease process disrupts the execution of the process. disease causes disruption of (disease to process) - cjm + 2017-11-05T03:51:09Z disease causes disruption of @@ -8135,7 +8132,7 @@ Environmental exposures include those imposed by natural environments, experimen disease causes dysfunction of (disease to anatomical entity) - cjm + 2017-11-05T03:58:20Z disease causes dysfunction of @@ -8159,7 +8156,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. - cjm + 2017-11-05T04:06:02Z disease has location @@ -8181,7 +8178,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity - cjm + 2017-12-26T19:37:31Z disease has inflammation site @@ -8199,7 +8196,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - cjm + 2017-12-26T19:45:49Z realized in response to stimulus @@ -8220,7 +8217,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. - cjm + 2017-12-26T19:50:53Z disease has feature @@ -8233,7 +8230,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. - cjm + 2017-12-26T19:58:44Z disease arises from alteration in structure @@ -8249,7 +8246,7 @@ Environmental exposures include those imposed by natural environments, experimen Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - cjm + 2018-01-25T23:20:13Z enables subfunction @@ -8265,7 +8262,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:30Z acts upstream of or within, positive effect @@ -8283,7 +8280,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:51Z acts upstream of or within, negative effect @@ -8302,7 +8299,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - cjm + 2018-01-26T23:53:14Z acts upstream of, positive effect @@ -8322,7 +8319,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - cjm + 2018-01-26T23:53:22Z acts upstream of, negative effect @@ -8336,7 +8333,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:05Z causally upstream of or within, negative effect @@ -8348,7 +8345,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:19Z causally upstream of or within, positive effect @@ -8480,7 +8477,7 @@ Environmental exposures include those imposed by natural environments, experimen "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. - Damion Dooley + has substance added @@ -8495,7 +8492,7 @@ Environmental exposures include those imposed by natural environments, experimen 'egg white' 'has substance removed' some 'egg yolk' "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. - Damion Dooley + has substance removed @@ -8510,7 +8507,7 @@ Environmental exposures include those imposed by natural environments, experimen sardines 'immersed in' some 'oil and mustard' "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. - Damion Dooley + immersed in @@ -8524,7 +8521,7 @@ Environmental exposures include those imposed by natural environments, experimen sardine has consumer some homo sapiens 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. - Damion Dooley + has consumer @@ -8538,7 +8535,7 @@ Environmental exposures include those imposed by natural environments, experimen bread 'has primary substance added' some 'flour' 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance. - Damion Dooley + has primary substance added @@ -8558,10 +8555,10 @@ Environmental exposures include those imposed by natural environments, experimen An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - Austin Meier - Chris Mungall - David Osumi-Sutherland - Marie Angelique Laporte + + + + triggered by process realized in response to https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit @@ -8624,7 +8621,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - Vasundra Touré + regulates activity of @@ -8637,7 +8634,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. - Vasundra Touré + regulates quantity of @@ -8650,7 +8647,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. - Vasundra Touré + indirectly regulates activity of @@ -8665,7 +8662,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + decreases by repression quantity of @@ -8680,7 +8677,7 @@ For example, protein A (transcription factor) indirectly decreases by repression The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + increases by expression quantity of @@ -8693,7 +8690,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly positively regulates the quantity of B. - Vasundra Touré + directly positively regulates quantity of @@ -8706,7 +8703,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly negatively regulates the quantity of B. - Vasundra Touré + directly negatively regulates quantity of @@ -8719,7 +8716,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. - Vasundra Touré + indirectly activates indirectly positively regulates activity of @@ -8734,7 +8731,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. - Vasundra Touré + destabilizes quantity of @@ -8748,7 +8745,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. - Vasundra Touré + stabilizes quantity of @@ -8759,7 +8756,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. - Vasundra Touré + indirectly inhibits indirectly negatively regulates activity of @@ -8771,7 +8768,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. - Vasundra Touré + directly regulates quantity of @@ -8782,7 +8779,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. - Vasundra Touré + indirectly regulates quantity of @@ -8793,7 +8790,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. - Vasundra Touré + indirectly negatively regulates quantity of @@ -8804,7 +8801,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. - Vasundra Touré + indirectly positively regulates quantity of @@ -8815,8 +8812,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is regulated by the small molecule continuant + pg 2020-04-22T20:27:26Z has small molecule regulator @@ -8828,8 +8825,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is activated by the small molecule continuant + pg 2020-04-22T20:28:37Z has small molecule activator @@ -8841,8 +8838,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant + pg 2020-04-22T20:28:54Z has small molecule inhibitor @@ -8853,8 +8850,8 @@ For example, protein A (transcription factor) indirectly increases by expression - p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + p acts on population of c iff c' is a collection, has members of type c, and p has participant c + pg 2020-06-08T17:21:33Z @@ -8868,8 +8865,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process + pg 2020-06-24T13:15:17Z is small molecule regulator of @@ -8881,8 +8878,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process + pg 2020-06-24T13:15:26Z is small molecule activator of @@ -8894,8 +8891,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process + pg 2020-06-24T13:15:35Z is small molecule inhibitor of @@ -8906,8 +8903,8 @@ For example, protein A (transcription factor) indirectly increases by expression - The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. + pg 2020-08-27T08:13:59Z results in adhesion of @@ -8918,7 +8915,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + pg 2021-02-26T07:28:29Z @@ -8933,7 +8930,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + pg 2022-09-26T06:01:01Z @@ -8947,7 +8944,7 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + pg 2022-09-26T06:06:20Z @@ -8961,7 +8958,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + pg 2022-09-26T06:07:17Z indirectly causally upstream of @@ -8974,7 +8971,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + pg 2022-09-26T06:08:01Z indirectly regulates @@ -9139,7 +9136,7 @@ For example, protein A (transcription factor) indirectly increases by expression transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data]) A relation between a material entity and some data in which the data is taken as exemplifying the material entity. C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C. - Patrick Ray + This relation is not meant to capture the relation between occurrents and data. has exemplar data @@ -9150,7 +9147,7 @@ For example, protein A (transcription factor) indirectly increases by expression - Patrick Ray + exemplar data of @@ -9163,7 +9160,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relation between a group and another group it is part of but does not fully constitute. X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. - Shawn Tan + This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. subcluster of @@ -9211,7 +9208,7 @@ For example, protein A (transcription factor) indirectly increases by expression q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. - This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. + This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. increased in magnitude relative to @@ -9230,7 +9227,7 @@ For example, protein A (transcription factor) indirectly increases by expression q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. - This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. + This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. decreased in magnitude relative to @@ -9269,7 +9266,7 @@ For example, protein A (transcription factor) indirectly increases by expression s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. - Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. + Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. has cross section @@ -9285,7 +9282,7 @@ For example, protein A (transcription factor) indirectly increases by expression q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. - There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. + There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. reciprocal of @@ -9354,7 +9351,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - http://orcid.org/0000-0002-7463-6306 + 2021-11-05T17:30:44Z has disease https://github.com/oborel/obo-relations/issues/478 @@ -9384,8 +9381,8 @@ For example, protein A (transcription factor) indirectly increases by expression A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - https://orcid.org/0000-0001-9625-1899 - https://orcid.org/0000-0003-2620-0345 + + A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z @@ -9540,7 +9537,7 @@ For example, protein A (transcription factor) indirectly increases by expression This relation groups relations between diseases and any other kind of entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. - cjm + 2018-09-26T00:00:32Z disease relationship @@ -9552,7 +9549,7 @@ For example, protein A (transcription factor) indirectly increases by expression p has anatomical participant c iff p has participant c, and c is an anatomical entity - cjm + 2018-09-26T01:08:58Z results in changes to anatomical or cellular structure @@ -9613,7 +9610,7 @@ For example, protein A (transcription factor) indirectly increases by expression Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. - dos + dos 2018-05-22T16:43:28Z This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. has increased age-specific mortality rate @@ -10198,8 +10195,8 @@ For example, protein A (transcription factor) indirectly increases by expression An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes. A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism. This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions. - Chris Mungall - cjm + + 2017-06-05T17:55:39Z exposure event or process https://github.com/oborel/obo-relations/pull/173 @@ -10218,7 +10215,7 @@ For example, protein A (transcription factor) indirectly increases by expression Any entity that is ordered in discrete units along a linear axis. - Chris Mungall + sequentially ordered entity @@ -10229,7 +10226,7 @@ For example, protein A (transcription factor) indirectly increases by expression Any individual unit of a collection of like units arranged in a linear order - Chris Mungall + An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair. sequence atomic unit @@ -10241,7 +10238,7 @@ For example, protein A (transcription factor) indirectly increases by expression Any entity that can be divided into parts such that each part is an atomical unit of a sequence - Chris Mungall + Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence. sequence bearer @@ -10254,7 +10251,7 @@ For example, protein A (transcription factor) indirectly increases by expression A material entity consisting of multiple components that are causally integrated. May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 - Chris Mungall + http://www.jbiomedsem.com/content/4/1/43 system @@ -10301,8 +10298,8 @@ For example, protein A (transcription factor) indirectly increases by expression - This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. + @@ -10437,15 +10434,15 @@ For example, protein A (transcription factor) indirectly increases by expression - - - + + + @@ -10455,15 +10452,15 @@ For example, protein A (transcription factor) indirectly increases by expression - - - + + + @@ -10524,8 +10521,8 @@ For example, protein A (transcription factor) indirectly increases by expression true - MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z - infer input from direct reg + MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z + infer input from direct reg @@ -10654,8 +10651,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP + GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' + involved in BP @@ -10965,9 +10962,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -10976,9 +10973,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -11010,9 +11007,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -11021,9 +11018,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -11055,9 +11052,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -11066,9 +11063,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -11100,9 +11097,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -11111,9 +11108,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -11145,9 +11142,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -11156,9 +11153,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -11190,7 +11187,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -11201,7 +11198,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -11218,7 +11215,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -11228,7 +11225,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -11246,7 +11243,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -11257,7 +11254,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -11274,7 +11271,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -11284,7 +11281,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -11301,7 +11298,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -11312,7 +11309,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -11345,9 +11342,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -11356,9 +11353,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -11389,9 +11386,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -11400,9 +11397,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -11433,9 +11430,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -11444,9 +11441,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -11477,9 +11474,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -11488,9 +11485,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -11522,8 +11519,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -11533,8 +11530,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -11561,5 +11558,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + diff --git a/src/ontology/generated-axioms.owl b/src/ontology/generated-axioms.owl index 5eff3f88..4adb7c15 100644 --- a/src/ontology/generated-axioms.owl +++ b/src/ontology/generated-axioms.owl @@ -148,5 +148,5 @@ - + diff --git a/src/ontology/subsets/ro-causal.obo b/src/ontology/subsets/ro-causal.obo index 35c639dc..9472403f 100644 --- a/src/ontology/subsets/ro-causal.obo +++ b/src/ontology/subsets/ro-causal.obo @@ -13,7 +13,7 @@ id: acquires_nutrients_from name: acquires nutrients from subset: ro-eco xref: RO:0002457 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for @@ -58,7 +58,7 @@ property_value: RO:0004050 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:22Z [Typedef] @@ -71,7 +71,7 @@ property_value: RO:0004049 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:14Z [Typedef] @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z [Typedef] @@ -103,7 +103,7 @@ xref: RO:0004032 property_value: RO:0004049 RO:0002264 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z [Typedef] @@ -120,7 +120,7 @@ property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cy property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 domain: BFO:0000004 range: BFO:0000004 @@ -131,7 +131,7 @@ id: allelopath_of name: allelopath of subset: ro-eco xref: RO:0002555 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string @@ -153,7 +153,7 @@ def: "x anabranch_of y if x is a distributary of y (i.e. it channels a from a la subset: ro-eco xref: RO:0002378 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "anastomoses with" xsd:string is_a: distributary_of ! distributary of disjoint_from: proper_distributary_of ! proper distributary of @@ -165,7 +165,7 @@ name: attached to def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] subset: ro-eco xref: RO:0002371 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: attached_to_part_of ! attached to part of @@ -189,9 +189,8 @@ def: "Relation between a neuron and some structure its axon forms (chemical) syn xref: RO:0002102 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in @@ -202,7 +201,7 @@ id: biomechanically_related_to name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] xref: RO:0002567 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: CARO:0000003 range: CARO:0000003 @@ -214,7 +213,7 @@ name: biotically interacts with def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] subset: ro-eco xref: RO:0002437 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string @@ -231,7 +230,7 @@ def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\ comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco xref: RO:0002007 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 is_a: part_of @@ -242,7 +241,7 @@ def: "x bounds the sequence of y iff the upstream-most part of x is upstream of xref: RO:0002522 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to inverse_of: is_bound_by_sequence_of ! is bound by sequence of @@ -254,7 +253,7 @@ def: "x is a branching part of y if and only if x is part of y and x is connecte subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso FMA:85994 xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with @@ -269,7 +268,7 @@ subset: ro-eco xref: RO:0002215 property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 @@ -302,7 +301,7 @@ id: capable_of_part_of name: capable of part of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ is_a: causal_agent_in_process ! causal agent in process @@ -350,7 +349,7 @@ id: causal_relation_between_entities name: causal relation between entities xref: RO:0002506 property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000002 @@ -363,7 +362,7 @@ name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] xref: RO:0002595 property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 range: BFO:0000015 @@ -374,7 +373,7 @@ id: causal_relation_between_processes name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 @@ -389,7 +388,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: OGMS:0000031 is_a: causally_related_to ! causally related to is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:50:54Z [Typedef] @@ -398,7 +397,7 @@ name: causally downstream of def: "inverse of upstream of" [] xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within is_a: preceded_by inverse_of: causally_upstream_of ! causally upstream of @@ -409,7 +408,7 @@ name: causally downstream of or within def: "inverse of causally upstream of or within" [] subset: RO:0002259 xref: RO:0002427 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -418,7 +417,7 @@ is_a: causal_relation_between_processes ! causal relation between processes id: causally_influenced_by name: causally influenced by xref: RO:0002559 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: causal_relation_between_entities ! causal relation between entities @@ -429,8 +428,8 @@ id: causally_influences name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] xref: RO:0002566 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 @@ -443,7 +442,7 @@ name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] @@ -453,7 +452,7 @@ def: "p is causally upstream of q iff p is causally related to q, the end of p p subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes @@ -465,7 +464,7 @@ def: "p is causally upstream of, negative effect q iff p is casually upstream of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -478,7 +477,7 @@ comment: holds between x and y if and only if x is causally upstream of y and th subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -490,7 +489,7 @@ def: "p is 'causally upstream or within' q iff p is causally related to q, and t synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -502,7 +501,7 @@ name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -511,7 +510,7 @@ name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -537,7 +536,7 @@ name: child nucleus of def: "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" [] xref: RO:0002476 property_value: IAO:0000112 "ABal nucleus child nucleus of ABa nucleus (in C elegans)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." xsd:string domain: GO:0005634 range: GO:0005634 @@ -548,7 +547,7 @@ id: child_nucleus_of_in_hermaphrodite name: child nucleus of in hermaphrodite def: "A child nucleus relationship in which the cells are part of a hermaphroditic organism" [] xref: RO:0002477 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -556,7 +555,7 @@ id: child_nucleus_of_in_male name: child nucleus of in male def: "A child nucleus relationship in which the cells are part of a male organism" [] xref: RO:0002478 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -576,7 +575,7 @@ comment: Example: if we define region of chromosome as any subdivision of a chro subset: ro-eco xref: RO:0002008 property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -585,9 +584,8 @@ name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 -property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -599,7 +597,7 @@ name: commensually interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] subset: ro-eco xref: RO:0002441 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -610,7 +608,7 @@ def: "x composed_primarily_of y if and only if more than half of the mass of x i subset: ro-eco xref: RO:0002473 property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 @@ -639,7 +637,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: BFO:0000017 is_a: causally_related_to ! causally related to inverse_of: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:38:20Z [Typedef] @@ -648,7 +646,7 @@ name: conduit for def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] subset: ro-eco xref: RO:0002570 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 UBERON:cjm xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 @@ -661,7 +659,7 @@ name: confers advantage in subset: ro-eco xref: RO:0002322 property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "adapted for" xsd:string range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -727,7 +725,7 @@ name: continuous with def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 @@ -746,7 +744,7 @@ property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a het property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -771,7 +769,7 @@ id: contributes_to_morphology_of name: contributes to morphology of def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] xref: RO:0002433 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -796,7 +794,7 @@ id: decreases_by_repression_quantity_of name: decreases by repression quantity of def: "The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011007 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_negatively_regulates_quantity_of ! indirectly negatively regulates quantity of @@ -808,8 +806,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in wh xref: RO:0002121 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in @@ -821,7 +819,7 @@ name: destabilizes quantity of def: "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." [] xref: RO:0011014 property_value: IAO:0000112 "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_quantity_of ! directly negatively regulates quantity of @@ -832,11 +830,11 @@ name: determined by def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] subset: ro-eco xref: RO:0002507 -property_value: http://purl.org/dc/terms/creator "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/creator "Pier Buttigieg" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-4366-3088 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "A coral reef environment is determined by a particular coral reef" xsd:string property_value: IAO:0000116 "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602 property_value: IAO:0000589 "determined by (system to material entity)" xsd:string domain: RO:0002577 @@ -852,7 +850,7 @@ name: determined by part of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] subset: ro-eco xref: RO:0002509 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 range: BFO:0000040 is_a: causal_relation_between_entities ! causal relation between entities @@ -865,7 +863,7 @@ def: "inverse of determined by" [] subset: ro-eco subset: RO:0002259 xref: RO:0002508 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "determines (material entity to system)" xsd:string is_a: causally_influences ! causally influences @@ -876,7 +874,7 @@ def: "inverse of has developmental contribution from" [] subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to @@ -886,9 +884,9 @@ name: developmentally induced by def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] xref: RO:0002256 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string property_value: IAO:0000119 GO:0001759 xsd:string @@ -905,7 +903,7 @@ name: developmentally induces def: "Inverse of developmentally induced by" [] xref: RO:0002257 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_induce ! has potential to developmentally induce @@ -917,7 +915,7 @@ comment: This relation groups together various other developmental relations. It xref: RO:0002258 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string domain: BFO:0000002 range: BFO:0000002 @@ -929,7 +927,7 @@ id: developmentally_related_to name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] xref: RO:0002324 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] @@ -939,7 +937,7 @@ def: "x developmentally replaces y if and only if there is some developmental pr xref: RO:0002285 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "replaces" xsd:string is_a: developmentally_preceded_by ! developmentally preceded by @@ -949,7 +947,7 @@ name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] xref: RO:0002286 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -959,10 +957,10 @@ def: "x develops from y if and only if either (a) x directly develops from y or comment: This is the transitive form of the develops from relation xref: RO:0002202 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 domain: BFO:0000004 range: BFO:0000004 is_transitive: true @@ -975,7 +973,7 @@ name: develops from part of def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] xref: RO:0002225 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: develops_from ! develops from [Typedef] @@ -984,7 +982,7 @@ name: develops in def: "x develops_in y if x is located in y whilst x is developing" [] xref: RO:0002226 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string domain: CARO:0000000 @@ -997,9 +995,9 @@ def: "inverse of develops from" [] subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 is_transitive: true is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into @@ -1010,11 +1008,11 @@ id: directly_develops_from name: directly develops from def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] xref: RO:0002207 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "has developmental precursor" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000119 "FBbt" xsd:string property_value: RO:0002575 RO:0002202 is_a: develops_from ! develops from @@ -1060,8 +1058,8 @@ name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] xref: RO:0002449 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1072,7 +1070,7 @@ id: directly_negatively_regulates_quantity_of name: directly negatively regulates quantity of def: "The entity A has an activity that directly negatively regulates the quantity of B." [] xref: RO:0011010 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1107,8 +1105,8 @@ name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] xref: RO:0002450 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1119,7 +1117,7 @@ id: directly_positively_regulates_quantity_of name: directly positively regulates quantity of def: "The entity A has an activity that directly positively regulates the quantity of B." [] xref: RO:0011009 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1142,7 +1140,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002578 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string property_value: RO:0002575 RO:0002211 @@ -1155,8 +1153,8 @@ name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] xref: RO:0002448 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: molecularly_interacts_with ! molecularly interacts with @@ -1167,7 +1165,7 @@ id: directly_regulates_quantity_of name: directly regulates quantity of def: "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B." [] xref: RO:0011021 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -1177,7 +1175,7 @@ def: "A relationship between a disease and an anatomical structure where the mat xref: RO:0004030 range: CARO:0000003 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z [Typedef] @@ -1189,7 +1187,7 @@ property_value: IAO:0000589 "disease causes disruption of (disease to process)" domain: OGMS:0000031 range: BFO:0000015 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:51:09Z [Typedef] @@ -1200,7 +1198,7 @@ property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomica domain: OGMS:0000031 range: CARO:0000006 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z [Typedef] @@ -1210,7 +1208,7 @@ xref: RO:0004019 domain: OGMS:0000031 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject is_a: realizable_has_basis_in ! realizable has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:26:47Z [Typedef] @@ -1221,7 +1219,7 @@ xref: RO:0004021 property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:37:52Z [Typedef] @@ -1232,7 +1230,7 @@ xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string range: CARO:0000006 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z [Typedef] @@ -1243,7 +1241,7 @@ xref: RO:0004022 domain: OGMS:0000031 is_a: disease_has_basis_in ! disease has basis in is_a: has_phenotype ! has phenotype -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:46:07Z [Typedef] @@ -1253,7 +1251,7 @@ def: "A relationship between a disease and some feature of that disease, where t xref: RO:0004029 domain: OGMS:0000031 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:50:53Z [Typedef] @@ -1272,7 +1270,7 @@ xref: RO:0004027 domain: OGMS:0000031 range: BFO:0000004 is_a: disease_has_location ! disease has location -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:37:31Z [Typedef] @@ -1285,7 +1283,7 @@ property_value: IAO:0000232 "This relation is intentionally very general, and co domain: OGMS:0000031 range: BFO:0000004 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T04:06:02Z [Typedef] @@ -1294,7 +1292,7 @@ name: disease relationship def: "This relation groups relations between diseases and any other kind of entity." [] xref: RO:0040035 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z [Typedef] @@ -1306,7 +1304,7 @@ subset: ro-eco xref: RO:0002377 property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string @@ -1316,10 +1314,10 @@ is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: does_not_overlap_sequence_of name: does not overlap sequence of -def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] xref: RO:0002527 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "disconnected from" xsd:string is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -1338,7 +1336,7 @@ id: eats name: eats subset: ro-eco xref: RO:0002470 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -1359,7 +1357,7 @@ def: "A relationship that is mediated in some way by the environment or environm subset: ro-eco xref: RO:0002321 property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string [Typedef] @@ -1377,7 +1375,7 @@ name: electrically_synapsed_to def: "A relation that holds between two neurons that are electrically coupled via gap junctions." [] xref: RO:0002003 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: connected_to ! connected to [Typedef] @@ -1386,7 +1384,7 @@ name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: has_participant @@ -1397,7 +1395,7 @@ def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string property_value: IAO:0000118 "has" xsd:string @@ -1413,7 +1411,7 @@ name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] xref: RO:0004031 is_a: functionally_related_to ! functionally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z [Typedef] @@ -1430,14 +1428,14 @@ inverse_of: has_endoparasite ! has endoparasite id: ends subset: ro-eco xref: RO:0002229 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: ends_with subset: ro-eco xref: RO:0002230 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -1462,7 +1460,7 @@ name: exports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002345 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -1479,7 +1477,7 @@ def: "relationship between a neuron and a neuron projection bundle (e.g.- tract xref: RO:0002101 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 @@ -1492,7 +1490,7 @@ inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron proje id: formed_as_result_of name: formed as result of xref: RO:0002354 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of [Typedef] @@ -1500,7 +1498,7 @@ id: functionally_related_to name: functionally related to def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] xref: RO:0002328 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string [Typedef] @@ -1509,7 +1507,7 @@ name: genetically interacts with xref: RO:0002435 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with @@ -1517,7 +1515,7 @@ is_a: interacts_with ! interacts with [Typedef] id: has_2D_boundary xref: RO:0002002 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1557,7 +1555,7 @@ def: "inverse of branching part of" [] subset: ro-eco subset: RO:0002259 xref: RO:0002569 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: has_part is_a: in_branching_relationship_with ! in branching relationship with @@ -1593,7 +1591,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 "Bill Duncan (https://orcid.org/0000-0001-9625-1899)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant @@ -1622,7 +1620,7 @@ id: has_dendrite_location name: has dendrite location xref: RO:0002360 property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -1632,7 +1630,7 @@ def: "x has developmental contribution from y iff x has some part z such that z xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by @@ -1644,7 +1642,7 @@ name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to @@ -1656,7 +1654,7 @@ def: "p has direct input c iff c is a participant in p, c is present at the star xref: RO:0002400 property_value: IAO:0000112 "'protein catabolic process' SubClassOf has_direct_input some protein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly consumes" xsd:string property_value: IAO:0000232 "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" xsd:string is_a: has_input ! has input @@ -1666,7 +1664,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1711,7 +1709,7 @@ def: "x 'has end location' y if and only if there exists some process z such tha subset: ro-eco xref: RO:0002232 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -1724,7 +1722,7 @@ def: "x has end sequence y if the end of x is identical to the end of y, and x h xref: RO:0002518 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -1776,11 +1774,11 @@ id: has_exposure_stimulus name: has exposure stimulus def: "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002309 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 is_a: related_via_exposure_to ! related via exposure to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:35:04Z [Typedef] @@ -1806,7 +1804,7 @@ def: "The relation between a neuron projection bundle and a neuron projection th xref: RO:0002132 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 @@ -1828,7 +1826,7 @@ subset: ro-eco xref: RO:0002303 property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Pier Buttigieg" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string domain: CARO:0001010 range: ENVO:01000254 @@ -1851,7 +1849,7 @@ name: has host def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] subset: ro-eco xref: RO:0002454 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -1865,7 +1863,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 is_a: has_participant @@ -1886,7 +1884,7 @@ def: "p has intermediate c if and only if p has parts p1, p2 and p1 has output c subset: ro-eco xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string is_a: has_participant @@ -1924,7 +1922,7 @@ name: has major susceptibility factor xref: RO:0004005 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_susceptibility_factor_for ! is causal susceptibility factor for -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:26Z [Typedef] @@ -1935,7 +1933,7 @@ property_value: seeAlso Orphanet:410295 property_value: seeAlso Orphanet:410296 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_gain_of_function_germline_mutation_of_in ! is causal gain of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:20Z [Typedef] @@ -1945,7 +1943,7 @@ xref: RO:0004003 property_value: seeAlso Orphanet:317343 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_in ! is causal germline mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:54Z [Typedef] @@ -1954,7 +1952,7 @@ name: has material basis in loss of function germline mutation in xref: RO:0004002 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_loss_of_function_germline_mutation_of_in ! is causal loss of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:37Z [Typedef] @@ -1964,7 +1962,7 @@ xref: RO:0004004 property_value: seeAlso Orphanet:317344 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z [Typedef] @@ -1980,7 +1978,7 @@ id: has_muscle_antagonist name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string is_a: biomechanically_related_to ! biomechanically related to @@ -1989,7 +1987,7 @@ id: has_muscle_insertion name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} @@ -2001,7 +1999,7 @@ id: has_muscle_origin name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} @@ -2039,7 +2037,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string is_a: has_participant inverse_of: output_of ! output of @@ -2066,7 +2064,7 @@ name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] xref: RO:0002584 property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causal_relation_between_material_entity_and_a_process ! causal relation between material entity and a process is_a: functionally_related_to ! functionally related to @@ -2076,7 +2074,7 @@ name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco xref: RO:0002479 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 range: BFO:0000004 @@ -2086,7 +2084,7 @@ name: has partial material basis in germline mutation in xref: RO:0004006 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_partially_giving_rise_to ! is causal germline mutation partially giving rise to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:57Z [Typedef] @@ -2098,7 +2096,7 @@ id: has_pathogen name: has pathogen subset: ro-eco xref: RO:0002557 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2108,7 +2106,7 @@ def: "A relationship that holds between a biological entity and a phenotype. Her subset: ro-eco xref: RO:0002200 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: UPHENO:0001001 is_a: has_phenotype_or_disease ! has phenotype or disease inverse_of: phenotype_of ! phenotype of @@ -2129,9 +2127,9 @@ def: "Holds between a cell c and a protein complex or protein p if and only if t xref: RO:0002104 property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Alexander Diehl" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 @@ -2157,8 +2155,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in whi xref: RO:0002110 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "synapsed in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2172,7 +2170,7 @@ name: has potential to develop into def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] xref: RO:0002387 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2181,7 +2179,7 @@ name: has potential to developmentally contribute to def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] xref: RO:0002385 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2190,7 +2188,7 @@ name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] xref: RO:0002386 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2199,7 +2197,7 @@ name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] xref: RO:0002388 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_potential_to_develop_into ! has potential to develop into [Typedef] @@ -2223,7 +2221,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -2233,7 +2231,7 @@ def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c o subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -2244,7 +2242,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -2276,7 +2274,7 @@ name: has skeleton def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] xref: RO:0002551 property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 @@ -2321,7 +2319,7 @@ name: has soma location def: "Relation between a neuron and an anatomical structure that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 range: CARO:0000003 @@ -2335,7 +2333,7 @@ def: "x 'has starts location' y if and only if there exists some process z such subset: ro-eco xref: RO:0002231 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -2348,7 +2346,7 @@ def: "x has start sequence y if the start of x is identical to the start of y, a xref: RO:0002516 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2358,10 +2356,10 @@ inverse_of: is_start_sequence_of ! is start sequence of [Typedef] id: has_subsequence name: has subsequence -def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2375,7 +2373,7 @@ id: has_symptom name: has symptom def: "A relation that holds between a disease or an organism and a phenotype" [] xref: RO:0002452 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: OGMS:0000031 is_a: has_phenotype ! has phenotype @@ -2405,7 +2403,7 @@ def: "A general relation between a neuron and some structure in which it either xref: RO:0002130 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has synapse in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2417,7 +2415,7 @@ id: has_synaptic_terminal_of name: has synaptic terminal of xref: RO:0002006 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: overlaps ! overlaps inverse_of: has_synaptic_terminal_in ! has synaptic terminal in @@ -2429,7 +2427,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002339 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2440,7 +2438,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002338 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2448,7 +2446,7 @@ id: has_vector name: has vector subset: ro-eco xref: RO:0002460 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with [Typedef] @@ -2463,7 +2461,7 @@ id: host_of name: host of subset: ro-eco xref: RO:0002453 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2476,7 +2474,7 @@ synonym: "epiparasite of" RELATED [] synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string is_a: has_host ! has host @@ -2492,7 +2490,7 @@ synonym: "has epiparasite" RELATED [] synonym: "has hyperparasite" RELATED [] synonym: "hyperparasitoidized by" RELATED [] xref: RO:0002554 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2500,7 +2498,7 @@ id: immediate_transformation_of name: immediate transformation of def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] xref: RO:0002495 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002494 is_a: directly_develops_from ! directly develops from is_a: transformation_of ! transformation of @@ -2510,7 +2508,7 @@ id: immediately_causally_downstream_of name: immediately causally downstream of xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of is_a: immediately_preceded_by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of @@ -2520,7 +2518,7 @@ id: immediately_causally_upstream_of name: immediately causally upstream of def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: immediately_precedes @@ -2533,7 +2531,7 @@ xref: RO:0002087 id: immediately_precedes subset: ro-eco xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0002575 BFO:0000063 [Typedef] @@ -2542,7 +2540,7 @@ name: imports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002340 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -2551,7 +2549,7 @@ name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] xref: RO:0002375 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 @@ -2577,7 +2575,7 @@ id: increases_by_expression_quantity_of name: increases by expression quantity of def: "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011008 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_positively_regulates_quantity_of ! indirectly positively regulates quantity of @@ -2587,7 +2585,7 @@ id: increases_expression_of name: increases expression of def: "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." [] xref: RO:0003003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -2606,7 +2604,7 @@ id: indirectly_negatively_regulates name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true @@ -2618,7 +2616,7 @@ id: indirectly_negatively_regulates_activity_of name: indirectly negatively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B." [] xref: RO:0011016 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly inhibits" xsd:string is_a: indirectly_regulates_activity_of ! indirectly regulates activity of @@ -2627,7 +2625,7 @@ id: indirectly_negatively_regulates_quantity_of name: indirectly negatively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B." [] xref: RO:0011023 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2635,7 +2633,7 @@ id: indirectly_positively_regulates name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 is_transitive: true @@ -2647,7 +2645,7 @@ id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." [] xref: RO:0011013 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -2658,7 +2656,7 @@ id: indirectly_positively_regulates_quantity_of name: indirectly positively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B." [] xref: RO:0011024 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2676,7 +2674,7 @@ id: indirectly_regulates_activity_of name: indirectly regulates activity of def: "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." [] xref: RO:0011004 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: regulates_activity_of ! regulates activity of @@ -2686,7 +2684,7 @@ id: indirectly_regulates_quantity_of name: indirectly regulates quantity of def: "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B." [] xref: RO:0011022 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -2696,7 +2694,7 @@ def: "inverse of has input" [] subset: ro-eco subset: RO:0002259 xref: RO:0002352 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -2710,7 +2708,7 @@ xref: RO:0002434 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI domain: BFO:0000040 @@ -2723,7 +2721,7 @@ name: interacts with via parasite-host interaction def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] subset: ro-eco xref: RO:0002443 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2751,7 +2749,7 @@ id: involved_in name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] xref: RO:0002331 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in @@ -2763,7 +2761,7 @@ id: involved_in_negative_regulation_of name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] xref: RO:0002430 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2773,7 +2771,7 @@ name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in_process ! causal agent in process @@ -2784,7 +2782,7 @@ id: involved_in_positive_regulation_of name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] xref: RO:0002429 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2793,7 +2791,7 @@ id: involved_in_regulation_of name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] xref: RO:0002428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of @@ -2804,7 +2802,7 @@ def: "c executes activity in d if and only if c enables p and p occurs_in d. As synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -2853,7 +2851,7 @@ id: is_basis_for_realizable name: is basis for realizable xref: RO:0004018 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:29Z [Typedef] @@ -2863,7 +2861,7 @@ def: "inverse of bounds sequence of" [] subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to @@ -2874,7 +2872,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004011 property_value: seeAlso Orphanet:410296 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:55:51Z [Typedef] @@ -2885,7 +2883,7 @@ xref: RO:0004013 property_value: seeAlso Orphanet:317343 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:40Z [Typedef] @@ -2896,7 +2894,7 @@ xref: RO:0004016 property_value: seeAlso Orphanet:317346 is_a: contributes_to_condition ! contributes to condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:58:43Z [Typedef] @@ -2906,7 +2904,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004012 property_value: seeAlso Orphanet:410295 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:06Z [Typedef] @@ -2917,7 +2915,7 @@ xref: RO:0004014 property_value: seeAlso Orphanet:317344 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:07Z [Typedef] @@ -2927,7 +2925,7 @@ def: "Relates a gene to condition, such that a mutation in this gene predisposes xref: RO:0004015 property_value: seeAlso Orphanet:317345 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:43Z [Typedef] @@ -2937,7 +2935,7 @@ def: "x is a consecutive sequence of y iff x has subsequence y, and all the part xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: has_subsequence ! has subsequence @@ -2947,7 +2945,7 @@ name: is downstream of sequence of def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] xref: RO:0002529 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of @@ -2957,7 +2955,7 @@ id: is_eaten_by name: is eaten by subset: ro-eco xref: RO:0002471 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -2969,7 +2967,7 @@ def: "inverse of has end sequence" [] subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2982,7 +2980,7 @@ xref: RO:0004010 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string range: BFO:0000017 is_a: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:53:08Z [Typedef] @@ -2992,7 +2990,7 @@ def: "x is immediately downstream of the sequence of y iff either (1) x and y ha xref: RO:0002530 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002529 is_a: is_downstream_of_sequence_of ! is downstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3004,7 +3002,7 @@ def: "inverse of immediately downstream of" [] xref: RO:0002531 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: is_upstream_of_sequence_of ! is upstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3031,7 +3029,7 @@ def: "x is sequentially aligned with if a significant portion bases of x and y c xref: RO:0002521 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -3071,7 +3069,7 @@ def: "inverse of has start sequence" [] subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3084,7 +3082,7 @@ def: "inverse of has subsequence" [] subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of @@ -3107,7 +3105,7 @@ name: is treated by substance def: "Inverse of 'is substance that treats'" [] subset: RO:0002259 xref: RO:0002302 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 is_a: causally_related_to ! causally related to inverse_of: is_substance_that_treats ! is substance that treats @@ -3117,7 +3115,7 @@ name: is upstream of sequence of def: "inverse of downstream of sequence of" [] xref: RO:0002528 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -3127,7 +3125,7 @@ name: is vector for subset: ro-eco xref: RO:0002459 property_value: IAO:0000112 "Anopheles is a vector for Plasmodium" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: has_vector ! has vector @@ -3179,7 +3177,7 @@ name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco xref: RO:0002571 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:cjm xsd:string range: BFO:0000040 is_a: part_of @@ -3190,7 +3188,7 @@ name: luminal space of def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] subset: ro-eco xref: RO:0002572 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000141 is_a: lumen_of ! lumen of @@ -3202,7 +3200,7 @@ subset: ro-eco xref: RO:0002381 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with is_a: part_of @@ -3212,7 +3210,7 @@ id: mereotopologically_related_to name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] xref: RO:0002323 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string property_value: RO:0001900 RO:0001901 @@ -3230,7 +3228,7 @@ name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 @@ -3243,7 +3241,7 @@ name: mutualistically interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] subset: ro-eco xref: RO:0002442 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -3270,7 +3268,7 @@ name: negatively regulated by def: "inverse of negatively regulates" [] subset: RO:0002259 xref: RO:0002335 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3281,7 +3279,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 @@ -3330,7 +3328,7 @@ def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -3351,10 +3349,10 @@ expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://p [Typedef] id: overlaps_sequence_of name: overlaps sequence of -def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] xref: RO:0002526 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: overlaps ! overlaps is_a: sequentially_related_to ! sequentially related to @@ -3366,7 +3364,7 @@ subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string is_a: has_host ! has host @@ -3379,7 +3377,7 @@ name: parasitized by subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string @@ -3418,7 +3416,7 @@ name: part of developmental precursor of xref: RO:0002287 property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by [Typedef] @@ -3426,7 +3424,7 @@ id: part_of_structure_that_is_capable_of name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] xref: RO:0002329 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean is_a: functionally_related_to ! functionally related to @@ -3455,7 +3453,7 @@ subset: ro-eco synonym: "semibiotically interacts with" RELATED [] xref: RO:0002446 property_value: IAO:0000112 "Porifiera attaches to substrate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: biotically_interacts_with ! biotically interacts with @@ -3464,7 +3462,7 @@ id: participates_in_a_biotic-biotic_interaction_with name: participates in a biotic-biotic interaction with subset: ro-eco xref: RO:0002574 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 domain: CARO:0001010 range: CARO:0001010 @@ -3474,7 +3472,7 @@ is_a: biotically_interacts_with ! biotically interacts with id: partner_in name: partner in xref: RO:0002461 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string is_a: participates_in @@ -3483,7 +3481,7 @@ id: pathogen_of name: pathogen of subset: ro-eco xref: RO:0002556 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_host ! has host inverse_of: has_pathogen ! has pathogen @@ -3495,7 +3493,7 @@ subset: ro-eco subset: RO:0002259 xref: RO:0002201 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_functional: true [Typedef] @@ -3503,7 +3501,7 @@ id: phosphorylates name: phosphorylates xref: RO:0002447 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: molecularly_interacts_with ! molecularly interacts with @@ -3512,7 +3510,7 @@ id: pollinated_by name: pollinated by subset: ro-eco xref: RO:0002456 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string @@ -3525,7 +3523,7 @@ subset: ro-eco xref: RO:0002455 property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with @@ -3537,7 +3535,7 @@ name: positively regulated by def: "inverse of positively regulates" [] subset: RO:0002259 xref: RO:0002336 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3548,7 +3546,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002211 @@ -3583,7 +3581,7 @@ def: "inverse of preys on" [] subset: ro-eco subset: RO:0002259 xref: RO:0002458 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string @@ -3598,9 +3596,9 @@ subset: ro-eco xref: RO:0002439 property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Jorrit Poelen" xsd:string -property_value: IAO:0000117 "Katja Shulz" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7134-3324 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string @@ -3623,7 +3621,7 @@ def: "x proper_distributary_of y iff x distributary_of y and x does not flow bac subset: ro-eco xref: RO:0002382 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: distributary_of ! distributary of [Typedef] @@ -3633,7 +3631,7 @@ def: "x proper_tributary_of y iff x tributary_of y and x does not originate from subset: ro-eco xref: RO:0002383 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: tributary_of ! tributary of [Typedef] @@ -3642,7 +3640,7 @@ name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string @@ -3654,7 +3652,7 @@ id: provides_nutrients_for name: provides nutrients for subset: ro-eco xref: RO:0002469 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3663,7 +3661,7 @@ name: realizable has basis in xref: RO:0004017 is_a: causally_related_to ! causally related to inverse_of: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:01Z [Typedef] @@ -3672,10 +3670,10 @@ name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] synonym: "triggered by process" EXACT [RO:cjm] xref: RO:0009501 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "David Osumi-Sutherland" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string @@ -3692,7 +3690,7 @@ xref: RO:0004028 domain: BFO:0000017 range: BFO:0000040 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:45:49Z [Typedef] @@ -3700,7 +3698,7 @@ id: receives_input_from name: receives input from xref: RO:0002485 property_value: IAO:0000116 "See notes for inverse relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to inverse_of: sends_output_to ! sends output to @@ -3740,7 +3738,7 @@ name: regulated by def: "inverse of regulates" [] subset: RO:0002259 xref: RO:0002334 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 range: BFO:0000015 @@ -3755,9 +3753,9 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Hill" xsd:string -property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 +property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string @@ -3774,7 +3772,7 @@ id: regulates_activity_of name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] xref: RO:0011002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3794,7 +3792,7 @@ id: regulates_in_other_organism name: regulates in other organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] xref: RO:0002010 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 range: BFO:0000015 is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -3805,7 +3803,7 @@ name: regulates levels of def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] xref: RO:0002332 property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 @@ -3817,7 +3815,7 @@ id: regulates_quantity_of name: regulates quantity of def: "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." [] xref: RO:0011003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3836,7 +3834,7 @@ id: related_via_localization_to name: related via localization to def: "A relationship that holds via some process of localization" [] xref: RO:0002337 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 range: BFO:0000002 @@ -3857,7 +3855,7 @@ id: represses_expression_of name: represses expression of def: "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." [] xref: RO:0003002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3871,7 +3869,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -3916,7 +3914,7 @@ name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] @@ -3936,7 +3934,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002348 property_value: IAO:0000112 "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3948,7 +3946,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002349 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3962,7 +3960,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3972,7 +3970,7 @@ id: results_in_developmental_induction_of name: results in developmental induction of def: "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." [] xref: RO:0002357 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3982,7 +3980,7 @@ def: "p results in the developmental progression of s iff p is a developmental p xref: RO:0002295 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 range: CARO:0000000 @@ -3994,7 +3992,7 @@ name: results in developmental regression of xref: RO:0002301 property_value: IAO:0000112 "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4004,7 +4002,7 @@ name: results in disappearance of xref: RO:0002300 property_value: IAO:0000112 "foramen ovale closure SubClassOf results in disappearance of foramen ovale" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4020,7 +4018,7 @@ id: results_in_ending_of name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4034,7 +4032,7 @@ xref: RO:0002297 property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4056,7 +4054,7 @@ id: results_in_growth_of name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4071,7 +4069,7 @@ xref: RO:0002299 property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4087,7 +4085,7 @@ xref: RO:0002298 property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4100,7 +4098,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002565 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4126,7 +4124,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002356 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4135,7 +4133,7 @@ id: results_in_structural_organization_of name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4151,7 +4149,7 @@ name: results in transport across def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002342 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: occurs_across ! occurs across is_a: results_in_transport_to_from_or_in ! results in transport to from or in @@ -4160,7 +4158,7 @@ id: results_in_transport_along name: results in transport along def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] xref: RO:0002341 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4168,7 +4166,7 @@ id: results_in_transport_to_from_or_in name: results in transport to from or in xref: RO:0002344 property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4183,7 +4181,7 @@ id: sends_output_to name: sends output to xref: RO:0002486 property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to [Typedef] @@ -4225,7 +4223,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcript" xsd:string property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -4235,7 +4233,7 @@ name: sequentially related to def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string @@ -4248,7 +4246,7 @@ name: skeleton of def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 is_a: part_of @@ -4259,7 +4257,7 @@ name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] xref: RO:0002379 property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: overlaps ! overlaps @@ -4271,7 +4269,7 @@ subset: ro-eco xref: RO:0002163 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 @@ -4285,7 +4283,7 @@ name: stabilizes quantity of def: "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." [] xref: RO:0011015 property_value: IAO:0000112 "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_quantity_of ! directly positively regulates quantity of @@ -4294,14 +4292,14 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates id: starts subset: ro-eco xref: RO:0002223 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: starts_with subset: ro-eco xref: RO:0002224 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -4317,7 +4315,7 @@ name: subcluster of def: "A relation between a group and another group it is part of but does not fully constitute." [] xref: RO:0015003 property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." xsd:string -property_value: IAO:0000117 "Shawn Tan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true is_a: part_of @@ -4326,7 +4324,7 @@ is_a: part_of id: subject_participant_in name: subject participant in xref: RO:0002462 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4345,7 +4343,7 @@ name: surrounded by def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] xref: RO:0002219 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to inverse_of: surrounds ! surrounds @@ -4357,7 +4355,7 @@ def: "inverse of surrounded by" [] subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to @@ -4367,7 +4365,7 @@ name: symbiotically interacts with def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] subset: ro-eco xref: RO:0002440 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true @@ -4380,8 +4378,8 @@ def: "Relation between an anatomical structure (including cells) and a neuron th xref: RO:0002103 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: receives_input_from ! receives input from inverse_of: synapsed_to ! synapsed to @@ -4406,8 +4404,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002108 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" [] @@ -4420,8 +4418,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002109 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4434,8 +4432,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002112 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4448,8 +4446,8 @@ comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part som xref: RO:0002120 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: sends_output_to ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -4473,8 +4471,8 @@ def: "A relation between a motor neuron and a muscle that it synapses to via a t comment: Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) xref: RO:0002107 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_II_bouton ! synapsed_by_via_type_II_bouton @@ -4488,8 +4486,8 @@ comment: Expands to: has_part some ('type Ib terminal button' that has_part some xref: RO:0002105 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Ib_bouton ! synapsed_by_via_type_Ib_bouton @@ -4503,8 +4501,8 @@ comment: Expands to: has_part some ('type Is terminal button' that has_part some xref: RO:0002106 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Is_bouton ! synapsed_by_via_type_Is_bouton @@ -4514,7 +4512,7 @@ expand_expression_to: "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that id: target_participant_in name: target participant in xref: RO:0002463 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4523,7 +4521,7 @@ id: temporally_related_to subset: ro-eco xref: RO:0002222 property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string [Typedef] @@ -4531,7 +4529,7 @@ id: transformation_of name: transformation of def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] xref: RO:0002494 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: develops_from ! develops from @@ -4541,7 +4539,7 @@ name: transitively provides input for def: "transitive form of directly_provides_input_for" [] xref: RO:0002414 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." xsd:string property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string domain: BFO:0000015 @@ -4556,7 +4554,7 @@ def: "A relationship that holds between a disease and organism" [] xref: RO:0002451 property_value: IAO:0000112 "all dengue disease transmitted by some mosquito" xsd:string property_value: IAO:0000116 "Add domain and range constraints" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -4576,7 +4574,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002313 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "regulates localization of" xsd:string is_a: related_via_localization_to ! related via localization to is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4590,7 +4588,7 @@ xref: RO:0002376 property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string @@ -4608,7 +4606,7 @@ name: trophically interacts with def: "An interaction relationship in which the partners are related via a feeding relationship." [] subset: ro-eco xref: RO:0002438 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4618,7 +4616,7 @@ name: ubiquitinates def: "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" [] xref: RO:0002480 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with [Typedef] diff --git a/src/ontology/subsets/ro-causal.owl b/src/ontology/subsets/ro-causal.owl index 7ef14d05..d6ac9788 100644 --- a/src/ontology/subsets/ro-causal.owl +++ b/src/ontology/subsets/ro-causal.owl @@ -409,7 +409,7 @@ - David Osumi-Sutherland + RO:0002002 has_2D_boundary @@ -421,7 +421,7 @@ A relation that holds between two neurons that are electrically coupled via gap junctions. - David Osumi-Sutherland + RO:0002003 electrically_synapsed_to @@ -435,7 +435,7 @@ - David Osumi-Sutherland + RO:0002006 has_synaptic_terminal_of @@ -469,7 +469,7 @@ has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland + RO:0002007 bounding_layer_of @@ -505,9 +505,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. + A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. Note from NCEAS meeting: consider changing primary label - David Osumi-Sutherland + RO:0002008 coincident_with @@ -524,7 +524,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - David Osumi-Sutherland + RO:0002010 regulates_in_other_organism regulates in other organism @@ -553,7 +553,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + dos 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -568,7 +568,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + dos 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -584,7 +584,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + dos 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -599,7 +599,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -613,7 +613,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -630,7 +630,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + dos 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -644,7 +644,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + dos 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -658,7 +658,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + dos 2017-07-20T17:11:08Z RO:0002020 transports @@ -672,7 +672,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + dos 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -686,7 +686,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -697,7 +697,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + GOC:dos @@ -708,7 +708,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + dos 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -718,7 +718,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + GOC:dos @@ -729,7 +729,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + dos 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -739,7 +739,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + GOC:dos @@ -750,7 +750,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + dos 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -761,7 +761,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + GOC:dos @@ -780,7 +780,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + dos 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -797,7 +797,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + GOC:dos @@ -814,7 +814,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + RO:0002090 @@ -831,7 +831,7 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure that its soma is part of. - David Osumi-Sutherland + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -852,9 +852,9 @@ Examples include: the relationship between two channels collected simultaneously relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - David Osumi-Sutherland + fasciculates with - (forall (?x ?y) + (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) @@ -890,9 +890,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure its axon forms (chemical) synapses in. - Chris Mungall - David Osumi-Sutherland - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -924,8 +923,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -945,9 +944,9 @@ Examples include: the relationship between two channels collected simultaneously Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - Alexander Diehl - Chris Mungall - Lindsay Cowell + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) @@ -965,8 +964,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -985,8 +984,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -1005,8 +1004,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) RO:0002107 @@ -1023,8 +1022,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1043,8 +1042,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1064,8 +1063,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - Chris Mungall - David Osumi-Sutherland + + synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( @@ -1085,8 +1084,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1168,8 +1167,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -1196,8 +1195,8 @@ N1 SubclassOf ( Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -1218,7 +1217,7 @@ N1 SubclassOf ( A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - David Osumi-Sutherland + has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) @@ -1267,9 +1266,9 @@ N1 SubclassOf ( The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - David Osumi-Sutherland + has fasciculating component - (forall (?x ?y) + (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) @@ -1309,8 +1308,8 @@ N1 SubclassOf ( - X continuous_with Y if and only if X and Y share a fiat boundary. - David Osumi-Sutherland + X continuous_with Y if and only if X and Y share a fiat boundary. + connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) @@ -1329,8 +1328,8 @@ N1 SubclassOf ( x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom - proper overlaps - (forall (?x ?y) + proper overlaps + (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and @@ -1353,7 +1352,7 @@ N1 SubclassOf ( A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - Chris Mungall + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) @@ -1361,7 +1360,7 @@ N1 SubclassOf ( RO:0002163 spatially_disjoint_from - spatially disjoint from + spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern @@ -1498,7 +1497,7 @@ N1 SubclassOf ( A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - Chris Mungall + RO:0002200 has_phenotype @@ -1513,7 +1512,7 @@ N1 SubclassOf ( inverse of has phenotype - Chris Mungall + RO:0002201 @@ -1533,10 +1532,10 @@ N1 SubclassOf ( x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - Terry Meehan + + + + RO:0002202 develops_from This is the transitive form of the develops from relation @@ -1554,9 +1553,9 @@ N1 SubclassOf ( inverse of develops from - Chris Mungall - David Osumi-Sutherland - Terry Meehan + + + RO:0002203 develops_into @@ -1588,12 +1587,12 @@ N1 SubclassOf ( Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - Chris Mungall - David Osumi-Sutherland - has developmental precursor + + FBbt RO:0002207 + has developmental precursor directly_develops_from TODO - add child relations from DOS directly develops from @@ -1651,9 +1650,9 @@ N1 SubclassOf ( p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - Chris Mungall - David Hill - Tanya Berardini + + + GO Regulation precludes parthood; the regulatory process may not be within the regulated process. @@ -1676,7 +1675,7 @@ N1 SubclassOf ( p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - Chris Mungall + negatively regulates (process to process) @@ -1698,7 +1697,7 @@ N1 SubclassOf ( p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - Chris Mungall + positively regulates (process to process) @@ -1721,7 +1720,7 @@ N1 SubclassOf ( mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - Chris Mungall + has function realized in @@ -1740,7 +1739,7 @@ N1 SubclassOf ( c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - Chris Mungall + has function in RO:0002216 capable_of_part_of @@ -1757,7 +1756,7 @@ N1 SubclassOf ( x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - Chris Mungall + RO:0002219 surrounded_by @@ -1779,7 +1778,7 @@ N1 SubclassOf ( x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - Chris Mungall + RO:0002220 @@ -1803,7 +1802,7 @@ N1 SubclassOf ( inverse of surrounded by - Chris Mungall + RO:0002221 @@ -1816,7 +1815,7 @@ N1 SubclassOf ( - Chris Mungall + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 @@ -1830,7 +1829,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002223 starts @@ -1842,7 +1841,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002224 starts_with @@ -1856,7 +1855,7 @@ N1 SubclassOf ( x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - Chris Mungall + RO:0002225 develops_from_part_of develops from part of @@ -1871,7 +1870,7 @@ N1 SubclassOf ( x develops_in y if x is located in y whilst x is developing - Chris Mungall + EHDAA2 Jonathan Bard, EHDAA2 RO:0002226 @@ -1909,7 +1908,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002229 ends @@ -1921,7 +1920,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002230 ends_with @@ -1937,7 +1936,7 @@ N1 SubclassOf ( x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - Chris Mungall + starts with process that occurs in RO:0002231 @@ -1955,7 +1954,7 @@ N1 SubclassOf ( x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - Chris Mungall + ends with process that occurs in RO:0002232 @@ -1973,7 +1972,7 @@ N1 SubclassOf ( p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + consumes RO:0002233 @@ -1993,7 +1992,7 @@ N1 SubclassOf ( p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - Chris Mungall + produces RO:0002234 @@ -2047,7 +2046,7 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - Bill Duncan (https://orcid.org/0000-0001-9625-1899) + This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. @@ -2196,7 +2195,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y - Chris Mungall + RO:0002254 has_developmental_contribution_from has developmental contribution from @@ -2211,7 +2210,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho inverse of has developmental contribution from - Chris Mungall + RO:0002255 developmentally_contributes_to @@ -2229,9 +2228,9 @@ If you need an axiom that says 'has_participant min 2 object', you sho t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - Chris Mungall - David Osumi-Sutherland - Melissa Haendel + + + induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) @@ -2251,7 +2250,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally induced by - Chris Mungall + RO:0002257 developmentally_induces developmentally induces @@ -2269,7 +2268,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - Chris Mungall + In general you should not use this relation to make assertions - use one of the more specific relations below this one RO:0002258 developmentally_preceded_by @@ -2317,7 +2316,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - Chris Mungall + replaces RO:0002285 developmentally_replaces @@ -2332,7 +2331,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally preceded by - Chris Mungall + RO:0002286 developmentally_succeeded_by developmentally succeeded by @@ -2346,7 +2345,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - Chris Mungall + RO:0002287 part_of_developmental_precursor_of part of developmental precursor of @@ -2363,7 +2362,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - Chris Mungall + RO:0002295 results_in_developmental_progression_of results in developmental progression of @@ -2380,7 +2379,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - Chris Mungall + http://www.geneontology.org/GO.doc.development.shtml RO:0002296 @@ -2401,7 +2400,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002297 @@ -2422,7 +2421,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002298 @@ -2443,7 +2442,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002299 @@ -2461,7 +2460,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho foramen ovale closure SubClassOf results in disappearance of foramen ovale - Chris Mungall + May be merged into parent relation RO:0002300 results_in_disappearance_of @@ -2476,7 +2475,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) - Chris Mungall + May be merged into parent relation RO:0002301 results_in_developmental_regression_of @@ -2491,7 +2490,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of 'is substance that treats' - cjm + RO:0002302 is_treated_by_substance @@ -2511,7 +2510,7 @@ where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. - Pier Buttigieg + adapted for living in RO:0002303 @@ -2529,7 +2528,7 @@ where p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - cjm + RO:0002304 @@ -2547,7 +2546,7 @@ where p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - cjm + RO:0002305 @@ -2562,10 +2561,10 @@ where A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. - Austin Meier - Chris Mungall - Marie Angelique Laporte - cjm + + + + 2017-06-05T17:35:04Z RO:0002309 has_exposure_stimulus @@ -2580,7 +2579,7 @@ where Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. - Chris Mungall + regulates localization of RO:0002313 @@ -2600,7 +2599,7 @@ where an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002315 @@ -2617,7 +2616,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions RO:0002321 @@ -2633,7 +2632,7 @@ where An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. - Chris Mungall + adapted for RO:0002322 @@ -2647,7 +2646,7 @@ where A mereological relationship or a topological relationship - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships RO:0002323 @@ -2661,7 +2660,7 @@ where A relationship that holds between entities participating in some developmental process (GO:0032502) - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development RO:0002324 developmentally_related_to @@ -2678,9 +2677,8 @@ where Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. - Chris Mungall + In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - Gene Ontology Consortium RO:0002325 colocalizes_with @@ -2708,7 +2706,7 @@ then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. - Chris Mungall + In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 @@ -2725,7 +2723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - Chris Mungall + catalyzes executes has @@ -2744,7 +2742,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 functionally_related_to @@ -2758,7 +2756,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati this relation holds between c and p when c is part of some c', and c' is capable of p. - Chris Mungall + false RO:0002329 part_of_structure_that_is_capable_of @@ -2773,7 +2771,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati c involved_in p if and only if c enables some process p', and p' is part of p - Chris Mungall + actively involved in enables part of RO:0002331 @@ -2792,7 +2790,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - Chris Mungall + regulates levels of (process to entity) RO:0002332 @@ -2808,7 +2806,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables - Chris Mungall + RO:0002333 enabled_by @@ -2825,7 +2823,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of regulates - Chris Mungall + regulated by (processual) RO:0002334 @@ -2840,7 +2838,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of negatively regulates - Chris Mungall + RO:0002335 negatively_regulated_by @@ -2854,7 +2852,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of positively regulates - Chris Mungall + RO:0002336 positively_regulated_by @@ -2869,7 +2867,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds via some process of localization - Chris Mungall + Do not use this relation directly. It is a grouping relation. RO:0002337 related_via_localization_to @@ -2883,7 +2881,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - Chris Mungall + RO:0002338 @@ -2899,7 +2897,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - Chris Mungall + RO:0002339 @@ -2915,7 +2913,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. - Chris Mungall + RO:0002340 imports @@ -2929,7 +2927,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - Chris Mungall + RO:0002341 results_in_transport_along results in transport along @@ -2943,7 +2941,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - Chris Mungall + RO:0002342 results_in_transport_across @@ -2958,7 +2956,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'pollen tube growth' results_in growth_of some 'pollen tube' - Chris Mungall + RO:0002343 results_in_growth_of results in growth of @@ -2971,7 +2969,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - Chris Mungall + RO:0002344 results_in_transport_to_from_or_in results in transport to from or in @@ -2983,8 +2981,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. - Chris Mungall + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. + RO:0002345 exports @@ -3000,7 +2998,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - Chris Mungall + RO:0002348 @@ -3017,7 +3015,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - Chris Mungall + RO:0002349 @@ -3034,7 +3032,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has input - Chris Mungall + RO:0002352 @@ -3050,7 +3048,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has output - Chris Mungall + RO:0002353 @@ -3064,7 +3062,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002354 formed_as_result_of formed as result of @@ -3078,7 +3076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. - Chris Mungall + RO:0002355 results_in_structural_organization_of results in structural organization of @@ -3092,7 +3090,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - Chris Mungall + RO:0002356 @@ -3108,7 +3106,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. - Chris Mungall + RO:0002357 results_in_developmental_induction_of results in developmental induction of @@ -3120,7 +3118,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + http://neurolex.org/wiki/Property:DendriteLocation RO:0002360 has_dendrite_location @@ -3136,7 +3134,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - Chris Mungall + attached to (anatomical structure to anatomical structure) RO:0002371 @@ -3153,7 +3151,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002372 has_muscle_origin @@ -3176,7 +3174,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002373 has_muscle_insertion @@ -3200,7 +3198,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) @@ -3222,7 +3220,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - Chris Mungall + drains into drains to tributary channel of @@ -3247,7 +3245,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Deschutes River distributary_of Little Lava Lake x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - Chris Mungall + branch of distributary channel of http://en.wikipedia.org/wiki/Distributary @@ -3273,7 +3271,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. - Chris Mungall + anastomoses with RO:0002378 @@ -3289,7 +3287,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - Chris Mungall + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios RO:0002379 spatially_coextensive_with @@ -3312,7 +3310,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - Chris Mungall + RO:0002380 branching_part_of @@ -3331,7 +3329,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. - Chris Mungall + RO:0002381 main_stem_of @@ -3347,7 +3345,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_distributary_of y iff x distributary_of y and x does not flow back into y - Chris Mungall + RO:0002382 proper_distributary_of @@ -3362,7 +3360,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_tributary_of y iff x tributary_of y and x does not originate from y - Chris Mungall + RO:0002383 proper_tributary_of @@ -3379,7 +3377,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - Chris Mungall + RO:0002384 has_developmental_potential_involving has developmental potential involving @@ -3393,7 +3391,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - Chris Mungall + RO:0002385 has_potential_to_developmentally_contribute_to has potential to developmentally contribute to @@ -3407,7 +3405,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - Chris Mungall + RO:0002386 has_potential_to_developmentally_induce has potential to developmentally induce @@ -3421,7 +3419,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has the potential to develop into y iff x develops into y or if x is capable of developing into y - Chris Mungall + RO:0002387 has_potential_to_develop_into has potential to develop into @@ -3435,7 +3433,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - Chris Mungall + RO:0002388 has_potential_to_directly_develop_into has potential to directly develop into @@ -3450,7 +3448,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' RO:0002400 @@ -3468,7 +3466,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of upstream of - Chris Mungall + RO:0002404 causally_downstream_of causally downstream of @@ -3483,7 +3481,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002405 immediately_causally_downstream_of immediately causally downstream of @@ -3498,7 +3496,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - Chris Mungall + indirectly activates RO:0002407 @@ -3515,7 +3513,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - Chris Mungall + indirectly inhibits RO:0002409 @@ -3544,7 +3542,7 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002410 causally_related_to @@ -3566,7 +3564,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - Chris Mungall + RO:0002411 @@ -3582,7 +3580,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - Chris Mungall + RO:0002412 immediately_causally_upstream_of @@ -3598,7 +3596,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit - Chris Mungall + directly provides input for directly provides input for (process to process) @@ -3618,7 +3616,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different transitive form of directly_provides_input_for - Chris Mungall + This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. transitively provides input for (process to process) RO:0002414 @@ -3636,7 +3634,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall + influences (processual) RO:0002418 affects @@ -3652,7 +3650,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - Chris Mungall + RO:0002427 @@ -3668,7 +3666,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - Chris Mungall + RO:0002428 involved_in_regulation_of involved in regulation of @@ -3681,7 +3679,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - Chris Mungall + RO:0002429 involved_in_positive_regulation_of @@ -3695,7 +3693,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - Chris Mungall + RO:0002430 involved_in_negative_regulation_of @@ -3712,7 +3710,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - Chris Mungall + involved in or reguates RO:0002431 involved_in_or_involved_in_regulation_of @@ -3728,7 +3726,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall + executes activity in RO:0002432 enables activity in @@ -3740,8 +3738,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + GOC:cjm + GOC:dos @@ -3751,7 +3749,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - Chris Mungall + RO:0002433 contributes_to_morphology_of contributes to morphology of @@ -3768,7 +3766,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. - Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. RO:0002434 in pairwise interaction with @@ -3787,7 +3785,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) - Chris Mungall + RO:0002435 genetically_interacts_with genetically interacts with @@ -3803,7 +3801,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - Chris Mungall + binds molecularly binds with RO:0002436 @@ -3824,7 +3822,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - Chris Mungall + interacts with on organism level RO:0002437 @@ -3841,7 +3839,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the partners are related via a feeding relationship. - Chris Mungall + RO:0002438 trophically_interacts_with @@ -3859,9 +3857,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] Baleen whale preys on krill An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - Chris Mungall - Jorrit Poelen - Katja Shulz + + + is subject of predation interaction with preys upon RO:0002439 @@ -3880,7 +3878,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A biotic interaction in which the two organisms live together in more or less intimate association. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism RO:0002440 @@ -3896,7 +3894,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002441 @@ -3911,7 +3909,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002442 @@ -3926,7 +3924,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 This relation groups a pair of inverse relations, parasite of and parasitized by RO:0002443 @@ -3944,7 +3942,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human - Chris Mungall + parasitizes RO:0002444 direct parasite of @@ -3961,7 +3959,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + has parasite parasitised by RO:0002445 @@ -3980,7 +3978,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - Chris Mungall + RO:0002446 semibiotically interacts with @@ -3996,7 +3994,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. RO:0002447 phosphorylates @@ -4015,8 +4013,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - Chris Mungall - Vasundra Touré + + RO:0002448 molecularly controls directly_regulates_activity_of @@ -4033,8 +4031,8 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly inhibits RO:0002449 molecularly decreases activity of @@ -4052,8 +4050,8 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly activates RO:0002450 molecularly increases activity of @@ -4070,7 +4068,7 @@ For example, A and B may be gene products and binding of B by A positively regul all dengue disease transmitted by some mosquito A relationship that holds between a disease and organism Add domain and range constraints - Chris Mungall + RO:0002451 transmitted_by transmitted by @@ -4084,7 +4082,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between a disease or an organism and a phenotype - Chris Mungall + RO:0002452 has_symptom has symptom @@ -4096,7 +4094,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) RO:0002453 @@ -4111,7 +4109,7 @@ For example, A and B may be gene products and binding of B by A positively regul X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y - Chris Mungall + RO:0002454 has_host @@ -4128,7 +4126,7 @@ For example, A and B may be gene products and binding of B by A positively regul Bees pollinate Flowers This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - Chris Mungall + is subject of pollination interaction with RO:0002455 @@ -4143,7 +4141,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + has polinator is target of pollination interaction with RO:0002456 @@ -4160,7 +4158,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4175,7 +4173,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of preys on - Chris Mungall + has predator is target of predation interaction with RO:0002458 @@ -4195,7 +4193,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anopheles is a vector for Plasmodium - Chris Mungall + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism RO:0002459 @@ -4209,7 +4207,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002460 has_vector @@ -4222,7 +4220,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target RO:0002461 partner_in @@ -4235,7 +4233,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002462 subject_participant_in @@ -4248,7 +4246,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002463 target_participant_in @@ -4261,7 +4259,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002469 provides_nutrients_for @@ -4274,7 +4272,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is subject of eating interaction with RO:0002470 @@ -4288,7 +4286,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + eaten by is target of eating interaction with RO:0002471 @@ -4307,7 +4305,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - Chris Mungall + RO:0002473 @@ -4326,7 +4324,7 @@ For example, A and B may be gene products and binding of B by A positively regul ABal nucleus child nucleus of ABa nucleus (in C elegans) c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d - Chris Mungall + This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. RO:0002476 child_nucleus_of @@ -4340,7 +4338,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a hermaphroditic organism - Chris Mungall + RO:0002477 child_nucleus_of_in_hermaphrodite child nucleus of in hermaphrodite @@ -4353,7 +4351,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a male organism - Chris Mungall + RO:0002478 child_nucleus_of_in_male child nucleus of in male @@ -4367,7 +4365,7 @@ For example, A and B may be gene products and binding of B by A positively regul p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall + RO:0002479 has_part_that_occurs_in @@ -4382,7 +4380,7 @@ For example, A and B may be gene products and binding of B by A positively regul An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y Axiomatization to GO to be added later - Chris Mungall + RO:0002480 ubiquitinates ubiquitinates @@ -4396,7 +4394,7 @@ For example, A and B may be gene products and binding of B by A positively regul See notes for inverse relation - Chris Mungall + RO:0002485 receives_input_from receives input from @@ -4409,7 +4407,7 @@ For example, A and B may be gene products and binding of B by A positively regul This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - Chris Mungall + RO:0002486 sends_output_to sends output to @@ -4423,7 +4421,7 @@ For example, A and B may be gene products and binding of B by A positively regul x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - Chris Mungall + RO:0002494 transformation_of transformation of @@ -4437,7 +4435,7 @@ For example, A and B may be gene products and binding of B by A positively regul x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - Chris Mungall + RO:0002495 immediate_transformation_of @@ -4467,7 +4465,7 @@ For example, A and B may be gene products and binding of B by A positively regul p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002501 @@ -4483,7 +4481,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c - Chris Mungall + has intermediate product RO:0002505 @@ -4500,7 +4498,7 @@ For example, A and B may be gene products and binding of B by A positively regul The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002506 @@ -4522,11 +4520,11 @@ For example, A and B may be gene products and binding of B by A positively regul A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future - Chris Mungall + determined by (system to material entity) - Chris Mungall - Pier Buttigieg + + RO:0002507 determined_by @@ -4540,7 +4538,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of determined by - Chris Mungall + determines (material entity to system) RO:0002508 @@ -4559,7 +4557,7 @@ For example, A and B may be gene products and binding of B by A positively regul s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. - Chris Mungall + RO:0002509 determined_by_part_of @@ -4574,7 +4572,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between two entities that have the property of being sequences or having sequences. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. @@ -4594,7 +4592,7 @@ For example, A and B may be gene products and binding of B by A positively regul Two consecutive DNA residues are sequentially adjacent Two exons on a processed transcript that were previously connected by an intron are adjacent x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002515 @@ -4612,7 +4610,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as a start sequence the start codon for that transcript x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence - Chris Mungall + started by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4629,7 +4627,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has start sequence - Chris Mungall + starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4649,7 +4647,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence - Chris Mungall + ended by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4666,7 +4664,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has end sequence - Chris Mungall + ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4684,7 +4682,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. In the SO paper, this was defined as an instance-type relation - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002520 @@ -4701,7 +4699,7 @@ For example, A and B may be gene products and binding of B by A positively regul Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering - Chris Mungall + RO:0002521 is_sequentially_aligned_with @@ -4718,7 +4716,7 @@ For example, A and B may be gene products and binding of B by A positively regul The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y - Chris Mungall + RO:0002522 bounds_sequence_of @@ -4733,7 +4731,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of bounds sequence of - Chris Mungall + RO:0002523 @@ -4751,8 +4749,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x has subsequence y iff all of the sequence parts of x are sequence parts of y - Chris Mungall + x has subsequence y iff all of the sequence parts of y are sequence parts of x + contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4771,7 +4769,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has subsequence - Chris Mungall + contained by RO:0002525 @@ -4788,8 +4786,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. - Chris Mungall + x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. + RO:0002526 overlaps_sequence_of @@ -4803,8 +4801,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. - Chris Mungall + x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + disconnected from RO:0002527 @@ -4820,7 +4818,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of downstream of sequence of - Chris Mungall + RO:0002528 is_upstream_of_sequence_of @@ -4836,7 +4834,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. - Chris Mungall + RO:0002529 is_downstream_of_sequence_of @@ -4852,7 +4850,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y - Chris Mungall + RO:0002530 @@ -4869,7 +4867,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript inverse of immediately downstream of - Chris Mungall + RO:0002531 is_immediately_upstream_of_sequence_of @@ -4889,7 +4887,7 @@ For example, A and B may be gene products and binding of B by A positively regul Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - Chris Mungall + has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). RO:0002551 @@ -4911,7 +4909,7 @@ For example, A and B may be gene products and binding of B by A positively regul p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. - Chris Mungall + RO:0002552 results_in_ending_of results in ending of @@ -4926,7 +4924,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - Chris Mungall + http://eol.org/schema/terms/hyperparasitoidOf https://en.wikipedia.org/wiki/Hyperparasite RO:0002553 @@ -4944,7 +4942,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of hyperparasite of - Chris Mungall + RO:0002554 has epiparasite has hyperparasite @@ -4961,7 +4959,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + http://en.wikipedia.org/wiki/Allelopathy RO:0002555 @@ -4978,7 +4976,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002556 pathogen_of @@ -4991,7 +4989,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002557 has_pathogen @@ -5005,7 +5003,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + causally influenced by (entity-centric) RO:0002559 @@ -5020,7 +5018,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - Chris Mungall + RO:0002565 @@ -5039,8 +5037,8 @@ For example, A and B may be gene products and binding of B by A positively regul The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - Chris Mungall - Vasundra Touré + + causally influences (entity-centric) RO:0002566 @@ -5057,7 +5055,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between elements of a musculoskeletal system or its analogs. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. RO:0002567 biomechanically_related_to @@ -5071,7 +5069,7 @@ For example, A and B may be gene products and binding of B by A positively regul m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - Chris Mungall + Wikipedia:Antagonist_(muscle) RO:0002568 has_muscle_antagonist @@ -5087,7 +5085,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of branching part of - Chris Mungall + RO:0002569 @@ -5104,7 +5102,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - Chris Mungall + UBERON:cjm This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. RO:0002570 @@ -5121,7 +5119,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - Chris Mungall + GOC:cjm RO:0002571 @@ -5137,7 +5135,7 @@ For example, A and B may be gene products and binding of B by A positively regul s is luminal space of x iff s is lumen_of x and s is an immaterial entity - Chris Mungall + RO:0002572 luminal_space_of @@ -5152,7 +5150,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002574 participates_in_a_biotic-biotic_interaction_with @@ -5169,7 +5167,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has skeleton - Chris Mungall + RO:0002576 skeleton_of @@ -5184,7 +5182,7 @@ For example, A and B may be gene products and binding of B by A positively regul p directly regulates q iff p is immediately causally upstream of q and p regulates q. - Chris Mungall + directly regulates (processual) @@ -5205,7 +5203,7 @@ For example, A and B may be gene products and binding of B by A positively regul gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - Chris Mungall + RO:0002584 has_part_structure_that_is_capable_of has part structure that is capable of @@ -5320,7 +5318,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall + RO:0002595 causal_relation_between_material_entity_and_a_process @@ -5723,7 +5721,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. - Vasundra Touré + RO:0003002 represses_expression_of represses expression of @@ -5738,7 +5736,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. - Vasundra Touré + RO:0003003 increases_expression_of increases expression of @@ -5883,7 +5881,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:38:20Z RO:0004000 condition_has_genetic_basis_in @@ -5897,7 +5895,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:20Z RO:0004001 has_material_basis_in_gain_of_function_germline_mutation_in @@ -5913,7 +5911,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:37Z RO:0004002 has_material_basis_in_loss_of_function_germline_mutation_in @@ -5927,7 +5925,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:54Z RO:0004003 has_material_basis_in_germline_mutation_in @@ -5942,7 +5940,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:07Z RO:0004004 has_material_basis_in_somatic_mutation_in @@ -5957,7 +5955,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:26Z RO:0004005 has_major_susceptibility_factor @@ -5971,7 +5969,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:57Z RO:0004006 has_partial_material_basis_in_germline_mutation_in @@ -5985,7 +5983,7 @@ Environmental exposures include those imposed by natural environments, experimen p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - cjm + 2018-12-13T11:26:17Z RO:0004007 @@ -6001,7 +5999,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - cjm + 2018-12-13T11:26:32Z RO:0004008 @@ -6012,8 +6010,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6027,7 +6025,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - cjm + 2018-12-13T11:26:56Z RO:0004009 @@ -6038,8 +6036,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6053,7 +6051,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:53:08Z RO:0004010 is_genetic_basis_for_condition @@ -6067,7 +6065,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:55:51Z RO:0004011 is_causal_gain_of_function_germline_mutation_of_in @@ -6082,7 +6080,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:06Z RO:0004012 is_causal_loss_of_function_germline_mutation_of_in @@ -6098,7 +6096,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:40Z RO:0004013 is_causal_germline_mutation_in @@ -6114,7 +6112,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:57:07Z RO:0004014 is_causal_somatic_mutation_in @@ -6129,7 +6127,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. - cjm + 2017-11-05T02:57:43Z RO:0004015 is_causal_susceptibility_factor_for @@ -6145,7 +6143,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. - cjm + 2017-11-05T02:58:43Z RO:0004016 is_causal_germline_mutation_partially_giving_rise_to @@ -6160,7 +6158,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:01Z RO:0004017 realizable_has_basis_in @@ -6173,7 +6171,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:29Z RO:0004018 is_basis_for_realizable @@ -6188,7 +6186,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:26:47Z RO:0004019 disease_has_basis_in @@ -6204,7 +6202,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) - cjm + 2017-11-05T03:29:32Z RO:0004020 disease_has_basis_in_dysfunction_of @@ -6220,7 +6218,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. disease has basis in disruption of (disease to process) - cjm + 2017-11-05T03:37:52Z RO:0004021 disease_has_basis_in_disruption_of @@ -6244,7 +6242,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. - cjm + 2017-11-05T03:46:07Z RO:0004022 disease_has_basis_in_feature @@ -6260,7 +6258,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. - cjm + 2017-11-05T03:50:54Z RO:0004023 causal_relationship_with_disease_as_subject @@ -6277,7 +6275,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and a process where the disease process disrupts the execution of the process. disease causes disruption of (disease to process) - cjm + 2017-11-05T03:51:09Z RO:0004024 disease_causes_disruption_of @@ -6293,7 +6291,7 @@ Environmental exposures include those imposed by natural environments, experimen disease causes dysfunction of (disease to anatomical entity) - cjm + 2017-11-05T03:58:20Z RO:0004025 disease_causes_dysfunction_of @@ -6319,7 +6317,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. - cjm + 2017-11-05T04:06:02Z RO:0004026 disease_has_location @@ -6343,7 +6341,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity - cjm + 2017-12-26T19:37:31Z RO:0004027 disease_has_inflammation_site @@ -6359,7 +6357,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - cjm + 2017-12-26T19:45:49Z RO:0004028 realized_in_response_to_stimulus @@ -6382,7 +6380,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. - cjm + 2017-12-26T19:50:53Z RO:0004029 disease_has_feature @@ -6397,7 +6395,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. - cjm + 2017-12-26T19:58:44Z RO:0004030 disease_arises_from_alteration_in_structure @@ -6411,7 +6409,7 @@ Environmental exposures include those imposed by natural environments, experimen Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - cjm + 2018-01-25T23:20:13Z RO:0004031 enables_subfunction @@ -6425,7 +6423,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:30Z RO:0004032 @@ -6441,7 +6439,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:51Z RO:0004033 @@ -6458,7 +6456,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - cjm + 2018-01-26T23:53:14Z RO:0004034 @@ -6476,7 +6474,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - cjm + 2018-01-26T23:53:22Z RO:0004035 @@ -6492,7 +6490,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:05Z RO:0004046 causally_upstream_of_or_within,_negative_effect @@ -6506,7 +6504,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:19Z RO:0004047 causally_upstream_of_or_within,_positive_effect @@ -6633,10 +6631,10 @@ Environmental exposures include those imposed by natural environments, experimen An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - Austin Meier - Chris Mungall - David Osumi-Sutherland - Marie Angelique Laporte + + + + RO:0009501 triggered by process realized_in_response_to @@ -6659,7 +6657,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - Vasundra Touré + RO:0011002 regulates_activity_of regulates activity of @@ -6674,7 +6672,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. - Vasundra Touré + RO:0011003 regulates_quantity_of regulates quantity of @@ -6689,7 +6687,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. - Vasundra Touré + RO:0011004 indirectly_regulates_activity_of indirectly regulates activity of @@ -6706,7 +6704,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011007 decreases_by_repression_quantity_of decreases by repression quantity of @@ -6723,7 +6721,7 @@ For example, protein A (transcription factor) indirectly decreases by repression The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011008 increases_by_expression_quantity_of increases by expression quantity of @@ -6738,7 +6736,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly positively regulates the quantity of B. - Vasundra Touré + RO:0011009 directly_positively_regulates_quantity_of directly positively regulates quantity of @@ -6753,7 +6751,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly negatively regulates the quantity of B. - Vasundra Touré + RO:0011010 directly_negatively_regulates_quantity_of directly negatively regulates quantity of @@ -6768,7 +6766,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. - Vasundra Touré + indirectly activates RO:0011013 indirectly_positively_regulates_activity_of @@ -6785,7 +6783,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. - Vasundra Touré + RO:0011014 destabilizes_quantity_of destabilizes quantity of @@ -6801,7 +6799,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. - Vasundra Touré + RO:0011015 stabilizes_quantity_of stabilizes quantity of @@ -6814,7 +6812,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. - Vasundra Touré + indirectly inhibits RO:0011016 indirectly_negatively_regulates_activity_of @@ -6828,7 +6826,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. - Vasundra Touré + RO:0011021 directly_regulates_quantity_of directly regulates quantity of @@ -6841,7 +6839,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011022 indirectly_regulates_quantity_of indirectly regulates quantity of @@ -6854,7 +6852,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011023 indirectly_negatively_regulates_quantity_of indirectly negatively regulates quantity of @@ -6867,7 +6865,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011024 indirectly_positively_regulates_quantity_of indirectly positively regulates quantity of @@ -6880,8 +6878,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is regulated by the small molecule continuant + pg 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -6895,8 +6893,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is activated by the small molecule continuant + pg 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -6910,8 +6908,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant + pg 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -6924,8 +6922,8 @@ For example, protein A (transcription factor) indirectly increases by expression - p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + p acts on population of c iff c' is a collection, has members of type c, and p has participant c + pg 2020-06-08T17:21:33Z RO:0012003 @@ -6941,8 +6939,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process + pg 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -6956,8 +6954,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process + pg 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of @@ -6971,8 +6969,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process + pg 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of @@ -6985,8 +6983,8 @@ For example, protein A (transcription factor) indirectly increases by expression - The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. + pg 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -6999,7 +6997,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + pg 2021-02-26T07:28:29Z RO:0012008 @@ -7016,7 +7014,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + pg 2022-09-26T06:01:01Z RO:0012009 @@ -7032,7 +7030,7 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + pg 2022-09-26T06:06:20Z RO:0012010 @@ -7048,7 +7046,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + pg 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7063,7 +7061,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + pg 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7229,7 +7227,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relation between a group and another group it is part of but does not fully constitute. X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. - Shawn Tan + This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. RO:0015003 subcluster_of @@ -7301,7 +7299,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - http://orcid.org/0000-0002-7463-6306 + 2021-11-05T17:30:44Z RO:0016002 has_disease @@ -7457,7 +7455,7 @@ For example, protein A (transcription factor) indirectly increases by expression This relation groups relations between diseases and any other kind of entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. - cjm + 2018-09-26T00:00:32Z RO:0040035 disease_relationship @@ -7471,7 +7469,7 @@ For example, protein A (transcription factor) indirectly increases by expression p has anatomical participant c iff p has participant c, and c is an anatomical entity - cjm + 2018-09-26T01:08:58Z RO:0040036 results_in_changes_to_anatomical_or_cellular_structure diff --git a/src/ontology/subsets/ro-chado.obo b/src/ontology/subsets/ro-chado.obo index f0eedbec..300fa699 100644 --- a/src/ontology/subsets/ro-chado.obo +++ b/src/ontology/subsets/ro-chado.obo @@ -26,7 +26,7 @@ property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations O property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2023-01-04" xsd:string +property_value: owl:versionInfo "2023-02-19" xsd:string [Typedef] id: BFO:0000050 @@ -823,6 +823,7 @@ transitive_over: BFO:0000050 ! part of id: RO:0002207 name: directly_develops_from def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] +synonym: "has developmental precursor" EXACT [] is_a: RO:0002202 ! develops from inverse_of: RO:0002210 ! directly develops into @@ -2390,7 +2391,7 @@ is_a: RO:0002514 ! sequentially related to [Typedef] id: RO:0002524 name: has_subsequence -def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] is_transitive: true is_a: BFO:0000051 ! has part is_a: RO:0002522 ! bounds sequence of @@ -2409,7 +2410,7 @@ is_a: RO:0002526 ! overlaps sequence of [Typedef] id: RO:0002526 name: overlaps_sequence_of -def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] holds_over_chain: RO:0002524 RO:0002525 is_symmetric: true is_a: RO:0002131 ! overlaps @@ -2418,7 +2419,7 @@ is_a: RO:0002514 ! sequentially related to [Typedef] id: RO:0002527 name: does_not_overlap_sequence_of -def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] is_symmetric: true is_a: RO:0002514 ! sequentially related to diff --git a/src/ontology/subsets/ro-chado.obo.tmp b/src/ontology/subsets/ro-chado.obo.tmp index 7bd7cf91..1b4b78ac 100644 --- a/src/ontology/subsets/ro-chado.obo.tmp +++ b/src/ontology/subsets/ro-chado.obo.tmp @@ -25,7 +25,7 @@ property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations O property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2023-01-04" xsd:string +property_value: owl:versionInfo "2023-02-19" xsd:string owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: ()\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\n) [Typedef] @@ -823,6 +823,7 @@ transitive_over: BFO:0000050 ! part of id: RO:0002207 name: directly develops from def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] +synonym: "has developmental precursor" EXACT [] is_a: RO:0002202 ! develops from inverse_of: RO:0002210 ! directly develops into @@ -2390,7 +2391,7 @@ is_a: RO:0002514 ! sequentially related to [Typedef] id: RO:0002524 name: has subsequence -def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] is_transitive: true is_a: BFO:0000051 ! has part is_a: RO:0002522 ! bounds sequence of @@ -2409,7 +2410,7 @@ is_a: RO:0002526 ! overlaps sequence of [Typedef] id: RO:0002526 name: overlaps sequence of -def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] holds_over_chain: RO:0002524 RO:0002525 is_symmetric: true is_a: RO:0002131 ! overlaps @@ -2418,7 +2419,7 @@ is_a: RO:0002514 ! sequentially related to [Typedef] id: RO:0002527 name: does not overlap sequence of -def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] is_symmetric: true is_a: RO:0002514 ! sequentially related to diff --git a/src/ontology/subsets/ro-developmental.obo b/src/ontology/subsets/ro-developmental.obo index 3e95c217..0d29373a 100644 --- a/src/ontology/subsets/ro-developmental.obo +++ b/src/ontology/subsets/ro-developmental.obo @@ -13,7 +13,7 @@ id: acquires_nutrients_from name: acquires nutrients from subset: ro-eco xref: RO:0002457 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for @@ -58,7 +58,7 @@ property_value: RO:0004050 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:22Z [Typedef] @@ -71,7 +71,7 @@ property_value: RO:0004049 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:14Z [Typedef] @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z [Typedef] @@ -103,7 +103,7 @@ xref: RO:0004032 property_value: RO:0004049 RO:0002264 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z [Typedef] @@ -120,7 +120,7 @@ property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cy property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 domain: BFO:0000004 range: BFO:0000004 @@ -131,7 +131,7 @@ id: allelopath_of name: allelopath of subset: ro-eco xref: RO:0002555 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string @@ -153,7 +153,7 @@ def: "x anabranch_of y if x is a distributary of y (i.e. it channels a from a la subset: ro-eco xref: RO:0002378 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "anastomoses with" xsd:string is_a: distributary_of ! distributary of disjoint_from: proper_distributary_of ! proper distributary of @@ -165,7 +165,7 @@ name: attached to def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] subset: ro-eco xref: RO:0002371 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: attached_to_part_of ! attached to part of @@ -189,9 +189,8 @@ def: "Relation between a neuron and some structure its axon forms (chemical) syn xref: RO:0002102 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in @@ -202,7 +201,7 @@ id: biomechanically_related_to name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] xref: RO:0002567 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: CARO:0000003 range: CARO:0000003 @@ -214,7 +213,7 @@ name: biotically interacts with def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] subset: ro-eco xref: RO:0002437 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string @@ -231,7 +230,7 @@ def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\ comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco xref: RO:0002007 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 is_a: part_of @@ -242,7 +241,7 @@ def: "x bounds the sequence of y iff the upstream-most part of x is upstream of xref: RO:0002522 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to inverse_of: is_bound_by_sequence_of ! is bound by sequence of @@ -254,7 +253,7 @@ def: "x is a branching part of y if and only if x is part of y and x is connecte subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso FMA:85994 xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with @@ -269,7 +268,7 @@ subset: ro-eco xref: RO:0002215 property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 @@ -302,7 +301,7 @@ id: capable_of_part_of name: capable of part of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ is_a: causal_agent_in_process ! causal agent in process @@ -350,7 +349,7 @@ id: causal_relation_between_entities name: causal relation between entities xref: RO:0002506 property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000002 @@ -363,7 +362,7 @@ name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] xref: RO:0002595 property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 range: BFO:0000015 @@ -374,7 +373,7 @@ id: causal_relation_between_processes name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 @@ -389,7 +388,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: OGMS:0000031 is_a: causally_related_to ! causally related to is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:50:54Z [Typedef] @@ -398,7 +397,7 @@ name: causally downstream of def: "inverse of upstream of" [] xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within is_a: preceded_by inverse_of: causally_upstream_of ! causally upstream of @@ -409,7 +408,7 @@ name: causally downstream of or within def: "inverse of causally upstream of or within" [] subset: RO:0002259 xref: RO:0002427 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -418,7 +417,7 @@ is_a: causal_relation_between_processes ! causal relation between processes id: causally_influenced_by name: causally influenced by xref: RO:0002559 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: causal_relation_between_entities ! causal relation between entities @@ -429,8 +428,8 @@ id: causally_influences name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] xref: RO:0002566 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 @@ -443,7 +442,7 @@ name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] @@ -453,7 +452,7 @@ def: "p is causally upstream of q iff p is causally related to q, the end of p p subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes @@ -465,7 +464,7 @@ def: "p is causally upstream of, negative effect q iff p is casually upstream of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -478,7 +477,7 @@ comment: holds between x and y if and only if x is causally upstream of y and th subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -490,7 +489,7 @@ def: "p is 'causally upstream or within' q iff p is causally related to q, and t synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -502,7 +501,7 @@ name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -511,7 +510,7 @@ name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -537,7 +536,7 @@ name: child nucleus of def: "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" [] xref: RO:0002476 property_value: IAO:0000112 "ABal nucleus child nucleus of ABa nucleus (in C elegans)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." xsd:string domain: GO:0005634 range: GO:0005634 @@ -548,7 +547,7 @@ id: child_nucleus_of_in_hermaphrodite name: child nucleus of in hermaphrodite def: "A child nucleus relationship in which the cells are part of a hermaphroditic organism" [] xref: RO:0002477 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -556,7 +555,7 @@ id: child_nucleus_of_in_male name: child nucleus of in male def: "A child nucleus relationship in which the cells are part of a male organism" [] xref: RO:0002478 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -576,7 +575,7 @@ comment: Example: if we define region of chromosome as any subdivision of a chro subset: ro-eco xref: RO:0002008 property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -585,9 +584,8 @@ name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 -property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -599,7 +597,7 @@ name: commensually interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] subset: ro-eco xref: RO:0002441 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -610,7 +608,7 @@ def: "x composed_primarily_of y if and only if more than half of the mass of x i subset: ro-eco xref: RO:0002473 property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 @@ -639,7 +637,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: BFO:0000017 is_a: causally_related_to ! causally related to inverse_of: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:38:20Z [Typedef] @@ -648,7 +646,7 @@ name: conduit for def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] subset: ro-eco xref: RO:0002570 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 UBERON:cjm xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 @@ -661,7 +659,7 @@ name: confers advantage in subset: ro-eco xref: RO:0002322 property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "adapted for" xsd:string range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -727,7 +725,7 @@ name: continuous with def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 @@ -746,7 +744,7 @@ property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a het property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -771,7 +769,7 @@ id: contributes_to_morphology_of name: contributes to morphology of def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] xref: RO:0002433 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -796,7 +794,7 @@ id: decreases_by_repression_quantity_of name: decreases by repression quantity of def: "The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011007 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_negatively_regulates_quantity_of ! indirectly negatively regulates quantity of @@ -808,8 +806,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in wh xref: RO:0002121 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in @@ -821,7 +819,7 @@ name: destabilizes quantity of def: "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." [] xref: RO:0011014 property_value: IAO:0000112 "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_quantity_of ! directly negatively regulates quantity of @@ -832,11 +830,11 @@ name: determined by def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] subset: ro-eco xref: RO:0002507 -property_value: http://purl.org/dc/terms/creator "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/creator "Pier Buttigieg" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-4366-3088 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "A coral reef environment is determined by a particular coral reef" xsd:string property_value: IAO:0000116 "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602 property_value: IAO:0000589 "determined by (system to material entity)" xsd:string domain: RO:0002577 @@ -852,7 +850,7 @@ name: determined by part of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] subset: ro-eco xref: RO:0002509 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 range: BFO:0000040 is_a: causal_relation_between_entities ! causal relation between entities @@ -865,7 +863,7 @@ def: "inverse of determined by" [] subset: ro-eco subset: RO:0002259 xref: RO:0002508 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "determines (material entity to system)" xsd:string is_a: causally_influences ! causally influences @@ -876,7 +874,7 @@ def: "inverse of has developmental contribution from" [] subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to @@ -886,9 +884,9 @@ name: developmentally induced by def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] xref: RO:0002256 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string property_value: IAO:0000119 GO:0001759 xsd:string @@ -905,7 +903,7 @@ name: developmentally induces def: "Inverse of developmentally induced by" [] xref: RO:0002257 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_induce ! has potential to developmentally induce @@ -917,7 +915,7 @@ comment: This relation groups together various other developmental relations. It xref: RO:0002258 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string domain: BFO:0000002 range: BFO:0000002 @@ -929,7 +927,7 @@ id: developmentally_related_to name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] xref: RO:0002324 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] @@ -939,7 +937,7 @@ def: "x developmentally replaces y if and only if there is some developmental pr xref: RO:0002285 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "replaces" xsd:string is_a: developmentally_preceded_by ! developmentally preceded by @@ -949,7 +947,7 @@ name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] xref: RO:0002286 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -959,10 +957,10 @@ def: "x develops from y if and only if either (a) x directly develops from y or comment: This is the transitive form of the develops from relation xref: RO:0002202 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 domain: BFO:0000004 range: BFO:0000004 is_transitive: true @@ -975,7 +973,7 @@ name: develops from part of def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] xref: RO:0002225 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: develops_from ! develops from [Typedef] @@ -984,7 +982,7 @@ name: develops in def: "x develops_in y if x is located in y whilst x is developing" [] xref: RO:0002226 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string domain: CARO:0000000 @@ -997,9 +995,9 @@ def: "inverse of develops from" [] subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 is_transitive: true is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into @@ -1010,11 +1008,11 @@ id: directly_develops_from name: directly develops from def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] xref: RO:0002207 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "has developmental precursor" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000119 "FBbt" xsd:string property_value: RO:0002575 RO:0002202 is_a: develops_from ! develops from @@ -1060,8 +1058,8 @@ name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] xref: RO:0002449 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1072,7 +1070,7 @@ id: directly_negatively_regulates_quantity_of name: directly negatively regulates quantity of def: "The entity A has an activity that directly negatively regulates the quantity of B." [] xref: RO:0011010 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1107,8 +1105,8 @@ name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] xref: RO:0002450 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1119,7 +1117,7 @@ id: directly_positively_regulates_quantity_of name: directly positively regulates quantity of def: "The entity A has an activity that directly positively regulates the quantity of B." [] xref: RO:0011009 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1142,7 +1140,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002578 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string property_value: RO:0002575 RO:0002211 @@ -1155,8 +1153,8 @@ name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] xref: RO:0002448 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: molecularly_interacts_with ! molecularly interacts with @@ -1167,7 +1165,7 @@ id: directly_regulates_quantity_of name: directly regulates quantity of def: "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B." [] xref: RO:0011021 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -1177,7 +1175,7 @@ def: "A relationship between a disease and an anatomical structure where the mat xref: RO:0004030 range: CARO:0000003 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z [Typedef] @@ -1189,7 +1187,7 @@ property_value: IAO:0000589 "disease causes disruption of (disease to process)" domain: OGMS:0000031 range: BFO:0000015 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:51:09Z [Typedef] @@ -1200,7 +1198,7 @@ property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomica domain: OGMS:0000031 range: CARO:0000006 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z [Typedef] @@ -1210,7 +1208,7 @@ xref: RO:0004019 domain: OGMS:0000031 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject is_a: realizable_has_basis_in ! realizable has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:26:47Z [Typedef] @@ -1221,7 +1219,7 @@ xref: RO:0004021 property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:37:52Z [Typedef] @@ -1232,7 +1230,7 @@ xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string range: CARO:0000006 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z [Typedef] @@ -1243,7 +1241,7 @@ xref: RO:0004022 domain: OGMS:0000031 is_a: disease_has_basis_in ! disease has basis in is_a: has_phenotype ! has phenotype -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:46:07Z [Typedef] @@ -1253,7 +1251,7 @@ def: "A relationship between a disease and some feature of that disease, where t xref: RO:0004029 domain: OGMS:0000031 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:50:53Z [Typedef] @@ -1272,7 +1270,7 @@ xref: RO:0004027 domain: OGMS:0000031 range: BFO:0000004 is_a: disease_has_location ! disease has location -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:37:31Z [Typedef] @@ -1285,7 +1283,7 @@ property_value: IAO:0000232 "This relation is intentionally very general, and co domain: OGMS:0000031 range: BFO:0000004 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T04:06:02Z [Typedef] @@ -1294,7 +1292,7 @@ name: disease relationship def: "This relation groups relations between diseases and any other kind of entity." [] xref: RO:0040035 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z [Typedef] @@ -1306,7 +1304,7 @@ subset: ro-eco xref: RO:0002377 property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string @@ -1316,10 +1314,10 @@ is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: does_not_overlap_sequence_of name: does not overlap sequence of -def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] xref: RO:0002527 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "disconnected from" xsd:string is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -1338,7 +1336,7 @@ id: eats name: eats subset: ro-eco xref: RO:0002470 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -1359,7 +1357,7 @@ def: "A relationship that is mediated in some way by the environment or environm subset: ro-eco xref: RO:0002321 property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string [Typedef] @@ -1377,7 +1375,7 @@ name: electrically_synapsed_to def: "A relation that holds between two neurons that are electrically coupled via gap junctions." [] xref: RO:0002003 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: connected_to ! connected to [Typedef] @@ -1386,7 +1384,7 @@ name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: has_participant @@ -1397,7 +1395,7 @@ def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string property_value: IAO:0000118 "has" xsd:string @@ -1413,7 +1411,7 @@ name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] xref: RO:0004031 is_a: functionally_related_to ! functionally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z [Typedef] @@ -1430,14 +1428,14 @@ inverse_of: has_endoparasite ! has endoparasite id: ends subset: ro-eco xref: RO:0002229 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: ends_with subset: ro-eco xref: RO:0002230 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -1462,7 +1460,7 @@ name: exports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002345 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -1479,7 +1477,7 @@ def: "relationship between a neuron and a neuron projection bundle (e.g.- tract xref: RO:0002101 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 @@ -1492,7 +1490,7 @@ inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron proje id: formed_as_result_of name: formed as result of xref: RO:0002354 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of [Typedef] @@ -1500,7 +1498,7 @@ id: functionally_related_to name: functionally related to def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] xref: RO:0002328 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string [Typedef] @@ -1509,7 +1507,7 @@ name: genetically interacts with xref: RO:0002435 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with @@ -1517,7 +1515,7 @@ is_a: interacts_with ! interacts with [Typedef] id: has_2D_boundary xref: RO:0002002 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1557,7 +1555,7 @@ def: "inverse of branching part of" [] subset: ro-eco subset: RO:0002259 xref: RO:0002569 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: has_part is_a: in_branching_relationship_with ! in branching relationship with @@ -1593,7 +1591,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 "Bill Duncan (https://orcid.org/0000-0001-9625-1899)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant @@ -1622,7 +1620,7 @@ id: has_dendrite_location name: has dendrite location xref: RO:0002360 property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -1632,7 +1630,7 @@ def: "x has developmental contribution from y iff x has some part z such that z xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by @@ -1644,7 +1642,7 @@ name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to @@ -1656,7 +1654,7 @@ def: "p has direct input c iff c is a participant in p, c is present at the star xref: RO:0002400 property_value: IAO:0000112 "'protein catabolic process' SubClassOf has_direct_input some protein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly consumes" xsd:string property_value: IAO:0000232 "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" xsd:string is_a: has_input ! has input @@ -1666,7 +1664,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1711,7 +1709,7 @@ def: "x 'has end location' y if and only if there exists some process z such tha subset: ro-eco xref: RO:0002232 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -1724,7 +1722,7 @@ def: "x has end sequence y if the end of x is identical to the end of y, and x h xref: RO:0002518 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -1776,11 +1774,11 @@ id: has_exposure_stimulus name: has exposure stimulus def: "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002309 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 is_a: related_via_exposure_to ! related via exposure to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:35:04Z [Typedef] @@ -1806,7 +1804,7 @@ def: "The relation between a neuron projection bundle and a neuron projection th xref: RO:0002132 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 @@ -1828,7 +1826,7 @@ subset: ro-eco xref: RO:0002303 property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Pier Buttigieg" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string domain: CARO:0001010 range: ENVO:01000254 @@ -1851,7 +1849,7 @@ name: has host def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] subset: ro-eco xref: RO:0002454 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -1865,7 +1863,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 is_a: has_participant @@ -1886,7 +1884,7 @@ def: "p has intermediate c if and only if p has parts p1, p2 and p1 has output c subset: ro-eco xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string is_a: has_participant @@ -1924,7 +1922,7 @@ name: has major susceptibility factor xref: RO:0004005 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_susceptibility_factor_for ! is causal susceptibility factor for -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:26Z [Typedef] @@ -1935,7 +1933,7 @@ property_value: seeAlso Orphanet:410295 property_value: seeAlso Orphanet:410296 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_gain_of_function_germline_mutation_of_in ! is causal gain of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:20Z [Typedef] @@ -1945,7 +1943,7 @@ xref: RO:0004003 property_value: seeAlso Orphanet:317343 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_in ! is causal germline mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:54Z [Typedef] @@ -1954,7 +1952,7 @@ name: has material basis in loss of function germline mutation in xref: RO:0004002 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_loss_of_function_germline_mutation_of_in ! is causal loss of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:37Z [Typedef] @@ -1964,7 +1962,7 @@ xref: RO:0004004 property_value: seeAlso Orphanet:317344 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z [Typedef] @@ -1980,7 +1978,7 @@ id: has_muscle_antagonist name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string is_a: biomechanically_related_to ! biomechanically related to @@ -1989,7 +1987,7 @@ id: has_muscle_insertion name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} @@ -2001,7 +1999,7 @@ id: has_muscle_origin name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} @@ -2039,7 +2037,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string is_a: has_participant inverse_of: output_of ! output of @@ -2066,7 +2064,7 @@ name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] xref: RO:0002584 property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causal_relation_between_material_entity_and_a_process ! causal relation between material entity and a process is_a: functionally_related_to ! functionally related to @@ -2076,7 +2074,7 @@ name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco xref: RO:0002479 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 range: BFO:0000004 @@ -2086,7 +2084,7 @@ name: has partial material basis in germline mutation in xref: RO:0004006 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_partially_giving_rise_to ! is causal germline mutation partially giving rise to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:57Z [Typedef] @@ -2098,7 +2096,7 @@ id: has_pathogen name: has pathogen subset: ro-eco xref: RO:0002557 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2108,7 +2106,7 @@ def: "A relationship that holds between a biological entity and a phenotype. Her subset: ro-eco xref: RO:0002200 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: UPHENO:0001001 is_a: has_phenotype_or_disease ! has phenotype or disease inverse_of: phenotype_of ! phenotype of @@ -2129,9 +2127,9 @@ def: "Holds between a cell c and a protein complex or protein p if and only if t xref: RO:0002104 property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Alexander Diehl" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 @@ -2157,8 +2155,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in whi xref: RO:0002110 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "synapsed in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2172,7 +2170,7 @@ name: has potential to develop into def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] xref: RO:0002387 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2181,7 +2179,7 @@ name: has potential to developmentally contribute to def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] xref: RO:0002385 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2190,7 +2188,7 @@ name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] xref: RO:0002386 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2199,7 +2197,7 @@ name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] xref: RO:0002388 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_potential_to_develop_into ! has potential to develop into [Typedef] @@ -2223,7 +2221,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -2233,7 +2231,7 @@ def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c o subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -2244,7 +2242,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -2276,7 +2274,7 @@ name: has skeleton def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] xref: RO:0002551 property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 @@ -2321,7 +2319,7 @@ name: has soma location def: "Relation between a neuron and an anatomical structure that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 range: CARO:0000003 @@ -2335,7 +2333,7 @@ def: "x 'has starts location' y if and only if there exists some process z such subset: ro-eco xref: RO:0002231 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -2348,7 +2346,7 @@ def: "x has start sequence y if the start of x is identical to the start of y, a xref: RO:0002516 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2358,10 +2356,10 @@ inverse_of: is_start_sequence_of ! is start sequence of [Typedef] id: has_subsequence name: has subsequence -def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2375,7 +2373,7 @@ id: has_symptom name: has symptom def: "A relation that holds between a disease or an organism and a phenotype" [] xref: RO:0002452 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: OGMS:0000031 is_a: has_phenotype ! has phenotype @@ -2405,7 +2403,7 @@ def: "A general relation between a neuron and some structure in which it either xref: RO:0002130 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has synapse in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2417,7 +2415,7 @@ id: has_synaptic_terminal_of name: has synaptic terminal of xref: RO:0002006 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: overlaps ! overlaps inverse_of: has_synaptic_terminal_in ! has synaptic terminal in @@ -2429,7 +2427,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002339 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2440,7 +2438,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002338 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2448,7 +2446,7 @@ id: has_vector name: has vector subset: ro-eco xref: RO:0002460 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with [Typedef] @@ -2463,7 +2461,7 @@ id: host_of name: host of subset: ro-eco xref: RO:0002453 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2476,7 +2474,7 @@ synonym: "epiparasite of" RELATED [] synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string is_a: has_host ! has host @@ -2492,7 +2490,7 @@ synonym: "has epiparasite" RELATED [] synonym: "has hyperparasite" RELATED [] synonym: "hyperparasitoidized by" RELATED [] xref: RO:0002554 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2500,7 +2498,7 @@ id: immediate_transformation_of name: immediate transformation of def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] xref: RO:0002495 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002494 is_a: directly_develops_from ! directly develops from is_a: transformation_of ! transformation of @@ -2510,7 +2508,7 @@ id: immediately_causally_downstream_of name: immediately causally downstream of xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of is_a: immediately_preceded_by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of @@ -2520,7 +2518,7 @@ id: immediately_causally_upstream_of name: immediately causally upstream of def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: immediately_precedes @@ -2533,7 +2531,7 @@ xref: RO:0002087 id: immediately_precedes subset: ro-eco xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0002575 BFO:0000063 [Typedef] @@ -2542,7 +2540,7 @@ name: imports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002340 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -2551,7 +2549,7 @@ name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] xref: RO:0002375 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 @@ -2577,7 +2575,7 @@ id: increases_by_expression_quantity_of name: increases by expression quantity of def: "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011008 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_positively_regulates_quantity_of ! indirectly positively regulates quantity of @@ -2587,7 +2585,7 @@ id: increases_expression_of name: increases expression of def: "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." [] xref: RO:0003003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -2606,7 +2604,7 @@ id: indirectly_negatively_regulates name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true @@ -2618,7 +2616,7 @@ id: indirectly_negatively_regulates_activity_of name: indirectly negatively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B." [] xref: RO:0011016 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly inhibits" xsd:string is_a: indirectly_regulates_activity_of ! indirectly regulates activity of @@ -2627,7 +2625,7 @@ id: indirectly_negatively_regulates_quantity_of name: indirectly negatively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B." [] xref: RO:0011023 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2635,7 +2633,7 @@ id: indirectly_positively_regulates name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 is_transitive: true @@ -2647,7 +2645,7 @@ id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." [] xref: RO:0011013 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -2658,7 +2656,7 @@ id: indirectly_positively_regulates_quantity_of name: indirectly positively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B." [] xref: RO:0011024 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2676,7 +2674,7 @@ id: indirectly_regulates_activity_of name: indirectly regulates activity of def: "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." [] xref: RO:0011004 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: regulates_activity_of ! regulates activity of @@ -2686,7 +2684,7 @@ id: indirectly_regulates_quantity_of name: indirectly regulates quantity of def: "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B." [] xref: RO:0011022 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -2696,7 +2694,7 @@ def: "inverse of has input" [] subset: ro-eco subset: RO:0002259 xref: RO:0002352 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -2710,7 +2708,7 @@ xref: RO:0002434 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI domain: BFO:0000040 @@ -2723,7 +2721,7 @@ name: interacts with via parasite-host interaction def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] subset: ro-eco xref: RO:0002443 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2751,7 +2749,7 @@ id: involved_in name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] xref: RO:0002331 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in @@ -2763,7 +2761,7 @@ id: involved_in_negative_regulation_of name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] xref: RO:0002430 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2773,7 +2771,7 @@ name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in_process ! causal agent in process @@ -2784,7 +2782,7 @@ id: involved_in_positive_regulation_of name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] xref: RO:0002429 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2793,7 +2791,7 @@ id: involved_in_regulation_of name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] xref: RO:0002428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of @@ -2804,7 +2802,7 @@ def: "c executes activity in d if and only if c enables p and p occurs_in d. As synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -2853,7 +2851,7 @@ id: is_basis_for_realizable name: is basis for realizable xref: RO:0004018 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:29Z [Typedef] @@ -2863,7 +2861,7 @@ def: "inverse of bounds sequence of" [] subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to @@ -2874,7 +2872,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004011 property_value: seeAlso Orphanet:410296 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:55:51Z [Typedef] @@ -2885,7 +2883,7 @@ xref: RO:0004013 property_value: seeAlso Orphanet:317343 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:40Z [Typedef] @@ -2896,7 +2894,7 @@ xref: RO:0004016 property_value: seeAlso Orphanet:317346 is_a: contributes_to_condition ! contributes to condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:58:43Z [Typedef] @@ -2906,7 +2904,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004012 property_value: seeAlso Orphanet:410295 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:06Z [Typedef] @@ -2917,7 +2915,7 @@ xref: RO:0004014 property_value: seeAlso Orphanet:317344 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:07Z [Typedef] @@ -2927,7 +2925,7 @@ def: "Relates a gene to condition, such that a mutation in this gene predisposes xref: RO:0004015 property_value: seeAlso Orphanet:317345 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:43Z [Typedef] @@ -2937,7 +2935,7 @@ def: "x is a consecutive sequence of y iff x has subsequence y, and all the part xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: has_subsequence ! has subsequence @@ -2947,7 +2945,7 @@ name: is downstream of sequence of def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] xref: RO:0002529 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of @@ -2957,7 +2955,7 @@ id: is_eaten_by name: is eaten by subset: ro-eco xref: RO:0002471 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -2969,7 +2967,7 @@ def: "inverse of has end sequence" [] subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2982,7 +2980,7 @@ xref: RO:0004010 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string range: BFO:0000017 is_a: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:53:08Z [Typedef] @@ -2992,7 +2990,7 @@ def: "x is immediately downstream of the sequence of y iff either (1) x and y ha xref: RO:0002530 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002529 is_a: is_downstream_of_sequence_of ! is downstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3004,7 +3002,7 @@ def: "inverse of immediately downstream of" [] xref: RO:0002531 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: is_upstream_of_sequence_of ! is upstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3031,7 +3029,7 @@ def: "x is sequentially aligned with if a significant portion bases of x and y c xref: RO:0002521 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -3071,7 +3069,7 @@ def: "inverse of has start sequence" [] subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3084,7 +3082,7 @@ def: "inverse of has subsequence" [] subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of @@ -3107,7 +3105,7 @@ name: is treated by substance def: "Inverse of 'is substance that treats'" [] subset: RO:0002259 xref: RO:0002302 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 is_a: causally_related_to ! causally related to inverse_of: is_substance_that_treats ! is substance that treats @@ -3117,7 +3115,7 @@ name: is upstream of sequence of def: "inverse of downstream of sequence of" [] xref: RO:0002528 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -3127,7 +3125,7 @@ name: is vector for subset: ro-eco xref: RO:0002459 property_value: IAO:0000112 "Anopheles is a vector for Plasmodium" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: has_vector ! has vector @@ -3179,7 +3177,7 @@ name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco xref: RO:0002571 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:cjm xsd:string range: BFO:0000040 is_a: part_of @@ -3190,7 +3188,7 @@ name: luminal space of def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] subset: ro-eco xref: RO:0002572 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000141 is_a: lumen_of ! lumen of @@ -3202,7 +3200,7 @@ subset: ro-eco xref: RO:0002381 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with is_a: part_of @@ -3212,7 +3210,7 @@ id: mereotopologically_related_to name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] xref: RO:0002323 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string property_value: RO:0001900 RO:0001901 @@ -3230,7 +3228,7 @@ name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 @@ -3243,7 +3241,7 @@ name: mutualistically interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] subset: ro-eco xref: RO:0002442 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -3270,7 +3268,7 @@ name: negatively regulated by def: "inverse of negatively regulates" [] subset: RO:0002259 xref: RO:0002335 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3281,7 +3279,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 @@ -3330,7 +3328,7 @@ def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -3351,10 +3349,10 @@ expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://p [Typedef] id: overlaps_sequence_of name: overlaps sequence of -def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] xref: RO:0002526 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: overlaps ! overlaps is_a: sequentially_related_to ! sequentially related to @@ -3366,7 +3364,7 @@ subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string is_a: has_host ! has host @@ -3379,7 +3377,7 @@ name: parasitized by subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string @@ -3418,7 +3416,7 @@ name: part of developmental precursor of xref: RO:0002287 property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by [Typedef] @@ -3426,7 +3424,7 @@ id: part_of_structure_that_is_capable_of name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] xref: RO:0002329 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean is_a: functionally_related_to ! functionally related to @@ -3455,7 +3453,7 @@ subset: ro-eco synonym: "semibiotically interacts with" RELATED [] xref: RO:0002446 property_value: IAO:0000112 "Porifiera attaches to substrate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: biotically_interacts_with ! biotically interacts with @@ -3464,7 +3462,7 @@ id: participates_in_a_biotic-biotic_interaction_with name: participates in a biotic-biotic interaction with subset: ro-eco xref: RO:0002574 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 domain: CARO:0001010 range: CARO:0001010 @@ -3474,7 +3472,7 @@ is_a: biotically_interacts_with ! biotically interacts with id: partner_in name: partner in xref: RO:0002461 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string is_a: participates_in @@ -3483,7 +3481,7 @@ id: pathogen_of name: pathogen of subset: ro-eco xref: RO:0002556 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_host ! has host inverse_of: has_pathogen ! has pathogen @@ -3495,7 +3493,7 @@ subset: ro-eco subset: RO:0002259 xref: RO:0002201 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_functional: true [Typedef] @@ -3503,7 +3501,7 @@ id: phosphorylates name: phosphorylates xref: RO:0002447 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: molecularly_interacts_with ! molecularly interacts with @@ -3512,7 +3510,7 @@ id: pollinated_by name: pollinated by subset: ro-eco xref: RO:0002456 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string @@ -3525,7 +3523,7 @@ subset: ro-eco xref: RO:0002455 property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with @@ -3537,7 +3535,7 @@ name: positively regulated by def: "inverse of positively regulates" [] subset: RO:0002259 xref: RO:0002336 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3548,7 +3546,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002211 @@ -3583,7 +3581,7 @@ def: "inverse of preys on" [] subset: ro-eco subset: RO:0002259 xref: RO:0002458 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string @@ -3598,9 +3596,9 @@ subset: ro-eco xref: RO:0002439 property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Jorrit Poelen" xsd:string -property_value: IAO:0000117 "Katja Shulz" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7134-3324 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string @@ -3623,7 +3621,7 @@ def: "x proper_distributary_of y iff x distributary_of y and x does not flow bac subset: ro-eco xref: RO:0002382 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: distributary_of ! distributary of [Typedef] @@ -3633,7 +3631,7 @@ def: "x proper_tributary_of y iff x tributary_of y and x does not originate from subset: ro-eco xref: RO:0002383 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: tributary_of ! tributary of [Typedef] @@ -3642,7 +3640,7 @@ name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string @@ -3654,7 +3652,7 @@ id: provides_nutrients_for name: provides nutrients for subset: ro-eco xref: RO:0002469 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3663,7 +3661,7 @@ name: realizable has basis in xref: RO:0004017 is_a: causally_related_to ! causally related to inverse_of: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:01Z [Typedef] @@ -3672,10 +3670,10 @@ name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] synonym: "triggered by process" EXACT [RO:cjm] xref: RO:0009501 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "David Osumi-Sutherland" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string @@ -3692,7 +3690,7 @@ xref: RO:0004028 domain: BFO:0000017 range: BFO:0000040 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:45:49Z [Typedef] @@ -3700,7 +3698,7 @@ id: receives_input_from name: receives input from xref: RO:0002485 property_value: IAO:0000116 "See notes for inverse relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to inverse_of: sends_output_to ! sends output to @@ -3740,7 +3738,7 @@ name: regulated by def: "inverse of regulates" [] subset: RO:0002259 xref: RO:0002334 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 range: BFO:0000015 @@ -3755,9 +3753,9 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Hill" xsd:string -property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 +property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string @@ -3774,7 +3772,7 @@ id: regulates_activity_of name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] xref: RO:0011002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3794,7 +3792,7 @@ id: regulates_in_other_organism name: regulates in other organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] xref: RO:0002010 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 range: BFO:0000015 is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -3805,7 +3803,7 @@ name: regulates levels of def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] xref: RO:0002332 property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 @@ -3817,7 +3815,7 @@ id: regulates_quantity_of name: regulates quantity of def: "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." [] xref: RO:0011003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3836,7 +3834,7 @@ id: related_via_localization_to name: related via localization to def: "A relationship that holds via some process of localization" [] xref: RO:0002337 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 range: BFO:0000002 @@ -3857,7 +3855,7 @@ id: represses_expression_of name: represses expression of def: "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." [] xref: RO:0003002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3871,7 +3869,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -3916,7 +3914,7 @@ name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] @@ -3936,7 +3934,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002348 property_value: IAO:0000112 "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3948,7 +3946,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002349 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3962,7 +3960,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3972,7 +3970,7 @@ id: results_in_developmental_induction_of name: results in developmental induction of def: "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." [] xref: RO:0002357 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3982,7 +3980,7 @@ def: "p results in the developmental progression of s iff p is a developmental p xref: RO:0002295 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 range: CARO:0000000 @@ -3994,7 +3992,7 @@ name: results in developmental regression of xref: RO:0002301 property_value: IAO:0000112 "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4004,7 +4002,7 @@ name: results in disappearance of xref: RO:0002300 property_value: IAO:0000112 "foramen ovale closure SubClassOf results in disappearance of foramen ovale" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4020,7 +4018,7 @@ id: results_in_ending_of name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4034,7 +4032,7 @@ xref: RO:0002297 property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4056,7 +4054,7 @@ id: results_in_growth_of name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4071,7 +4069,7 @@ xref: RO:0002299 property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4087,7 +4085,7 @@ xref: RO:0002298 property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4100,7 +4098,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002565 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4126,7 +4124,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002356 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4135,7 +4133,7 @@ id: results_in_structural_organization_of name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4151,7 +4149,7 @@ name: results in transport across def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002342 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: occurs_across ! occurs across is_a: results_in_transport_to_from_or_in ! results in transport to from or in @@ -4160,7 +4158,7 @@ id: results_in_transport_along name: results in transport along def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] xref: RO:0002341 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4168,7 +4166,7 @@ id: results_in_transport_to_from_or_in name: results in transport to from or in xref: RO:0002344 property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4183,7 +4181,7 @@ id: sends_output_to name: sends output to xref: RO:0002486 property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to [Typedef] @@ -4225,7 +4223,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcript" xsd:string property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -4235,7 +4233,7 @@ name: sequentially related to def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string @@ -4248,7 +4246,7 @@ name: skeleton of def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 is_a: part_of @@ -4259,7 +4257,7 @@ name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] xref: RO:0002379 property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: overlaps ! overlaps @@ -4271,7 +4269,7 @@ subset: ro-eco xref: RO:0002163 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 @@ -4285,7 +4283,7 @@ name: stabilizes quantity of def: "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." [] xref: RO:0011015 property_value: IAO:0000112 "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_quantity_of ! directly positively regulates quantity of @@ -4294,14 +4292,14 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates id: starts subset: ro-eco xref: RO:0002223 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: starts_with subset: ro-eco xref: RO:0002224 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -4317,7 +4315,7 @@ name: subcluster of def: "A relation between a group and another group it is part of but does not fully constitute." [] xref: RO:0015003 property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." xsd:string -property_value: IAO:0000117 "Shawn Tan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true is_a: part_of @@ -4326,7 +4324,7 @@ is_a: part_of id: subject_participant_in name: subject participant in xref: RO:0002462 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4345,7 +4343,7 @@ name: surrounded by def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] xref: RO:0002219 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to inverse_of: surrounds ! surrounds @@ -4357,7 +4355,7 @@ def: "inverse of surrounded by" [] subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to @@ -4367,7 +4365,7 @@ name: symbiotically interacts with def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] subset: ro-eco xref: RO:0002440 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true @@ -4380,8 +4378,8 @@ def: "Relation between an anatomical structure (including cells) and a neuron th xref: RO:0002103 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: receives_input_from ! receives input from inverse_of: synapsed_to ! synapsed to @@ -4406,8 +4404,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002108 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" [] @@ -4420,8 +4418,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002109 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4434,8 +4432,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002112 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4448,8 +4446,8 @@ comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part som xref: RO:0002120 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: sends_output_to ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -4473,8 +4471,8 @@ def: "A relation between a motor neuron and a muscle that it synapses to via a t comment: Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) xref: RO:0002107 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_II_bouton ! synapsed_by_via_type_II_bouton @@ -4488,8 +4486,8 @@ comment: Expands to: has_part some ('type Ib terminal button' that has_part some xref: RO:0002105 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Ib_bouton ! synapsed_by_via_type_Ib_bouton @@ -4503,8 +4501,8 @@ comment: Expands to: has_part some ('type Is terminal button' that has_part some xref: RO:0002106 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Is_bouton ! synapsed_by_via_type_Is_bouton @@ -4514,7 +4512,7 @@ expand_expression_to: "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that id: target_participant_in name: target participant in xref: RO:0002463 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4523,7 +4521,7 @@ id: temporally_related_to subset: ro-eco xref: RO:0002222 property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string [Typedef] @@ -4531,7 +4529,7 @@ id: transformation_of name: transformation of def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] xref: RO:0002494 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: develops_from ! develops from @@ -4541,7 +4539,7 @@ name: transitively provides input for def: "transitive form of directly_provides_input_for" [] xref: RO:0002414 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." xsd:string property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string domain: BFO:0000015 @@ -4556,7 +4554,7 @@ def: "A relationship that holds between a disease and organism" [] xref: RO:0002451 property_value: IAO:0000112 "all dengue disease transmitted by some mosquito" xsd:string property_value: IAO:0000116 "Add domain and range constraints" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -4576,7 +4574,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002313 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "regulates localization of" xsd:string is_a: related_via_localization_to ! related via localization to is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4590,7 +4588,7 @@ xref: RO:0002376 property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string @@ -4608,7 +4606,7 @@ name: trophically interacts with def: "An interaction relationship in which the partners are related via a feeding relationship." [] subset: ro-eco xref: RO:0002438 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4618,7 +4616,7 @@ name: ubiquitinates def: "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" [] xref: RO:0002480 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with [Typedef] diff --git a/src/ontology/subsets/ro-developmental.owl b/src/ontology/subsets/ro-developmental.owl index bdb02d0a..27c2e134 100644 --- a/src/ontology/subsets/ro-developmental.owl +++ b/src/ontology/subsets/ro-developmental.owl @@ -409,7 +409,7 @@ - David Osumi-Sutherland + RO:0002002 has_2D_boundary @@ -421,7 +421,7 @@ A relation that holds between two neurons that are electrically coupled via gap junctions. - David Osumi-Sutherland + RO:0002003 electrically_synapsed_to @@ -435,7 +435,7 @@ - David Osumi-Sutherland + RO:0002006 has_synaptic_terminal_of @@ -469,7 +469,7 @@ has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland + RO:0002007 bounding_layer_of @@ -505,9 +505,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. + A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. Note from NCEAS meeting: consider changing primary label - David Osumi-Sutherland + RO:0002008 coincident_with @@ -524,7 +524,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - David Osumi-Sutherland + RO:0002010 regulates_in_other_organism regulates in other organism @@ -553,7 +553,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + dos 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -568,7 +568,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + dos 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -584,7 +584,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + dos 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -599,7 +599,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -613,7 +613,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -630,7 +630,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + dos 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -644,7 +644,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + dos 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -658,7 +658,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + dos 2017-07-20T17:11:08Z RO:0002020 transports @@ -672,7 +672,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + dos 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -686,7 +686,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -697,7 +697,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + GOC:dos @@ -708,7 +708,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + dos 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -718,7 +718,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + GOC:dos @@ -729,7 +729,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + dos 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -739,7 +739,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + GOC:dos @@ -750,7 +750,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + dos 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -761,7 +761,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + GOC:dos @@ -780,7 +780,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + dos 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -797,7 +797,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + GOC:dos @@ -814,7 +814,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + RO:0002090 @@ -831,7 +831,7 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure that its soma is part of. - David Osumi-Sutherland + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -852,9 +852,9 @@ Examples include: the relationship between two channels collected simultaneously relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - David Osumi-Sutherland + fasciculates with - (forall (?x ?y) + (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) @@ -890,9 +890,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure its axon forms (chemical) synapses in. - Chris Mungall - David Osumi-Sutherland - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -924,8 +923,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -945,9 +944,9 @@ Examples include: the relationship between two channels collected simultaneously Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - Alexander Diehl - Chris Mungall - Lindsay Cowell + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) @@ -965,8 +964,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -985,8 +984,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -1005,8 +1004,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) RO:0002107 @@ -1023,8 +1022,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1043,8 +1042,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1064,8 +1063,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - Chris Mungall - David Osumi-Sutherland + + synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( @@ -1085,8 +1084,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1168,8 +1167,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -1196,8 +1195,8 @@ N1 SubclassOf ( Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -1218,7 +1217,7 @@ N1 SubclassOf ( A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - David Osumi-Sutherland + has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) @@ -1267,9 +1266,9 @@ N1 SubclassOf ( The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - David Osumi-Sutherland + has fasciculating component - (forall (?x ?y) + (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) @@ -1309,8 +1308,8 @@ N1 SubclassOf ( - X continuous_with Y if and only if X and Y share a fiat boundary. - David Osumi-Sutherland + X continuous_with Y if and only if X and Y share a fiat boundary. + connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) @@ -1329,8 +1328,8 @@ N1 SubclassOf ( x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom - proper overlaps - (forall (?x ?y) + proper overlaps + (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and @@ -1353,7 +1352,7 @@ N1 SubclassOf ( A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - Chris Mungall + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) @@ -1361,7 +1360,7 @@ N1 SubclassOf ( RO:0002163 spatially_disjoint_from - spatially disjoint from + spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern @@ -1498,7 +1497,7 @@ N1 SubclassOf ( A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - Chris Mungall + RO:0002200 has_phenotype @@ -1513,7 +1512,7 @@ N1 SubclassOf ( inverse of has phenotype - Chris Mungall + RO:0002201 @@ -1533,10 +1532,10 @@ N1 SubclassOf ( x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - Terry Meehan + + + + RO:0002202 develops_from This is the transitive form of the develops from relation @@ -1554,9 +1553,9 @@ N1 SubclassOf ( inverse of develops from - Chris Mungall - David Osumi-Sutherland - Terry Meehan + + + RO:0002203 develops_into @@ -1588,12 +1587,12 @@ N1 SubclassOf ( Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - Chris Mungall - David Osumi-Sutherland - has developmental precursor + + FBbt RO:0002207 + has developmental precursor directly_develops_from TODO - add child relations from DOS directly develops from @@ -1651,9 +1650,9 @@ N1 SubclassOf ( p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - Chris Mungall - David Hill - Tanya Berardini + + + GO Regulation precludes parthood; the regulatory process may not be within the regulated process. @@ -1676,7 +1675,7 @@ N1 SubclassOf ( p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - Chris Mungall + negatively regulates (process to process) @@ -1698,7 +1697,7 @@ N1 SubclassOf ( p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - Chris Mungall + positively regulates (process to process) @@ -1721,7 +1720,7 @@ N1 SubclassOf ( mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - Chris Mungall + has function realized in @@ -1740,7 +1739,7 @@ N1 SubclassOf ( c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - Chris Mungall + has function in RO:0002216 capable_of_part_of @@ -1757,7 +1756,7 @@ N1 SubclassOf ( x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - Chris Mungall + RO:0002219 surrounded_by @@ -1779,7 +1778,7 @@ N1 SubclassOf ( x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - Chris Mungall + RO:0002220 @@ -1803,7 +1802,7 @@ N1 SubclassOf ( inverse of surrounded by - Chris Mungall + RO:0002221 @@ -1816,7 +1815,7 @@ N1 SubclassOf ( - Chris Mungall + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 @@ -1830,7 +1829,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002223 starts @@ -1842,7 +1841,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002224 starts_with @@ -1856,7 +1855,7 @@ N1 SubclassOf ( x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - Chris Mungall + RO:0002225 develops_from_part_of develops from part of @@ -1871,7 +1870,7 @@ N1 SubclassOf ( x develops_in y if x is located in y whilst x is developing - Chris Mungall + EHDAA2 Jonathan Bard, EHDAA2 RO:0002226 @@ -1909,7 +1908,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002229 ends @@ -1921,7 +1920,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002230 ends_with @@ -1937,7 +1936,7 @@ N1 SubclassOf ( x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - Chris Mungall + starts with process that occurs in RO:0002231 @@ -1955,7 +1954,7 @@ N1 SubclassOf ( x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - Chris Mungall + ends with process that occurs in RO:0002232 @@ -1973,7 +1972,7 @@ N1 SubclassOf ( p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + consumes RO:0002233 @@ -1993,7 +1992,7 @@ N1 SubclassOf ( p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - Chris Mungall + produces RO:0002234 @@ -2047,7 +2046,7 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - Bill Duncan (https://orcid.org/0000-0001-9625-1899) + This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. @@ -2196,7 +2195,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y - Chris Mungall + RO:0002254 has_developmental_contribution_from has developmental contribution from @@ -2211,7 +2210,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho inverse of has developmental contribution from - Chris Mungall + RO:0002255 developmentally_contributes_to @@ -2229,9 +2228,9 @@ If you need an axiom that says 'has_participant min 2 object', you sho t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - Chris Mungall - David Osumi-Sutherland - Melissa Haendel + + + induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) @@ -2251,7 +2250,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally induced by - Chris Mungall + RO:0002257 developmentally_induces developmentally induces @@ -2269,7 +2268,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - Chris Mungall + In general you should not use this relation to make assertions - use one of the more specific relations below this one RO:0002258 developmentally_preceded_by @@ -2317,7 +2316,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - Chris Mungall + replaces RO:0002285 developmentally_replaces @@ -2332,7 +2331,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally preceded by - Chris Mungall + RO:0002286 developmentally_succeeded_by developmentally succeeded by @@ -2346,7 +2345,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - Chris Mungall + RO:0002287 part_of_developmental_precursor_of part of developmental precursor of @@ -2363,7 +2362,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - Chris Mungall + RO:0002295 results_in_developmental_progression_of results in developmental progression of @@ -2380,7 +2379,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - Chris Mungall + http://www.geneontology.org/GO.doc.development.shtml RO:0002296 @@ -2401,7 +2400,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002297 @@ -2422,7 +2421,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002298 @@ -2443,7 +2442,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002299 @@ -2461,7 +2460,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho foramen ovale closure SubClassOf results in disappearance of foramen ovale - Chris Mungall + May be merged into parent relation RO:0002300 results_in_disappearance_of @@ -2476,7 +2475,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) - Chris Mungall + May be merged into parent relation RO:0002301 results_in_developmental_regression_of @@ -2491,7 +2490,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of 'is substance that treats' - cjm + RO:0002302 is_treated_by_substance @@ -2511,7 +2510,7 @@ where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. - Pier Buttigieg + adapted for living in RO:0002303 @@ -2529,7 +2528,7 @@ where p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - cjm + RO:0002304 @@ -2547,7 +2546,7 @@ where p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - cjm + RO:0002305 @@ -2562,10 +2561,10 @@ where A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. - Austin Meier - Chris Mungall - Marie Angelique Laporte - cjm + + + + 2017-06-05T17:35:04Z RO:0002309 has_exposure_stimulus @@ -2580,7 +2579,7 @@ where Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. - Chris Mungall + regulates localization of RO:0002313 @@ -2600,7 +2599,7 @@ where an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002315 @@ -2617,7 +2616,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions RO:0002321 @@ -2633,7 +2632,7 @@ where An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. - Chris Mungall + adapted for RO:0002322 @@ -2647,7 +2646,7 @@ where A mereological relationship or a topological relationship - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships RO:0002323 @@ -2661,7 +2660,7 @@ where A relationship that holds between entities participating in some developmental process (GO:0032502) - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development RO:0002324 developmentally_related_to @@ -2678,9 +2677,8 @@ where Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. - Chris Mungall + In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - Gene Ontology Consortium RO:0002325 colocalizes_with @@ -2708,7 +2706,7 @@ then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. - Chris Mungall + In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 @@ -2725,7 +2723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - Chris Mungall + catalyzes executes has @@ -2744,7 +2742,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 functionally_related_to @@ -2758,7 +2756,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati this relation holds between c and p when c is part of some c', and c' is capable of p. - Chris Mungall + false RO:0002329 part_of_structure_that_is_capable_of @@ -2773,7 +2771,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati c involved_in p if and only if c enables some process p', and p' is part of p - Chris Mungall + actively involved in enables part of RO:0002331 @@ -2792,7 +2790,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - Chris Mungall + regulates levels of (process to entity) RO:0002332 @@ -2808,7 +2806,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables - Chris Mungall + RO:0002333 enabled_by @@ -2825,7 +2823,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of regulates - Chris Mungall + regulated by (processual) RO:0002334 @@ -2840,7 +2838,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of negatively regulates - Chris Mungall + RO:0002335 negatively_regulated_by @@ -2854,7 +2852,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of positively regulates - Chris Mungall + RO:0002336 positively_regulated_by @@ -2869,7 +2867,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds via some process of localization - Chris Mungall + Do not use this relation directly. It is a grouping relation. RO:0002337 related_via_localization_to @@ -2883,7 +2881,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - Chris Mungall + RO:0002338 @@ -2899,7 +2897,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - Chris Mungall + RO:0002339 @@ -2915,7 +2913,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. - Chris Mungall + RO:0002340 imports @@ -2929,7 +2927,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - Chris Mungall + RO:0002341 results_in_transport_along results in transport along @@ -2943,7 +2941,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - Chris Mungall + RO:0002342 results_in_transport_across @@ -2958,7 +2956,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'pollen tube growth' results_in growth_of some 'pollen tube' - Chris Mungall + RO:0002343 results_in_growth_of results in growth of @@ -2971,7 +2969,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - Chris Mungall + RO:0002344 results_in_transport_to_from_or_in results in transport to from or in @@ -2983,8 +2981,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. - Chris Mungall + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. + RO:0002345 exports @@ -3000,7 +2998,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - Chris Mungall + RO:0002348 @@ -3017,7 +3015,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - Chris Mungall + RO:0002349 @@ -3034,7 +3032,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has input - Chris Mungall + RO:0002352 @@ -3050,7 +3048,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has output - Chris Mungall + RO:0002353 @@ -3064,7 +3062,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002354 formed_as_result_of formed as result of @@ -3078,7 +3076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. - Chris Mungall + RO:0002355 results_in_structural_organization_of results in structural organization of @@ -3092,7 +3090,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - Chris Mungall + RO:0002356 @@ -3108,7 +3106,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. - Chris Mungall + RO:0002357 results_in_developmental_induction_of results in developmental induction of @@ -3120,7 +3118,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + http://neurolex.org/wiki/Property:DendriteLocation RO:0002360 has_dendrite_location @@ -3136,7 +3134,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - Chris Mungall + attached to (anatomical structure to anatomical structure) RO:0002371 @@ -3153,7 +3151,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002372 has_muscle_origin @@ -3176,7 +3174,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002373 has_muscle_insertion @@ -3200,7 +3198,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) @@ -3222,7 +3220,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - Chris Mungall + drains into drains to tributary channel of @@ -3247,7 +3245,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Deschutes River distributary_of Little Lava Lake x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - Chris Mungall + branch of distributary channel of http://en.wikipedia.org/wiki/Distributary @@ -3273,7 +3271,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. - Chris Mungall + anastomoses with RO:0002378 @@ -3289,7 +3287,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - Chris Mungall + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios RO:0002379 spatially_coextensive_with @@ -3312,7 +3310,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - Chris Mungall + RO:0002380 branching_part_of @@ -3331,7 +3329,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. - Chris Mungall + RO:0002381 main_stem_of @@ -3347,7 +3345,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_distributary_of y iff x distributary_of y and x does not flow back into y - Chris Mungall + RO:0002382 proper_distributary_of @@ -3362,7 +3360,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_tributary_of y iff x tributary_of y and x does not originate from y - Chris Mungall + RO:0002383 proper_tributary_of @@ -3379,7 +3377,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - Chris Mungall + RO:0002384 has_developmental_potential_involving has developmental potential involving @@ -3393,7 +3391,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - Chris Mungall + RO:0002385 has_potential_to_developmentally_contribute_to has potential to developmentally contribute to @@ -3407,7 +3405,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - Chris Mungall + RO:0002386 has_potential_to_developmentally_induce has potential to developmentally induce @@ -3421,7 +3419,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has the potential to develop into y iff x develops into y or if x is capable of developing into y - Chris Mungall + RO:0002387 has_potential_to_develop_into has potential to develop into @@ -3435,7 +3433,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - Chris Mungall + RO:0002388 has_potential_to_directly_develop_into has potential to directly develop into @@ -3450,7 +3448,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' RO:0002400 @@ -3468,7 +3466,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of upstream of - Chris Mungall + RO:0002404 causally_downstream_of causally downstream of @@ -3483,7 +3481,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002405 immediately_causally_downstream_of immediately causally downstream of @@ -3498,7 +3496,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - Chris Mungall + indirectly activates RO:0002407 @@ -3515,7 +3513,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - Chris Mungall + indirectly inhibits RO:0002409 @@ -3544,7 +3542,7 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002410 causally_related_to @@ -3566,7 +3564,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - Chris Mungall + RO:0002411 @@ -3582,7 +3580,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - Chris Mungall + RO:0002412 immediately_causally_upstream_of @@ -3598,7 +3596,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit - Chris Mungall + directly provides input for directly provides input for (process to process) @@ -3618,7 +3616,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different transitive form of directly_provides_input_for - Chris Mungall + This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. transitively provides input for (process to process) RO:0002414 @@ -3636,7 +3634,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall + influences (processual) RO:0002418 affects @@ -3652,7 +3650,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - Chris Mungall + RO:0002427 @@ -3668,7 +3666,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - Chris Mungall + RO:0002428 involved_in_regulation_of involved in regulation of @@ -3681,7 +3679,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - Chris Mungall + RO:0002429 involved_in_positive_regulation_of @@ -3695,7 +3693,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - Chris Mungall + RO:0002430 involved_in_negative_regulation_of @@ -3712,7 +3710,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - Chris Mungall + involved in or reguates RO:0002431 involved_in_or_involved_in_regulation_of @@ -3728,7 +3726,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall + executes activity in RO:0002432 enables activity in @@ -3740,8 +3738,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + GOC:cjm + GOC:dos @@ -3751,7 +3749,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - Chris Mungall + RO:0002433 contributes_to_morphology_of contributes to morphology of @@ -3768,7 +3766,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. - Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. RO:0002434 in pairwise interaction with @@ -3787,7 +3785,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) - Chris Mungall + RO:0002435 genetically_interacts_with genetically interacts with @@ -3803,7 +3801,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - Chris Mungall + binds molecularly binds with RO:0002436 @@ -3824,7 +3822,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - Chris Mungall + interacts with on organism level RO:0002437 @@ -3841,7 +3839,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the partners are related via a feeding relationship. - Chris Mungall + RO:0002438 trophically_interacts_with @@ -3859,9 +3857,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] Baleen whale preys on krill An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - Chris Mungall - Jorrit Poelen - Katja Shulz + + + is subject of predation interaction with preys upon RO:0002439 @@ -3880,7 +3878,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A biotic interaction in which the two organisms live together in more or less intimate association. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism RO:0002440 @@ -3896,7 +3894,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002441 @@ -3911,7 +3909,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002442 @@ -3926,7 +3924,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 This relation groups a pair of inverse relations, parasite of and parasitized by RO:0002443 @@ -3944,7 +3942,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human - Chris Mungall + parasitizes RO:0002444 direct parasite of @@ -3961,7 +3959,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + has parasite parasitised by RO:0002445 @@ -3980,7 +3978,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - Chris Mungall + RO:0002446 semibiotically interacts with @@ -3996,7 +3994,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. RO:0002447 phosphorylates @@ -4015,8 +4013,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - Chris Mungall - Vasundra Touré + + RO:0002448 molecularly controls directly_regulates_activity_of @@ -4033,8 +4031,8 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly inhibits RO:0002449 molecularly decreases activity of @@ -4052,8 +4050,8 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly activates RO:0002450 molecularly increases activity of @@ -4070,7 +4068,7 @@ For example, A and B may be gene products and binding of B by A positively regul all dengue disease transmitted by some mosquito A relationship that holds between a disease and organism Add domain and range constraints - Chris Mungall + RO:0002451 transmitted_by transmitted by @@ -4084,7 +4082,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between a disease or an organism and a phenotype - Chris Mungall + RO:0002452 has_symptom has symptom @@ -4096,7 +4094,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) RO:0002453 @@ -4111,7 +4109,7 @@ For example, A and B may be gene products and binding of B by A positively regul X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y - Chris Mungall + RO:0002454 has_host @@ -4128,7 +4126,7 @@ For example, A and B may be gene products and binding of B by A positively regul Bees pollinate Flowers This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - Chris Mungall + is subject of pollination interaction with RO:0002455 @@ -4143,7 +4141,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + has polinator is target of pollination interaction with RO:0002456 @@ -4160,7 +4158,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4175,7 +4173,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of preys on - Chris Mungall + has predator is target of predation interaction with RO:0002458 @@ -4195,7 +4193,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anopheles is a vector for Plasmodium - Chris Mungall + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism RO:0002459 @@ -4209,7 +4207,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002460 has_vector @@ -4222,7 +4220,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target RO:0002461 partner_in @@ -4235,7 +4233,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002462 subject_participant_in @@ -4248,7 +4246,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002463 target_participant_in @@ -4261,7 +4259,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002469 provides_nutrients_for @@ -4274,7 +4272,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is subject of eating interaction with RO:0002470 @@ -4288,7 +4286,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + eaten by is target of eating interaction with RO:0002471 @@ -4307,7 +4305,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - Chris Mungall + RO:0002473 @@ -4326,7 +4324,7 @@ For example, A and B may be gene products and binding of B by A positively regul ABal nucleus child nucleus of ABa nucleus (in C elegans) c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d - Chris Mungall + This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. RO:0002476 child_nucleus_of @@ -4340,7 +4338,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a hermaphroditic organism - Chris Mungall + RO:0002477 child_nucleus_of_in_hermaphrodite child nucleus of in hermaphrodite @@ -4353,7 +4351,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a male organism - Chris Mungall + RO:0002478 child_nucleus_of_in_male child nucleus of in male @@ -4367,7 +4365,7 @@ For example, A and B may be gene products and binding of B by A positively regul p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall + RO:0002479 has_part_that_occurs_in @@ -4382,7 +4380,7 @@ For example, A and B may be gene products and binding of B by A positively regul An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y Axiomatization to GO to be added later - Chris Mungall + RO:0002480 ubiquitinates ubiquitinates @@ -4396,7 +4394,7 @@ For example, A and B may be gene products and binding of B by A positively regul See notes for inverse relation - Chris Mungall + RO:0002485 receives_input_from receives input from @@ -4409,7 +4407,7 @@ For example, A and B may be gene products and binding of B by A positively regul This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - Chris Mungall + RO:0002486 sends_output_to sends output to @@ -4423,7 +4421,7 @@ For example, A and B may be gene products and binding of B by A positively regul x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - Chris Mungall + RO:0002494 transformation_of transformation of @@ -4437,7 +4435,7 @@ For example, A and B may be gene products and binding of B by A positively regul x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - Chris Mungall + RO:0002495 immediate_transformation_of @@ -4467,7 +4465,7 @@ For example, A and B may be gene products and binding of B by A positively regul p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002501 @@ -4483,7 +4481,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c - Chris Mungall + has intermediate product RO:0002505 @@ -4500,7 +4498,7 @@ For example, A and B may be gene products and binding of B by A positively regul The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002506 @@ -4522,11 +4520,11 @@ For example, A and B may be gene products and binding of B by A positively regul A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future - Chris Mungall + determined by (system to material entity) - Chris Mungall - Pier Buttigieg + + RO:0002507 determined_by @@ -4540,7 +4538,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of determined by - Chris Mungall + determines (material entity to system) RO:0002508 @@ -4559,7 +4557,7 @@ For example, A and B may be gene products and binding of B by A positively regul s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. - Chris Mungall + RO:0002509 determined_by_part_of @@ -4574,7 +4572,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between two entities that have the property of being sequences or having sequences. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. @@ -4594,7 +4592,7 @@ For example, A and B may be gene products and binding of B by A positively regul Two consecutive DNA residues are sequentially adjacent Two exons on a processed transcript that were previously connected by an intron are adjacent x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002515 @@ -4612,7 +4610,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as a start sequence the start codon for that transcript x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence - Chris Mungall + started by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4629,7 +4627,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has start sequence - Chris Mungall + starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4649,7 +4647,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence - Chris Mungall + ended by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4666,7 +4664,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has end sequence - Chris Mungall + ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4684,7 +4682,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. In the SO paper, this was defined as an instance-type relation - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002520 @@ -4701,7 +4699,7 @@ For example, A and B may be gene products and binding of B by A positively regul Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering - Chris Mungall + RO:0002521 is_sequentially_aligned_with @@ -4718,7 +4716,7 @@ For example, A and B may be gene products and binding of B by A positively regul The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y - Chris Mungall + RO:0002522 bounds_sequence_of @@ -4733,7 +4731,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of bounds sequence of - Chris Mungall + RO:0002523 @@ -4751,8 +4749,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x has subsequence y iff all of the sequence parts of x are sequence parts of y - Chris Mungall + x has subsequence y iff all of the sequence parts of y are sequence parts of x + contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4771,7 +4769,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has subsequence - Chris Mungall + contained by RO:0002525 @@ -4788,8 +4786,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. - Chris Mungall + x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. + RO:0002526 overlaps_sequence_of @@ -4803,8 +4801,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. - Chris Mungall + x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + disconnected from RO:0002527 @@ -4820,7 +4818,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of downstream of sequence of - Chris Mungall + RO:0002528 is_upstream_of_sequence_of @@ -4836,7 +4834,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. - Chris Mungall + RO:0002529 is_downstream_of_sequence_of @@ -4852,7 +4850,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y - Chris Mungall + RO:0002530 @@ -4869,7 +4867,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript inverse of immediately downstream of - Chris Mungall + RO:0002531 is_immediately_upstream_of_sequence_of @@ -4889,7 +4887,7 @@ For example, A and B may be gene products and binding of B by A positively regul Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - Chris Mungall + has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). RO:0002551 @@ -4911,7 +4909,7 @@ For example, A and B may be gene products and binding of B by A positively regul p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. - Chris Mungall + RO:0002552 results_in_ending_of results in ending of @@ -4926,7 +4924,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - Chris Mungall + http://eol.org/schema/terms/hyperparasitoidOf https://en.wikipedia.org/wiki/Hyperparasite RO:0002553 @@ -4944,7 +4942,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of hyperparasite of - Chris Mungall + RO:0002554 has epiparasite has hyperparasite @@ -4961,7 +4959,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + http://en.wikipedia.org/wiki/Allelopathy RO:0002555 @@ -4978,7 +4976,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002556 pathogen_of @@ -4991,7 +4989,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002557 has_pathogen @@ -5005,7 +5003,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + causally influenced by (entity-centric) RO:0002559 @@ -5020,7 +5018,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - Chris Mungall + RO:0002565 @@ -5039,8 +5037,8 @@ For example, A and B may be gene products and binding of B by A positively regul The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - Chris Mungall - Vasundra Touré + + causally influences (entity-centric) RO:0002566 @@ -5057,7 +5055,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between elements of a musculoskeletal system or its analogs. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. RO:0002567 biomechanically_related_to @@ -5071,7 +5069,7 @@ For example, A and B may be gene products and binding of B by A positively regul m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - Chris Mungall + Wikipedia:Antagonist_(muscle) RO:0002568 has_muscle_antagonist @@ -5087,7 +5085,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of branching part of - Chris Mungall + RO:0002569 @@ -5104,7 +5102,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - Chris Mungall + UBERON:cjm This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. RO:0002570 @@ -5121,7 +5119,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - Chris Mungall + GOC:cjm RO:0002571 @@ -5137,7 +5135,7 @@ For example, A and B may be gene products and binding of B by A positively regul s is luminal space of x iff s is lumen_of x and s is an immaterial entity - Chris Mungall + RO:0002572 luminal_space_of @@ -5152,7 +5150,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002574 participates_in_a_biotic-biotic_interaction_with @@ -5169,7 +5167,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has skeleton - Chris Mungall + RO:0002576 skeleton_of @@ -5184,7 +5182,7 @@ For example, A and B may be gene products and binding of B by A positively regul p directly regulates q iff p is immediately causally upstream of q and p regulates q. - Chris Mungall + directly regulates (processual) @@ -5205,7 +5203,7 @@ For example, A and B may be gene products and binding of B by A positively regul gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - Chris Mungall + RO:0002584 has_part_structure_that_is_capable_of has part structure that is capable of @@ -5320,7 +5318,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall + RO:0002595 causal_relation_between_material_entity_and_a_process @@ -5723,7 +5721,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. - Vasundra Touré + RO:0003002 represses_expression_of represses expression of @@ -5738,7 +5736,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. - Vasundra Touré + RO:0003003 increases_expression_of increases expression of @@ -5883,7 +5881,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:38:20Z RO:0004000 condition_has_genetic_basis_in @@ -5897,7 +5895,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:20Z RO:0004001 has_material_basis_in_gain_of_function_germline_mutation_in @@ -5913,7 +5911,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:37Z RO:0004002 has_material_basis_in_loss_of_function_germline_mutation_in @@ -5927,7 +5925,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:54Z RO:0004003 has_material_basis_in_germline_mutation_in @@ -5942,7 +5940,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:07Z RO:0004004 has_material_basis_in_somatic_mutation_in @@ -5957,7 +5955,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:26Z RO:0004005 has_major_susceptibility_factor @@ -5971,7 +5969,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:57Z RO:0004006 has_partial_material_basis_in_germline_mutation_in @@ -5985,7 +5983,7 @@ Environmental exposures include those imposed by natural environments, experimen p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - cjm + 2018-12-13T11:26:17Z RO:0004007 @@ -6001,7 +5999,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - cjm + 2018-12-13T11:26:32Z RO:0004008 @@ -6012,8 +6010,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6027,7 +6025,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - cjm + 2018-12-13T11:26:56Z RO:0004009 @@ -6038,8 +6036,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6053,7 +6051,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:53:08Z RO:0004010 is_genetic_basis_for_condition @@ -6067,7 +6065,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:55:51Z RO:0004011 is_causal_gain_of_function_germline_mutation_of_in @@ -6082,7 +6080,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:06Z RO:0004012 is_causal_loss_of_function_germline_mutation_of_in @@ -6098,7 +6096,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:40Z RO:0004013 is_causal_germline_mutation_in @@ -6114,7 +6112,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:57:07Z RO:0004014 is_causal_somatic_mutation_in @@ -6129,7 +6127,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. - cjm + 2017-11-05T02:57:43Z RO:0004015 is_causal_susceptibility_factor_for @@ -6145,7 +6143,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. - cjm + 2017-11-05T02:58:43Z RO:0004016 is_causal_germline_mutation_partially_giving_rise_to @@ -6160,7 +6158,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:01Z RO:0004017 realizable_has_basis_in @@ -6173,7 +6171,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:29Z RO:0004018 is_basis_for_realizable @@ -6188,7 +6186,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:26:47Z RO:0004019 disease_has_basis_in @@ -6204,7 +6202,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) - cjm + 2017-11-05T03:29:32Z RO:0004020 disease_has_basis_in_dysfunction_of @@ -6220,7 +6218,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. disease has basis in disruption of (disease to process) - cjm + 2017-11-05T03:37:52Z RO:0004021 disease_has_basis_in_disruption_of @@ -6244,7 +6242,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. - cjm + 2017-11-05T03:46:07Z RO:0004022 disease_has_basis_in_feature @@ -6260,7 +6258,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. - cjm + 2017-11-05T03:50:54Z RO:0004023 causal_relationship_with_disease_as_subject @@ -6277,7 +6275,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and a process where the disease process disrupts the execution of the process. disease causes disruption of (disease to process) - cjm + 2017-11-05T03:51:09Z RO:0004024 disease_causes_disruption_of @@ -6293,7 +6291,7 @@ Environmental exposures include those imposed by natural environments, experimen disease causes dysfunction of (disease to anatomical entity) - cjm + 2017-11-05T03:58:20Z RO:0004025 disease_causes_dysfunction_of @@ -6319,7 +6317,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. - cjm + 2017-11-05T04:06:02Z RO:0004026 disease_has_location @@ -6343,7 +6341,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity - cjm + 2017-12-26T19:37:31Z RO:0004027 disease_has_inflammation_site @@ -6359,7 +6357,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - cjm + 2017-12-26T19:45:49Z RO:0004028 realized_in_response_to_stimulus @@ -6382,7 +6380,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. - cjm + 2017-12-26T19:50:53Z RO:0004029 disease_has_feature @@ -6397,7 +6395,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. - cjm + 2017-12-26T19:58:44Z RO:0004030 disease_arises_from_alteration_in_structure @@ -6411,7 +6409,7 @@ Environmental exposures include those imposed by natural environments, experimen Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - cjm + 2018-01-25T23:20:13Z RO:0004031 enables_subfunction @@ -6425,7 +6423,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:30Z RO:0004032 @@ -6441,7 +6439,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:51Z RO:0004033 @@ -6458,7 +6456,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - cjm + 2018-01-26T23:53:14Z RO:0004034 @@ -6476,7 +6474,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - cjm + 2018-01-26T23:53:22Z RO:0004035 @@ -6492,7 +6490,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:05Z RO:0004046 causally_upstream_of_or_within,_negative_effect @@ -6506,7 +6504,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:19Z RO:0004047 causally_upstream_of_or_within,_positive_effect @@ -6633,10 +6631,10 @@ Environmental exposures include those imposed by natural environments, experimen An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - Austin Meier - Chris Mungall - David Osumi-Sutherland - Marie Angelique Laporte + + + + RO:0009501 triggered by process realized_in_response_to @@ -6659,7 +6657,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - Vasundra Touré + RO:0011002 regulates_activity_of regulates activity of @@ -6674,7 +6672,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. - Vasundra Touré + RO:0011003 regulates_quantity_of regulates quantity of @@ -6689,7 +6687,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. - Vasundra Touré + RO:0011004 indirectly_regulates_activity_of indirectly regulates activity of @@ -6706,7 +6704,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011007 decreases_by_repression_quantity_of decreases by repression quantity of @@ -6723,7 +6721,7 @@ For example, protein A (transcription factor) indirectly decreases by repression The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011008 increases_by_expression_quantity_of increases by expression quantity of @@ -6738,7 +6736,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly positively regulates the quantity of B. - Vasundra Touré + RO:0011009 directly_positively_regulates_quantity_of directly positively regulates quantity of @@ -6753,7 +6751,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly negatively regulates the quantity of B. - Vasundra Touré + RO:0011010 directly_negatively_regulates_quantity_of directly negatively regulates quantity of @@ -6768,7 +6766,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. - Vasundra Touré + indirectly activates RO:0011013 indirectly_positively_regulates_activity_of @@ -6785,7 +6783,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. - Vasundra Touré + RO:0011014 destabilizes_quantity_of destabilizes quantity of @@ -6801,7 +6799,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. - Vasundra Touré + RO:0011015 stabilizes_quantity_of stabilizes quantity of @@ -6814,7 +6812,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. - Vasundra Touré + indirectly inhibits RO:0011016 indirectly_negatively_regulates_activity_of @@ -6828,7 +6826,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. - Vasundra Touré + RO:0011021 directly_regulates_quantity_of directly regulates quantity of @@ -6841,7 +6839,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011022 indirectly_regulates_quantity_of indirectly regulates quantity of @@ -6854,7 +6852,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011023 indirectly_negatively_regulates_quantity_of indirectly negatively regulates quantity of @@ -6867,7 +6865,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011024 indirectly_positively_regulates_quantity_of indirectly positively regulates quantity of @@ -6880,8 +6878,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is regulated by the small molecule continuant + pg 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -6895,8 +6893,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is activated by the small molecule continuant + pg 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -6910,8 +6908,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant + pg 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -6924,8 +6922,8 @@ For example, protein A (transcription factor) indirectly increases by expression - p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + p acts on population of c iff c' is a collection, has members of type c, and p has participant c + pg 2020-06-08T17:21:33Z RO:0012003 @@ -6941,8 +6939,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process + pg 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -6956,8 +6954,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process + pg 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of @@ -6971,8 +6969,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process + pg 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of @@ -6985,8 +6983,8 @@ For example, protein A (transcription factor) indirectly increases by expression - The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. + pg 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -6999,7 +6997,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + pg 2021-02-26T07:28:29Z RO:0012008 @@ -7016,7 +7014,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + pg 2022-09-26T06:01:01Z RO:0012009 @@ -7032,7 +7030,7 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + pg 2022-09-26T06:06:20Z RO:0012010 @@ -7048,7 +7046,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + pg 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7063,7 +7061,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + pg 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7229,7 +7227,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relation between a group and another group it is part of but does not fully constitute. X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. - Shawn Tan + This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. RO:0015003 subcluster_of @@ -7301,7 +7299,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - http://orcid.org/0000-0002-7463-6306 + 2021-11-05T17:30:44Z RO:0016002 has_disease @@ -7457,7 +7455,7 @@ For example, protein A (transcription factor) indirectly increases by expression This relation groups relations between diseases and any other kind of entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. - cjm + 2018-09-26T00:00:32Z RO:0040035 disease_relationship @@ -7471,7 +7469,7 @@ For example, protein A (transcription factor) indirectly increases by expression p has anatomical participant c iff p has participant c, and c is an anatomical entity - cjm + 2018-09-26T01:08:58Z RO:0040036 results_in_changes_to_anatomical_or_cellular_structure diff --git a/src/ontology/subsets/ro-eco.obo b/src/ontology/subsets/ro-eco.obo index 59230f28..7f3fab39 100644 --- a/src/ontology/subsets/ro-eco.obo +++ b/src/ontology/subsets/ro-eco.obo @@ -58,7 +58,7 @@ def: "OBSOLETE A relation that holds between two neurons connected directly via comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_transitive: true is_obsolete: true @@ -70,7 +70,7 @@ def: "OBSOLETE A relation that holds between a neuron that is synapsed_to anothe comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_transitive: true is_obsolete: true @@ -82,7 +82,7 @@ def: "OBSOLETE A relation that holds between a neuron that is synapsed_by anothe comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_transitive: true is_obsolete: true @@ -150,13 +150,13 @@ id: RO:0002001 name: aligned with property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "May be obsoleted, see https://github.com/oborel/obo-relations/issues/260" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_transitive: true [Typedef] id: RO:0002002 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0002323 ! mereotopologically related to [Typedef] @@ -164,28 +164,28 @@ id: RO:0002003 name: electrically_synapsed_to def: "A relation that holds between two neurons that are electrically coupled via gap junctions." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0002170 ! connected to [Typedef] id: RO:0002004 name: tracheates def: "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to)." [] -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0001018 ! contained in [Typedef] id: RO:0002005 name: innervated_by property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 inverse_of: RO:0002134 ! innervates [Typedef] id: RO:0002006 name: has synaptic terminal of property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0002131 ! overlaps inverse_of: RO:0002130 ! has synaptic terminal in @@ -195,7 +195,7 @@ name: bounding layer of def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" [] comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: BFO:0000050 [Typedef] @@ -205,7 +205,7 @@ def: "A relation that holds between two linear structures that are approximately comment: Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. subset: ro-eco property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0002323 ! mereotopologically related to [Typedef] @@ -213,14 +213,14 @@ id: RO:0002009 name: cell expresses def: "A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g." [] property_value: http://purl.org/dc/terms/description "x 'cell expresses' y iff:\ncell(x)\nAND gene(y)\nAND exists some 'transcription, DNA templated (GO_0006351)'(t)\nAND t occurs_in x\nAND t has_input y" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0002292 ! expresses [Typedef] id: RO:0002010 name: regulates in other organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0002418 ! causally upstream of or within [Typedef] @@ -228,7 +228,7 @@ id: RO:0002011 name: regulates transport of def: "A relationship that holds between a process that regulates a transport process and the entity transported by that process." [] subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 holds_over_chain: RO:0002211 RO:0002313 [Typedef] @@ -364,13 +364,13 @@ creation_date: 2017-12-07T12:58:06Z [Typedef] id: RO:0002082 subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 [Typedef] id: RO:0002085 name: encompasses comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "di" xsd:string is_transitive: true is_a: RO:0002088 @@ -383,7 +383,7 @@ subset: ro-eco [Typedef] id: RO:0002090 subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0002575 BFO:0000063 holds_over_chain: RO:0002230 RO:0002224 @@ -404,7 +404,7 @@ id: RO:0002100 name: has soma location def: "Relation between a neuron and an anatomical structure that its soma is part of." [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002131 ! overlaps transitive_over: BFO:0000050 @@ -416,7 +416,7 @@ name: fasciculates with def: "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 @@ -429,9 +429,8 @@ name: axon synapses in def: "Relation between a neuron and some structure its axon forms (chemical) synapses in." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002113 ! has presynaptic terminal in transitive_over: BFO:0000050 @@ -443,8 +442,8 @@ name: synapsed by def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002485 ! receives input from inverse_of: RO:0002120 ! synapsed to @@ -456,9 +455,9 @@ name: has plasma membrane part def: "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." [] property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Alexander Diehl" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 is_a: BFO:0000051 @@ -471,8 +470,8 @@ def: "A relation between a motor neuron and a muscle that it synapses to via a t comment: Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002120 ! synapsed to inverse_of: RO:0002109 ! synapsed_by_via_type_Ib_bouton @@ -485,8 +484,8 @@ def: "A relation between a motor neuron and a muscle that it synapses to via a t comment: Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002120 ! synapsed to inverse_of: RO:0002112 ! synapsed_by_via_type_Is_bouton @@ -498,8 +497,8 @@ name: synapsed_via_type_II_bouton_to def: "A relation between a motor neuron and a muscle that it synapses to via a type II bouton." [] comment: Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002120 ! synapsed to inverse_of: RO:0002108 ! synapsed_by_via_type_II_bouton @@ -512,8 +511,8 @@ def: "Relation between a muscle and a motor neuron that synapses to it via a typ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002103 ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" [] @@ -525,8 +524,8 @@ def: "Relation between a muscle and a motor neuron that synapses to it via a typ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002103 ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -537,8 +536,8 @@ name: has postsynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "synapsed in" xsd:string property_value: RO:0001900 RO:0001901 is_a: RO:0002130 ! has synaptic terminal in @@ -559,8 +558,8 @@ def: "Relation between a muscle and a motor neuron that synapses to it via a typ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002103 ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -605,8 +604,8 @@ def: " Relation between a neuron and an anatomical structure (including cells) t comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n ‘synapse ; GO:0045202’ that has_part some (\n ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002486 ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -617,8 +616,8 @@ name: dendrite synapsed in def: "Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.\n\n " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002110 ! has postsynaptic terminal in transitive_over: BFO:0000050 @@ -630,7 +629,7 @@ name: has synaptic terminal in def: "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has synapse in" xsd:string property_value: RO:0001900 RO:0001901 is_a: RO:0002131 ! overlaps @@ -660,7 +659,7 @@ name: has fasciculating neuron projection def: "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 @@ -672,7 +671,7 @@ name: innervates def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 transitive_over: BFO:0000050 expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] @@ -682,7 +681,7 @@ id: RO:0002150 name: continuous with def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 @@ -749,7 +748,7 @@ def: "x only in taxon y if and only if x is in taxon y, and there is no other or property_value: IAO:0000112 "lactation SubClassOf 'only in taxon' some 'Mammalia'" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints @@ -762,8 +761,8 @@ def: "x is in taxon y if an only if y is an organism, and the relationship betwe comment: Connects a biological entity to its taxon of origin. subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Jennifer Deegan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints @@ -785,7 +784,7 @@ def: "A is spatially_disjoint_from B if and only if they have no parts in common subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 @@ -857,7 +856,7 @@ name: has phenotype def: "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0016001 ! has phenotype or disease inverse_of: RO:0002201 ! phenotype of @@ -868,7 +867,7 @@ def: "inverse of has phenotype" [] subset: ro-eco subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_functional: true [Typedef] @@ -877,10 +876,10 @@ name: develops from def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] comment: This is the transitive form of the develops from relation property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 is_transitive: true is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002203 ! develops into @@ -891,9 +890,9 @@ name: develops into def: "inverse of develops from" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 is_transitive: true is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002387 ! has potential to develop into @@ -905,7 +904,7 @@ name: gene product of def: "definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\"" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002512 RO:0002510 is_a: RO:0002330 ! genomically related to inverse_of: RO:0002205 ! has gene product @@ -917,7 +916,7 @@ def: "x has gene product y if and only if x is a gene (SO:0000704) that particip property_value: IAO:0000112 "every HOTAIR lncRNA is the gene product of some HOXC gene" xsd:string property_value: IAO:0000112 "every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002511 RO:0002513 is_a: RO:0002330 ! genomically related to @@ -927,7 +926,7 @@ name: expressed in def: "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" [] property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002330 ! genomically related to inverse_of: RO:0002292 ! expresses transitive_over: BFO:0000050 @@ -937,10 +936,10 @@ id: RO:0002207 name: directly develops from def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "has developmental precursor" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000119 "FBbt" xsd:string property_value: RO:0002575 RO:0002202 is_a: RO:0002202 ! develops from @@ -976,9 +975,9 @@ def: "p regulates q iff p is causally upstream of q, the execution of p is not c subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Hill" xsd:string -property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 +property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string @@ -998,7 +997,7 @@ def: "p negatively regulates q iff p regulates q, and p decreases the rate or ma subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 @@ -1014,7 +1013,7 @@ def: "p positively regulates q iff p regulates q, and p increases the rate or ma subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002211 @@ -1035,7 +1034,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" xsd:string property_value: IAO:0000116 "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants." xsd:string property_value: IAO:0000116 "TODO: add homeomorphy axiom" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 [Typedef] id: RO:0002215 @@ -1044,7 +1043,7 @@ def: "A relation between a material entity (such as a cell) and a process, in wh subset: ro-eco property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 @@ -1055,7 +1054,7 @@ is_a: RO:0002216 ! capable of part of id: RO:0002216 name: capable of part of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} @@ -1067,7 +1066,7 @@ id: RO:0002217 name: obsolete actively participates in def: "OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role" [] comment: Obsoleted as the inverse property was obsoleted. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "agent in" xsd:string is_obsolete: true replaced_by: RO:0002608 @@ -1076,7 +1075,7 @@ replaced_by: RO:0002608 id: RO:0002218 name: obsolete has active participant def: "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has agent" xsd:string is_obsolete: true replaced_by: RO:0002500 @@ -1086,7 +1085,7 @@ id: RO:0002219 name: surrounded by def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: RO:0002220 ! adjacent to inverse_of: RO:0002221 ! surrounds @@ -1104,7 +1103,7 @@ property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cy property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: RO:0002163 ! spatially disjoint from @@ -1114,7 +1113,7 @@ name: surrounds def: "inverse of surrounded by" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: RO:0002220 ! adjacent to @@ -1122,19 +1121,19 @@ is_a: RO:0002220 ! adjacent to id: RO:0002222 subset: ro-eco property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string [Typedef] id: RO:0002223 subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: BFO:0000050 [Typedef] id: RO:0002224 subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: BFO:0000051 [Typedef] @@ -1142,7 +1141,7 @@ id: RO:0002225 name: develops from part of def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002207 BFO:0000050 is_a: RO:0002202 ! develops from @@ -1151,7 +1150,7 @@ id: RO:0002226 name: develops in def: "x develops_in y if x is located in y whilst x is developing" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string holds_over_chain: RO:0002207 RO:0001025 @@ -1172,13 +1171,13 @@ is_a: RO:0002444 ! parasite of [Typedef] id: RO:0002229 subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: BFO:0000050 [Typedef] id: RO:0002230 subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: BFO:0000051 [Typedef] @@ -1187,7 +1186,7 @@ name: has start location def: "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts with process that occurs in" xsd:string holds_over_chain: RO:0002224 BFO:0000066 is_a: RO:0002479 ! has part that occurs in @@ -1198,7 +1197,7 @@ name: has end location def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends with process that occurs in" xsd:string holds_over_chain: RO:0002230 BFO:0000066 is_a: RO:0002479 ! has part that occurs in @@ -1212,7 +1211,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string holds_over_chain: RO:0002224 RO:0002233 inverse_of: RO:0002352 ! input of @@ -1226,7 +1225,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string holds_over_chain: RO:0002230 RO:0002234 inverse_of: RO:0002353 ! output of @@ -1253,7 +1252,7 @@ is_a: RO:0002444 ! parasite of id: RO:0002238 name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] -property_value: IAO:0000117 "Bill Duncan (https://orcid.org/0000-0001-9625-1899)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string [Typedef] @@ -1345,7 +1344,7 @@ name: has developmental contribution from def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000051 RO:0002202 is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002255 ! developmentally contributes to @@ -1356,7 +1355,7 @@ name: developmentally contributes to def: "inverse of has developmental contribution from" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002203 BFO:0000050 is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002385 ! has potential to developmentally contribute to @@ -1366,9 +1365,9 @@ id: RO:0002256 name: developmentally induced by def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string property_value: IAO:0000119 GO:0001759 xsd:string @@ -1382,7 +1381,7 @@ id: RO:0002257 name: developmentally induces def: "Inverse of developmentally induced by" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002386 ! has potential to developmentally induce @@ -1393,7 +1392,7 @@ def: "Candidate definition: x developmentally related to y if and only if there comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string is_a: RO:0002324 ! developmentally related to inverse_of: RO:0002286 ! developmentally succeeded by @@ -1425,7 +1424,7 @@ name: developmentally replaces def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "replaces" xsd:string is_a: RO:0002258 ! developmentally preceded by @@ -1434,7 +1433,7 @@ id: RO:0002286 name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] @@ -1442,7 +1441,7 @@ id: RO:0002287 name: part of developmental precursor of property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000050 RO:0002210 is_a: RO:0002286 ! developmentally succeeded by @@ -1452,7 +1451,7 @@ name: ubiquitously expressed in def: "x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002206 ! expressed in inverse_of: RO:0002293 ! ubiquitously expresses @@ -1461,7 +1460,7 @@ id: RO:0002292 name: expresses def: "Inverse of 'expressed in'" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002330 ! genomically related to [Typedef] @@ -1470,7 +1469,7 @@ name: ubiquitously expresses def: "inverse of ubiquiotously expressed in" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002292 ! expresses [Typedef] @@ -1479,7 +1478,7 @@ name: results in developmental progression of def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions is_a: RO:0002324 ! developmentally related to @@ -1492,7 +1491,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -1506,7 +1505,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: RO:0002234 ! has output is_a: RO:0002295 ! results in developmental progression of @@ -1522,7 +1521,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -1537,7 +1536,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -1547,7 +1546,7 @@ id: RO:0002300 name: results in disappearance of property_value: IAO:0000112 "foramen ovale closure SubClassOf results in disappearance of foramen ovale" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: RO:0002552 ! results in ending of @@ -1556,7 +1555,7 @@ id: RO:0002301 name: results in developmental regression of property_value: IAO:0000112 "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: RO:0002552 ! results in ending of @@ -1565,7 +1564,7 @@ id: RO:0002302 name: is treated by substance def: "Inverse of 'is substance that treats'" [] subset: RO:0002259 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 is_a: RO:0002410 ! causally related to inverse_of: RO:0002606 ! is substance that treats @@ -1577,7 +1576,7 @@ comment: A population of xs will possess adaptations (either evolved naturally o subset: ro-eco property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Pier Buttigieg" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string is_a: RO:0002321 ! ecologically related to @@ -1588,7 +1587,7 @@ def: "p is causally upstream of, positive effect q iff p is casually upstream of comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 is_a: RO:0002411 ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -1599,7 +1598,7 @@ name: causally upstream of, negative effect def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 is_a: RO:0002411 ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect @@ -1608,17 +1607,17 @@ is_a: RO:0004046 ! causally upstream of or within, negative effect id: RO:0002309 name: has exposure stimulus def: "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." [] -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 is_a: RO:0002244 ! related via exposure to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:35:04Z [Typedef] id: RO:0002312 name: evolutionary variant of -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002320 ! evolutionarily related to [Typedef] @@ -1628,7 +1627,7 @@ def: "Holds between p and c when p is a localization process (localization cover subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "regulates localization of" xsd:string is_a: RO:0002337 ! related via localization to is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -1638,7 +1637,7 @@ id: RO:0002314 name: characteristic of part of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 @@ -1654,7 +1653,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -1663,7 +1662,7 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure id: RO:0002320 name: evolutionarily related to def: "A relationship that holds via some environmental process" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." xsd:string [Typedef] @@ -1672,7 +1671,7 @@ name: ecologically related to def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] subset: ro-eco property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string [Typedef] @@ -1680,7 +1679,7 @@ id: RO:0002322 name: confers advantage in subset: ro-eco property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "adapted for" xsd:string is_a: RO:0002321 ! ecologically related to @@ -1688,7 +1687,7 @@ is_a: RO:0002321 ! ecologically related to id: RO:0002323 name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string property_value: RO:0001900 RO:0001901 @@ -1696,7 +1695,7 @@ property_value: RO:0001900 RO:0001901 id: RO:0002324 name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] @@ -1704,9 +1703,8 @@ id: RO:0002325 name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" xsd:string is_a: RO:0002323 ! mereotopologically related to @@ -1718,7 +1716,7 @@ property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a het property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string is_a: RO:0002216 ! capable of part of is_a: RO:0002329 ! part of structure that is capable of @@ -1729,7 +1727,7 @@ name: enables def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string property_value: IAO:0000118 "has" xsd:string @@ -1745,14 +1743,14 @@ transitive_over: RO:0002017 ! has component activity id: RO:0002328 name: functionally related to def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string [Typedef] id: RO:0002329 name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} is_a: RO:0002328 ! functionally related to @@ -1761,14 +1759,14 @@ is_a: RO:0002328 ! functionally related to id: RO:0002330 name: genomically related to def: "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" xsd:string [Typedef] id: RO:0002331 name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in @@ -1781,7 +1779,7 @@ id: RO:0002332 name: regulates levels of def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string is_a: RO:0002328 ! functionally related to @@ -1791,7 +1789,7 @@ id: RO:0002333 name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002328 ! functionally related to [Typedef] @@ -1799,7 +1797,7 @@ id: RO:0002334 name: regulated by def: "inverse of regulates" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "regulated by (processual)" xsd:string is_transitive: true is_a: RO:0002427 ! causally downstream of or within @@ -1809,7 +1807,7 @@ id: RO:0002335 name: negatively regulated by def: "inverse of negatively regulates" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002334 ! regulated by [Typedef] @@ -1817,14 +1815,14 @@ id: RO:0002336 name: positively regulated by def: "inverse of positively regulates" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002334 ! regulated by [Typedef] id: RO:0002337 name: related via localization to def: "A relationship that holds via some process of localization" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string [Typedef] @@ -1834,7 +1832,7 @@ def: "This relationship holds between p and l when p is a transport or localizat subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002344 ! results in transport to from or in transitive_over: BFO:0000050 @@ -1845,7 +1843,7 @@ def: "This relationship holds between p and l when p is a transport or localizat subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002344 ! results in transport to from or in transitive_over: BFO:0000050 @@ -1854,14 +1852,14 @@ id: RO:0002340 name: imports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002020 ! transports [Typedef] id: RO:0002341 name: results in transport along def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to [Typedef] @@ -1869,7 +1867,7 @@ id: RO:0002342 name: results in transport across def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002021 ! occurs across is_a: RO:0002344 ! results in transport to from or in @@ -1877,7 +1875,7 @@ is_a: RO:0002344 ! results in transport to from or in id: RO:0002343 name: results in growth of property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -1885,7 +1883,7 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure id: RO:0002344 name: results in transport to from or in property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to [Typedef] @@ -1893,7 +1891,7 @@ id: RO:0002345 name: exports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002020 ! transports [Typedef] @@ -1904,7 +1902,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of [Typedef] @@ -1914,7 +1912,7 @@ def: "p 'results in determination of' c if and only if p is a developmental proc subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of [Typedef] @@ -1923,7 +1921,7 @@ name: input of def: "inverse of has input" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002328 ! functionally related to [Typedef] @@ -1932,20 +1930,20 @@ name: output of def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002354 name: formed as result of -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002353 ! output of [Typedef] id: RO:0002355 name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -1956,21 +1954,21 @@ def: "The relationship linking a cell and its participation in a process that re subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of [Typedef] id: RO:0002357 name: results in developmental induction of def: "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of [Typedef] id: RO:0002360 name: has dendrite location property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002131 ! overlaps [Typedef] @@ -1978,7 +1976,7 @@ id: RO:0002371 name: attached to def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: RO:0002170 ! connected to @@ -1988,7 +1986,7 @@ is_a: RO:0002177 ! attached to part of id: RO:0002372 name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin is_a: RO:0002371 ! attached to @@ -1998,7 +1996,7 @@ is_a: RO:0002567 ! biomechanically related to id: RO:0002373 name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion is_a: RO:0002371 ! attached to @@ -2012,8 +2010,7 @@ comment: A has_fused_element B does not imply that A has_part some B: rather tha synonym: "has fused element" BROAD [] property_value: IAO:0000112 "false" xsd:boolean property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 is_a: RO:0002156 ! derived by descent from @@ -2022,7 +2019,7 @@ id: RO:0002375 name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 @@ -2038,7 +2035,7 @@ subset: ro-eco property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string @@ -2058,7 +2055,7 @@ comment: This is both a mereotopological relationship and a relationship defined subset: ro-eco property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string @@ -2071,7 +2068,7 @@ name: anabranch of def: "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." [] subset: ro-eco property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "anastomoses with" xsd:string is_a: RO:0002377 ! distributary of disjoint_from: RO:0002382 ! proper distributary of @@ -2082,7 +2079,7 @@ id: RO:0002379 name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: RO:0002131 ! overlaps @@ -2092,7 +2089,7 @@ name: branching part of def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] subset: ro-eco property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso FMA:85994 xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 holds_over_chain: RO:0002377 RO:0002381 @@ -2107,7 +2104,7 @@ def: "x main_stem_of y if y is a branching structure and x is a channel that tra subset: ro-eco property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: BFO:0000050 is_a: RO:0002375 ! in branching relationship with @@ -2118,7 +2115,7 @@ name: proper distributary of def: "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" [] subset: ro-eco property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002377 ! distributary of [Typedef] @@ -2127,7 +2124,7 @@ name: proper tributary of def: "x proper_tributary_of y iff x tributary_of y and x does not originate from y" [] subset: ro-eco property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002376 ! tributary of [Typedef] @@ -2135,7 +2132,7 @@ id: RO:0002384 name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002324 ! developmentally related to [Typedef] @@ -2143,7 +2140,7 @@ id: RO:0002385 name: has potential to developmentally contribute to def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] @@ -2151,7 +2148,7 @@ id: RO:0002386 name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] @@ -2159,7 +2156,7 @@ id: RO:0002387 name: has potential to develop into def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] @@ -2167,7 +2164,7 @@ id: RO:0002388 name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002387 ! has potential to develop into [Typedef] @@ -2176,7 +2173,7 @@ name: has direct input def: "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] property_value: IAO:0000112 "'protein catabolic process' SubClassOf has_direct_input some protein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly consumes" xsd:string property_value: IAO:0000232 "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" xsd:string holds_over_chain: RO:0002224 RO:0002400 @@ -2187,7 +2184,7 @@ id: RO:0002401 name: obsolete has indirect input comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_obsolete: true [Typedef] @@ -2196,7 +2193,7 @@ name: obsolete has direct output def: "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. " [] property_value: IAO:0000112 "translation SubClassOf has_direct_output some protein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly produces" xsd:string is_obsolete: true @@ -2205,7 +2202,7 @@ id: RO:0002403 name: obsolete has indirect output comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002411 RO:0002402 is_obsolete: true @@ -2214,7 +2211,7 @@ id: RO:0002404 name: causally downstream of def: "inverse of upstream of" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: BFO:0000062 is_a: RO:0002427 ! causally downstream of or within inverse_of: RO:0002411 ! causally upstream of @@ -2223,7 +2220,7 @@ inverse_of: RO:0002411 ! causally upstream of id: RO:0002405 name: immediately causally downstream of property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002404 ! causally downstream of inverse_of: RO:0002412 ! immediately causally upstream of @@ -2238,7 +2235,7 @@ replaced_by: RO:0002629 id: RO:0002407 name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 holds_over_chain: RO:0002409 RO:0002409 @@ -2260,7 +2257,7 @@ replaced_by: RO:0002630 id: RO:0002409 name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 holds_over_chain: RO:0002630 RO:0002409 @@ -2275,7 +2272,7 @@ id: RO:0002410 name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] @@ -2284,7 +2281,7 @@ name: causally upstream of def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: BFO:0000063 is_a: RO:0002418 ! causally upstream of or within @@ -2293,7 +2290,7 @@ is_a: RO:0002418 ! causally upstream of or within id: RO:0002412 name: immediately causally upstream of def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: RO:0002090 is_a: RO:0002411 ! causally upstream of @@ -2303,7 +2300,7 @@ id: RO:0002413 name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string @@ -2316,7 +2313,7 @@ id: RO:0002414 name: transitively provides input for def: "transitive form of directly_provides_input_for" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." xsd:string property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string is_transitive: true @@ -2328,7 +2325,7 @@ name: causally upstream of or within def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true is_a: RO:0002501 ! causal relation between processes @@ -2339,19 +2336,19 @@ id: RO:0002424 name: differs in comment: This is an exploratory relation property_value: IAO:0000116 "false" xsd:boolean -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions xsd:anyURI [Typedef] id: RO:0002425 name: differs in attribute of -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002424 ! differs in [Typedef] id: RO:0002426 name: differs in attribute -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002424 ! differs in [Typedef] @@ -2359,7 +2356,7 @@ id: RO:0002427 name: causally downstream of or within def: "inverse of causally upstream of or within" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: RO:0002501 ! causal relation between processes @@ -2368,7 +2365,7 @@ is_a: RO:0002501 ! causal relation between processes id: RO:0002428 name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002327 RO:0002211 holds_over_chain: RO:0002331 RO:0002211 is_a: RO:0002263 ! acts upstream of @@ -2378,7 +2375,7 @@ is_a: RO:0002431 ! involved in or involved in regulation of id: RO:0002429 name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002428 holds_over_chain: RO:0002327 RO:0002213 holds_over_chain: RO:0002331 RO:0002213 @@ -2388,7 +2385,7 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002430 name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 holds_over_chain: RO:0002327 RO:0002212 holds_over_chain: RO:0002331 RO:0002212 @@ -2399,7 +2396,7 @@ id: RO:0002431 name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: RO:0002264 ! acts upstream of or within is_a: RO:0002328 ! functionally related to @@ -2411,7 +2408,7 @@ name: is active in def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] synonym: "enables activity in" EXACT [] property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} is_a: RO:0002131 ! overlaps @@ -2421,7 +2418,7 @@ is_a: RO:0002328 ! functionally related to id: RO:0002433 name: contributes to morphology of def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002131 ! overlaps [Typedef] @@ -2433,7 +2430,7 @@ synonym: "in pairwise interaction with" EXACT [] property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI is_symmetric: true @@ -2443,7 +2440,7 @@ id: RO:0002435 name: genetically interacts with property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: RO:0002434 ! interacts with @@ -2453,7 +2450,7 @@ id: RO:0002436 name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 @@ -2465,7 +2462,7 @@ id: RO:0002437 name: biotically interacts with def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string @@ -2478,7 +2475,7 @@ id: RO:0002438 name: trophically interacts with def: "An interaction relationship in which the partners are related via a feeding relationship." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: RO:0002574 ! participates in a biotic-biotic interaction with @@ -2489,9 +2486,9 @@ def: "An interaction relationship involving a predation process, where the subje subset: ro-eco property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Jorrit Poelen" xsd:string -property_value: IAO:0000117 "Katja Shulz" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7134-3324 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string @@ -2504,7 +2501,7 @@ id: RO:0002440 name: symbiotically interacts with def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true @@ -2515,7 +2512,7 @@ id: RO:0002441 name: commensually interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: RO:0002440 ! symbiotically interacts with @@ -2524,7 +2521,7 @@ id: RO:0002442 name: mutualistically interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: RO:0002440 ! symbiotically interacts with @@ -2533,7 +2530,7 @@ id: RO:0002443 name: interacts with via parasite-host interaction def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: RO:0002440 ! symbiotically interacts with @@ -2544,7 +2541,7 @@ name: parasite of subset: ro-eco synonym: "direct parasite of" EXACT [] property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string is_a: RO:0002443 ! interacts with via parasite-host interaction @@ -2556,7 +2553,7 @@ id: RO:0002445 name: parasitized by subset: ro-eco synonym: "directly parasitized by" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string @@ -2570,7 +2567,7 @@ def: "A biotic interaction relationship in which one partner is an organism and subset: ro-eco synonym: "semibiotically interacts with" RELATED [] property_value: IAO:0000112 "Porifiera attaches to substrate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: RO:0002437 ! biotically interacts with @@ -2578,7 +2575,7 @@ is_a: RO:0002437 ! biotically interacts with id: RO:0002447 name: phosphorylates property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: RO:0002436 ! molecularly interacts with @@ -2587,8 +2584,8 @@ id: RO:0002448 name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0002436 ! molecularly interacts with is_a: RO:0011002 ! regulates activity of @@ -2597,8 +2594,8 @@ id: RO:0002449 name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly inhibits" xsd:string is_a: RO:0002448 ! directly regulates activity of @@ -2607,8 +2604,8 @@ id: RO:0002450 name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly activates" xsd:string is_a: RO:0002448 ! directly regulates activity of @@ -2618,21 +2615,21 @@ name: transmitted by def: "A relationship that holds between a disease and organism" [] property_value: IAO:0000112 "all dengue disease transmitted by some mosquito" xsd:string property_value: IAO:0000116 "Add domain and range constraints" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0002452 name: has symptom def: "A relation that holds between a disease or an organism and a phenotype" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002200 ! has phenotype [Typedef] id: RO:0002453 name: host of subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string is_a: RO:0002440 ! symbiotically interacts with @@ -2641,7 +2638,7 @@ id: RO:0002454 name: has host def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string is_a: RO:0002440 ! symbiotically interacts with @@ -2651,7 +2648,7 @@ name: pollinates subset: ro-eco property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string is_a: RO:0002442 ! mutualistically interacts with @@ -2661,7 +2658,7 @@ inverse_of: RO:0002456 ! pollinated by id: RO:0002456 name: pollinated by subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string @@ -2671,7 +2668,7 @@ is_a: RO:0002442 ! mutualistically interacts with id: RO:0002457 name: acquires nutrients from subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string is_a: RO:0002438 ! trophically interacts with inverse_of: RO:0002469 ! provides nutrients for @@ -2682,7 +2679,7 @@ name: preyed upon by def: "inverse of preys on" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string @@ -2694,7 +2691,7 @@ id: RO:0002459 name: is vector for subset: ro-eco property_value: IAO:0000112 "Anopheles is a vector for Plasmodium" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" xsd:string is_a: RO:0002574 ! participates in a biotic-biotic interaction with inverse_of: RO:0002460 ! has vector @@ -2703,71 +2700,71 @@ inverse_of: RO:0002460 ! has vector id: RO:0002460 name: has vector subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002461 name: partner in -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string [Typedef] id: RO:0002462 name: subject participant in -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: RO:0002461 ! partner in [Typedef] id: RO:0002463 name: target participant in -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: RO:0002461 ! partner in [Typedef] id: RO:0002464 name: helper property (not for use in curation) -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string [Typedef] id: RO:0002465 name: is symbiosis -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002563 ! interaction relation helper property [Typedef] id: RO:0002466 name: is commensalism -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002465 ! is symbiosis [Typedef] id: RO:0002467 name: is mutualism -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002465 ! is symbiosis [Typedef] id: RO:0002468 name: is parasitism -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002465 ! is symbiosis [Typedef] id: RO:0002469 name: provides nutrients for subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002438 ! trophically interacts with [Typedef] id: RO:0002470 name: eats subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: RO:0002438 ! trophically interacts with @@ -2775,7 +2772,7 @@ is_a: RO:0002438 ! trophically interacts with id: RO:0002471 name: is eaten by subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string is_a: RO:0002438 ! trophically interacts with @@ -2785,7 +2782,7 @@ id: RO:0002472 name: is evidence for def: "A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and \nthe a supports either the existence of b, or the truth value of b." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002616 ! related via evidence or inference to inverse_of: RO:0002558 ! has evidence @@ -2795,7 +2792,7 @@ name: composed primarily of def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] subset: ro-eco property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 is_a: BFO:0000051 @@ -2805,7 +2802,7 @@ id: RO:0002476 name: child nucleus of def: "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" [] property_value: IAO:0000112 "ABal nucleus child nucleus of ABa nucleus (in C elegans)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." xsd:string is_a: RO:0002258 ! developmentally preceded by @@ -2813,14 +2810,14 @@ is_a: RO:0002258 ! developmentally preceded by id: RO:0002477 name: child nucleus of in hermaphrodite def: "A child nucleus relationship in which the cells are part of a hermaphroditic organism" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002476 ! child nucleus of [Typedef] id: RO:0002478 name: child nucleus of in male def: "A child nucleus relationship in which the cells are part of a male organism" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002476 ! child nucleus of [Typedef] @@ -2828,7 +2825,7 @@ id: RO:0002479 name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} [Typedef] @@ -2836,26 +2833,26 @@ id: RO:0002480 name: ubiquitinates def: "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" [] property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002436 ! molecularly interacts with [Typedef] id: RO:0002481 name: is kinase activity -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002482 name: is ubiquitination -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002485 name: receives input from property_value: IAO:0000116 "See notes for inverse relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002170 ! connected to inverse_of: RO:0002486 ! sends output to @@ -2863,20 +2860,20 @@ inverse_of: RO:0002486 ! sends output to id: RO:0002486 name: sends output to property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002170 ! connected to [Typedef] id: RO:0002487 name: relation between physical entity and a process or stage -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." xsd:string [Typedef] id: RO:0002488 name: existence starts during def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002583 BFO:0000050 is_a: RO:0002490 ! existence overlaps is_a: RO:0002496 ! existence starts during or after @@ -2886,7 +2883,7 @@ transitive_over: BFO:0000050 id: RO:0002489 name: existence starts with def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002488 ! existence starts during [Typedef] @@ -2894,7 +2891,7 @@ id: RO:0002490 name: existence overlaps def: "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002487 ! relation between physical entity and a process or stage [Typedef] @@ -2903,7 +2900,7 @@ name: existence starts and ends during def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. synonym: "exists during" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002488 ! existence starts during is_a: RO:0002492 ! existence ends during @@ -2912,7 +2909,7 @@ id: RO:0002492 name: existence ends during def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002593 BFO:0000050 is_a: RO:0002490 ! existence overlaps is_a: RO:0002497 ! existence ends during or before @@ -2923,14 +2920,14 @@ id: RO:0002493 name: existence ends with def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002492 ! existence ends during [Typedef] id: RO:0002494 name: transformation of def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002202 ! develops from @@ -2938,7 +2935,7 @@ is_a: RO:0002202 ! develops from id: RO:0002495 name: immediate transformation of def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002494 is_a: RO:0002207 ! directly develops from is_a: RO:0002494 ! transformation of @@ -2948,7 +2945,7 @@ id: RO:0002496 name: existence starts during or after def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000050 RO:0002496 holds_over_chain: RO:0002258 RO:0002496 is_a: RO:0002487 ! relation between physical entity and a process or stage @@ -2961,7 +2958,7 @@ id: RO:0002497 name: existence ends during or before def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000050 RO:0002497 holds_over_chain: RO:0002286 RO:0002497 is_a: RO:0002487 ! relation between physical entity and a process or stage @@ -2981,7 +2978,7 @@ inverse_of: RO:0002608 ! process has causal agent id: RO:0002501 name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string is_a: RO:0002410 ! causally related to @@ -2989,7 +2986,7 @@ is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002502 name: depends on -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso BFO:0000169 [Typedef] @@ -2997,7 +2994,7 @@ id: RO:0002503 name: towards def: "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" [] property_value: IAO:0000116 "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 is_a: RO:0002502 ! depends on @@ -3007,14 +3004,14 @@ name: has intermediate def: "p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c" [] subset: ro-eco property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string [Typedef] id: RO:0002506 name: causal relation between entities property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string is_a: RO:0002410 ! causally related to @@ -3024,11 +3021,11 @@ id: RO:0002507 name: determined by def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] subset: ro-eco -property_value: http://purl.org/dc/terms/creator "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/creator "Pier Buttigieg" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-4366-3088 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "A coral reef environment is determined by a particular coral reef" xsd:string property_value: IAO:0000116 "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602 property_value: IAO:0000589 "determined by (system to material entity)" xsd:string is_a: BFO:0000050 @@ -3042,7 +3039,7 @@ name: determines def: "inverse of determined by" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "determines (material entity to system)" xsd:string is_a: RO:0002566 ! causally influences @@ -3051,7 +3048,7 @@ id: RO:0002509 name: determined by part of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002507 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002506 ! causal relation between entities @@ -3060,7 +3057,7 @@ is_a: RO:0002506 ! causal relation between entities id: RO:0002510 name: transcribed from def: "x is transcribed from y if and only if x is synthesized from template y" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to inverse_of: RO:0002511 ! transcribed to @@ -3070,7 +3067,7 @@ id: RO:0002511 name: transcribed to def: "inverse of transcribed from" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to @@ -3078,7 +3075,7 @@ is_a: RO:0002330 ! genomically related to id: RO:0002512 name: ribosomal translation of def: "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to inverse_of: RO:0002513 ! ribosomally translates to @@ -3087,7 +3084,7 @@ inverse_of: RO:0002513 ! ribosomally translates to id: RO:0002513 name: ribosomally translates to def: "inverse of ribosomal translation of" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to @@ -3096,7 +3093,7 @@ id: RO:0002514 name: sequentially related to def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string @@ -3109,7 +3106,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcript" xsd:string property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002527 ! does not overlap sequence of @@ -3119,7 +3116,7 @@ name: has start sequence def: "x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3132,7 +3129,7 @@ name: is start sequence of def: "inverse of has start sequence" [] subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3144,7 +3141,7 @@ name: has end sequence def: "x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3157,7 +3154,7 @@ name: is end sequence of def: "inverse of has end sequence" [] subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3169,7 +3166,7 @@ name: is consecutive sequence of def: "x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002524 ! has subsequence @@ -3179,7 +3176,7 @@ name: is sequentially aligned with def: "x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: RO:0002514 ! sequentially related to @@ -3189,7 +3186,7 @@ name: bounds sequence of def: "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002514 ! sequentially related to inverse_of: RO:0002523 ! is bound by sequence of @@ -3200,16 +3197,16 @@ name: is bound by sequence of def: "inverse of bounds sequence of" [] subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002514 ! sequentially related to [Typedef] id: RO:0002524 name: has subsequence -def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3224,7 +3221,7 @@ name: is subsequence of def: "inverse of has subsequence" [] subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: BFO:0000050 @@ -3234,9 +3231,9 @@ is_a: RO:0002526 ! overlaps sequence of [Typedef] id: RO:0002526 name: overlaps sequence of -def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002524 RO:0002525 is_symmetric: true is_a: RO:0002131 ! overlaps @@ -3245,9 +3242,9 @@ is_a: RO:0002514 ! sequentially related to [Typedef] id: RO:0002527 name: does not overlap sequence of -def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "disconnected from" xsd:string is_symmetric: true is_a: RO:0002514 ! sequentially related to @@ -3257,7 +3254,7 @@ id: RO:0002528 name: is upstream of sequence of def: "inverse of downstream of sequence of" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002527 ! does not overlap sequence of @@ -3266,7 +3263,7 @@ id: RO:0002529 name: is downstream of sequence of def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002527 ! does not overlap sequence of inverse_of: RO:0002529 ! is downstream of sequence of @@ -3277,7 +3274,7 @@ name: is immediately downstream of sequence of def: "x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002529 is_a: RO:0002515 ! sequentially adjacent to is_a: RO:0002529 ! is downstream of sequence of @@ -3288,7 +3285,7 @@ name: is immediately upstream of sequence of def: "inverse of immediately downstream of" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002515 ! sequentially adjacent to is_a: RO:0002528 ! is upstream of sequence of @@ -3297,7 +3294,7 @@ id: RO:0002551 name: has skeleton def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string is_a: BFO:0000051 @@ -3308,7 +3305,7 @@ is_asymmetric: true id: RO:0002552 name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -3320,7 +3317,7 @@ subset: ro-eco synonym: "epiparasite of" RELATED [] synonym: "hyperparasitoid of" NARROW [] property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string holds_over_chain: RO:0002444 RO:0002444 @@ -3336,7 +3333,7 @@ subset: RO:0002259 synonym: "has epiparasite" RELATED [] synonym: "has hyperparasite" RELATED [] synonym: "hyperparasitoidized by" RELATED [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002445 RO:0002445 is_a: RO:0002453 ! host of @@ -3344,7 +3341,7 @@ is_a: RO:0002453 ! host of id: RO:0002555 name: allelopath of subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string @@ -3354,7 +3351,7 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with id: RO:0002556 name: pathogen of subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002454 ! has host inverse_of: RO:0002557 ! has pathogen @@ -3362,7 +3359,7 @@ inverse_of: RO:0002557 ! has pathogen id: RO:0002557 name: has pathogen subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002453 ! host of [Typedef] @@ -3372,14 +3369,14 @@ def: "inverse of is evidence for" [] comment: x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/25052702 is_a: RO:0002616 ! related via evidence or inference to [Typedef] id: RO:0002559 name: causally influenced by -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: RO:0002506 ! causal relation between entities @@ -3388,7 +3385,7 @@ inverse_of: RO:0002566 ! causally influences [Typedef] id: RO:0002563 name: interaction relation helper property -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI is_a: RO:0002464 ! helper property (not for use in curation) @@ -3396,7 +3393,7 @@ is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 name: molecular interaction relation helper property -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002563 ! interaction relation helper property [Typedef] @@ -3406,7 +3403,7 @@ def: "Holds between p and c when p is locomotion process and the outcome of this subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "" xsd:string is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -3414,8 +3411,8 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure id: RO:0002566 name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string is_a: RO:0002506 ! causal relation between entities @@ -3424,7 +3421,7 @@ is_a: RO:0002506 ! causal relation between entities id: RO:0002567 name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string is_a: RO:0002328 ! functionally related to @@ -3432,7 +3429,7 @@ is_a: RO:0002328 ! functionally related to id: RO:0002568 name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string is_a: RO:0002567 ! biomechanically related to @@ -3442,7 +3439,7 @@ name: has branching part def: "inverse of branching part of" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: BFO:0000051 is_a: RO:0002375 ! in branching relationship with @@ -3452,7 +3449,7 @@ id: RO:0002570 name: conduit for def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 UBERON:cjm xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string is_a: RO:0002131 ! overlaps @@ -3462,7 +3459,7 @@ id: RO:0002571 name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:cjm xsd:string is_a: BFO:0000050 @@ -3471,7 +3468,7 @@ id: RO:0002572 name: luminal space of def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002571 ! lumen of [Typedef] @@ -3479,7 +3476,7 @@ id: RO:0002573 name: has modifier def: "A relation that holds between an attribute or a qualifier and another attribute." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." xsd:string @@ -3487,7 +3484,7 @@ property_value: IAO:0000232 "This relation is intended to be used in combination id: RO:0002574 name: participates in a biotic-biotic interaction with subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: RO:0002437 ! biotically interacts with @@ -3496,7 +3493,7 @@ id: RO:0002576 name: skeleton of def: "inverse of has skeleton" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: BFO:0000050 [Typedef] @@ -3506,7 +3503,7 @@ def: "p directly regulates q iff p is immediately causally upstream of q and p r subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string property_value: RO:0002575 RO:0002211 @@ -3524,7 +3521,7 @@ id: RO:0002584 name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000051 RO:0002215 is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process @@ -3591,7 +3588,7 @@ id: RO:0002595 name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002410 ! causally related to @@ -3857,7 +3854,7 @@ def: "a produces b if some process that occurs_in a has_output b, where a and b comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 inverse_of: RO:0003001 ! produced by [Typedef] @@ -3866,20 +3863,20 @@ name: produced by def: "a produced_by b iff some process that occurs_in b has_output a." [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 [Typedef] id: RO:0003002 name: represses expression of def: "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0002449 ! directly negatively regulates activity of [Typedef] id: RO:0003003 name: increases expression of def: "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0002450 ! directly positively regulates activity of [Typedef] @@ -3887,7 +3884,7 @@ id: RO:0003301 name: has role in modeling def: "A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." [] comment: The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate. -property_value: IAO:0000117 "Matthew Brush" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-1048-5019 property_value: IAO:0000118 "is used to study" xsd:string is_asymmetric: true @@ -3964,7 +3961,7 @@ name: condition has genetic basis in property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string is_a: RO:0002410 ! causally related to inverse_of: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:38:20Z [Typedef] @@ -3974,7 +3971,7 @@ property_value: seeAlso Orphanet:410295 property_value: seeAlso Orphanet:410296 is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004011 ! is causal gain of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:20Z [Typedef] @@ -3982,7 +3979,7 @@ id: RO:0004002 name: has material basis in loss of function germline mutation in is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004012 ! is causal loss of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:37Z [Typedef] @@ -3991,7 +3988,7 @@ name: has material basis in germline mutation in property_value: seeAlso Orphanet:317343 is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004013 ! is causal germline mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:54Z [Typedef] @@ -4000,7 +3997,7 @@ name: has material basis in somatic mutation in property_value: seeAlso Orphanet:317344 is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004014 ! is causal somatic mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z [Typedef] @@ -4008,7 +4005,7 @@ id: RO:0004005 name: has major susceptibility factor is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004015 ! is causal susceptibility factor for -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:26Z [Typedef] @@ -4016,7 +4013,7 @@ id: RO:0004006 name: has partial material basis in germline mutation in is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004016 ! is causal germline mutation partially giving rise to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:57Z [Typedef] @@ -4024,7 +4021,7 @@ id: RO:0004007 name: has primary input or output def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -4034,7 +4031,7 @@ def: "p has primary output c if (a) p has output c and (b) the goal of process i subset: http://purl.obolibrary.org/obo/valid_for_go_ontology is_a: RO:0002234 ! has output is_a: RO:0004007 ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -4044,7 +4041,7 @@ def: "p has primary input c if (a) p has input c and (b) the goal of process is subset: http://purl.obolibrary.org/obo/valid_for_go_ontology is_a: RO:0002233 ! has input is_a: RO:0004007 ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -4052,7 +4049,7 @@ id: RO:0004010 name: is genetic basis for condition property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string is_a: RO:0004018 ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:53:08Z [Typedef] @@ -4061,7 +4058,7 @@ name: is causal gain of function germline mutation of in def: "Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." [] property_value: seeAlso Orphanet:410296 is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:55:51Z [Typedef] @@ -4070,7 +4067,7 @@ name: is causal loss of function germline mutation of in def: "Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." [] property_value: seeAlso Orphanet:410295 is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:06Z [Typedef] @@ -4080,7 +4077,7 @@ def: "Relates a gene to condition, such that a mutation in this gene is sufficie property_value: seeAlso Orphanet:317343 is_a: RO:0003303 ! causes condition is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:40Z [Typedef] @@ -4090,7 +4087,7 @@ def: "Relates a gene to condition, such that a mutation in this gene is sufficie property_value: seeAlso Orphanet:317344 is_a: RO:0003303 ! causes condition is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:07Z [Typedef] @@ -4099,7 +4096,7 @@ name: is causal susceptibility factor for def: "Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]." [] property_value: seeAlso Orphanet:317345 is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:43Z [Typedef] @@ -4109,7 +4106,7 @@ def: "Relates a gene to condition, such that a mutation in this gene partially c property_value: seeAlso Orphanet:317346 is_a: RO:0003304 ! contributes to condition is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:58:43Z [Typedef] @@ -4117,14 +4114,14 @@ id: RO:0004017 name: realizable has basis in is_a: RO:0002410 ! causally related to inverse_of: RO:0004018 ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:01Z [Typedef] id: RO:0004018 name: is basis for realizable is_a: RO:0002410 ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:29Z [Typedef] @@ -4132,7 +4129,7 @@ id: RO:0004019 name: disease has basis in is_a: RO:0004017 ! realizable has basis in is_a: RO:0004023 ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:26:47Z [Typedef] @@ -4141,7 +4138,7 @@ name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string is_a: RO:0004019 ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z [Typedef] @@ -4150,7 +4147,7 @@ name: disease has basis in disruption of def: "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." [] property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string is_a: RO:0004019 ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:37:52Z [Typedef] @@ -4159,7 +4156,7 @@ name: disease has basis in feature def: "A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature." [] is_a: RO:0002200 ! has phenotype is_a: RO:0004019 ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:46:07Z [Typedef] @@ -4168,7 +4165,7 @@ name: causal relationship with disease as subject property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." xsd:string is_a: RO:0002410 ! causally related to is_a: RO:0040035 ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:50:54Z [Typedef] @@ -4179,7 +4176,7 @@ property_value: IAO:0000589 "disease causes disruption of (disease to process)" holds_over_chain: RO:0004025 RO:0002215 is_a: RO:0004023 ! causal relationship with disease as subject transitive_over: BFO:0000050 -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:51:09Z [Typedef] @@ -4188,7 +4185,7 @@ name: disease causes dysfunction of property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string is_a: RO:0004023 ! causal relationship with disease as subject transitive_over: BFO:0000050 -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z [Typedef] @@ -4198,7 +4195,7 @@ def: "A relationship between a disease and an anatomical entity where the diseas property_value: IAO:0000116 "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" xsd:string property_value: IAO:0000232 "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." xsd:string is_a: RO:0040035 ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T04:06:02Z [Typedef] @@ -4206,7 +4203,7 @@ id: RO:0004027 name: disease has inflammation site def: "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" [] is_a: RO:0004026 ! disease has location -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:37:31Z [Typedef] @@ -4215,7 +4212,7 @@ name: realized in response to stimulus def: "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." [] holds_over_chain: RO:0009501 RO:0002233 is_a: RO:0002410 ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:45:49Z [Typedef] @@ -4223,7 +4220,7 @@ id: RO:0004029 name: disease has feature def: "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." [] is_a: RO:0040035 ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:50:53Z [Typedef] @@ -4231,7 +4228,7 @@ id: RO:0004030 name: disease arises from alteration in structure def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." [] is_a: RO:0004019 ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z [Typedef] @@ -4240,7 +4237,7 @@ name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] holds_over_chain: RO:0002327 BFO:0000051 is_a: RO:0002328 ! functionally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z [Typedef] @@ -4251,7 +4248,7 @@ property_value: RO:0004049 RO:0002264 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z [Typedef] @@ -4261,7 +4258,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002264 holds_over_chain: RO:0002327 RO:0004046 is_a: RO:0002264 ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z [Typedef] @@ -4274,7 +4271,7 @@ property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of, holds_over_chain: RO:0002327 RO:0002304 is_a: RO:0002263 ! acts upstream of is_a: RO:0004032 ! acts upstream of or within, positive effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:14Z [Typedef] @@ -4287,7 +4284,7 @@ property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of, holds_over_chain: RO:0002327 RO:0002305 is_a: RO:0002263 ! acts upstream of is_a: RO:0004033 ! acts upstream of or within, negative effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:22Z [Typedef] @@ -4295,7 +4292,7 @@ id: RO:0004046 name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 is_a: RO:0002418 ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -4303,7 +4300,7 @@ id: RO:0004047 name: causally upstream of or within, positive effect property_value: RO:0004049 RO:0002418 is_a: RO:0002418 ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -4384,7 +4381,7 @@ def: "\"has substance added\" is a relation existing between a (physical) entity property_value: IAO:0000112 "muffin 'has substance added' some 'baking soda'" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." xsd:string -property_value: IAO:0000117 "Damion Dooley" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 [Typedef] id: RO:0009002 @@ -4392,7 +4389,7 @@ name: has substance removed def: "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." [] property_value: IAO:0000112 "'egg white' 'has substance removed' some 'egg yolk'" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Damion Dooley" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 [Typedef] id: RO:0009003 @@ -4400,7 +4397,7 @@ name: immersed in def: "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." [] property_value: IAO:0000112 "sardines 'immersed in' some 'oil and mustard'" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Damion Dooley" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 [Typedef] id: RO:0009004 @@ -4408,7 +4405,7 @@ name: has consumer def: "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect." [] property_value: IAO:0000112 "sardine has consumer some homo sapiens" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Damion Dooley" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 [Typedef] id: RO:0009005 @@ -4416,7 +4413,7 @@ name: has primary substance added def: "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." [] property_value: IAO:0000112 "bread 'has primary substance added' some 'flour'" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Damion Dooley" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 is_a: RO:0009001 ! has substance added [Typedef] @@ -4424,10 +4421,10 @@ id: RO:0009501 name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] synonym: "triggered by process" EXACT [RO:cjm] -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "David Osumi-Sutherland" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string @@ -4460,56 +4457,56 @@ property_value: IAO:0000119 "[072-ISO]" xsd:string id: RO:0011002 name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0002566 ! causally influences [Typedef] id: RO:0011003 name: regulates quantity of def: "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0002566 ! causally influences [Typedef] id: RO:0011004 name: indirectly regulates activity of def: "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011002 ! regulates activity of [Typedef] id: RO:0011007 name: decreases by repression quantity of def: "The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011023 ! indirectly negatively regulates quantity of [Typedef] id: RO:0011008 name: increases by expression quantity of def: "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011024 ! indirectly positively regulates quantity of [Typedef] id: RO:0011009 name: directly positively regulates quantity of def: "The entity A has an activity that directly positively regulates the quantity of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011021 ! directly regulates quantity of [Typedef] id: RO:0011010 name: directly negatively regulates quantity of def: "The entity A has an activity that directly negatively regulates the quantity of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011021 ! directly regulates quantity of [Typedef] id: RO:0011013 name: indirectly positively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly activates" xsd:string is_a: RO:0011004 ! indirectly regulates activity of @@ -4518,7 +4515,7 @@ id: RO:0011014 name: destabilizes quantity of def: "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." [] property_value: IAO:0000112 "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011010 ! directly negatively regulates quantity of [Typedef] @@ -4526,14 +4523,14 @@ id: RO:0011015 name: stabilizes quantity of def: "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." [] property_value: IAO:0000112 "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011009 ! directly positively regulates quantity of [Typedef] id: RO:0011016 name: indirectly negatively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly inhibits" xsd:string is_a: RO:0011004 ! indirectly regulates activity of @@ -4541,28 +4538,28 @@ is_a: RO:0011004 ! indirectly regulates activity of id: RO:0011021 name: directly regulates quantity of def: "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011003 ! regulates quantity of [Typedef] id: RO:0011022 name: indirectly regulates quantity of def: "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011003 ! regulates quantity of [Typedef] id: RO:0011023 name: indirectly negatively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011022 ! indirectly regulates quantity of [Typedef] id: RO:0011024 name: indirectly positively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011022 ! indirectly regulates quantity of [Typedef] @@ -4781,7 +4778,7 @@ name: has exemplar data def: "A relation between a material entity and some data in which the data is taken as exemplifying the material entity." [] property_value: IAO:0000112 "transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data])" xsd:string property_value: IAO:0000116 "C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C." xsd:string -property_value: IAO:0000117 "Patrick Ray" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-5260-9315 property_value: IAO:0000232 "This relation is not meant to capture the relation between occurrents and data." xsd:string inverse_of: RO:0015002 ! exemplar data of transitive_over: RO:0015003 ! subcluster of @@ -4789,14 +4786,14 @@ transitive_over: RO:0015003 ! subcluster of [Typedef] id: RO:0015002 name: exemplar data of -property_value: IAO:0000117 "Patrick Ray" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-5260-9315 [Typedef] id: RO:0015003 name: subcluster of def: "A relation between a group and another group it is part of but does not fully constitute." [] property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." xsd:string -property_value: IAO:0000117 "Shawn Tan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true is_a: BFO:0000050 @@ -4883,7 +4880,7 @@ property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:s id: RO:0016002 name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string is_a: RO:0016001 ! has phenotype or disease @@ -4903,8 +4900,8 @@ name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 +property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string holds_over_chain: RO:0002215 RO:0002233 @@ -4996,13 +4993,13 @@ id: RO:0040035 name: disease relationship def: "This relation groups relations between diseases and any other kind of entity." [] property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z [Typedef] id: RO:0040036 name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z diff --git a/src/ontology/subsets/ro-eco.owl b/src/ontology/subsets/ro-eco.owl index 6f1e3fe7..f85e1f99 100644 --- a/src/ontology/subsets/ro-eco.owl +++ b/src/ontology/subsets/ro-eco.owl @@ -147,7 +147,7 @@ tooth SubClassOf 'never in taxon' value 'Aves' x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. - Chris Mungall + Class: ?X DisjointWith: RO_0002162 some ?Y @@ -242,7 +242,7 @@ WHERE { S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. - https://orcid.org/0000-0002-6601-2165 + This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost dubious for taxon @@ -256,7 +256,7 @@ WHERE { S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S - https://orcid.org/0000-0002-6601-2165 + PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> @@ -631,7 +631,7 @@ Where we have an annotation assertion "directly P" "is direct form of" "P" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' - Chris Mungall + is direct form of @@ -643,7 +643,7 @@ Where we have an annotation assertion relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y - Chris Mungall + is indirect form of @@ -791,7 +791,7 @@ Where we have an annotation assertion true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation. - cjm + nominally disjoint with @@ -802,7 +802,7 @@ Where we have an annotation assertion Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" - cjm + 2018-03-13T23:59:29Z is directional form of @@ -813,7 +813,7 @@ Where we have an annotation assertion - cjm + 2018-03-14T00:03:16Z is positive form of @@ -824,7 +824,7 @@ Where we have an annotation assertion - cjm + 2018-03-14T00:03:24Z is negative form of @@ -837,7 +837,7 @@ Where we have an annotation assertion part-of is homeomorphic for independent continuants. R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. - cjm + 2018-10-21T19:46:34Z R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. is homeomorphic for @@ -1161,7 +1161,7 @@ Where we have an annotation assertion OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. - David Osumi-Sutherland + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). @@ -1177,7 +1177,7 @@ Where we have an annotation assertion OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first. - David Osumi-Sutherland + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). @@ -1193,7 +1193,7 @@ Where we have an annotation assertion OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first. - David Osumi-Sutherland + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). @@ -1308,7 +1308,7 @@ range: spatial region or site (immaterial continuant) May be obsoleted, see https://github.com/oborel/obo-relations/issues/260 - David Osumi-Sutherland + aligned with @@ -1319,7 +1319,7 @@ range: spatial region or site (immaterial continuant) - David Osumi-Sutherland + @@ -1329,7 +1329,7 @@ range: spatial region or site (immaterial continuant) A relation that holds between two neurons that are electrically coupled via gap junctions. - David Osumi-Sutherland + electrically_synapsed_to @@ -1341,7 +1341,7 @@ range: spatial region or site (immaterial continuant) The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). - David Osumi-Sutherland + tracheates @@ -1351,7 +1351,7 @@ range: spatial region or site (immaterial continuant) - David Osumi-Sutherland + http://www.ncbi.nlm.nih.gov/pubmed/22402613 innervated_by @@ -1363,7 +1363,7 @@ range: spatial region or site (immaterial continuant) - David Osumi-Sutherland + has synaptic terminal of @@ -1383,7 +1383,7 @@ range: spatial region or site (immaterial continuant) has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland + A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. bounding layer of @@ -1397,7 +1397,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. Note from NCEAS meeting: consider changing primary label - David Osumi-Sutherland + Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. coincident with @@ -1410,7 +1410,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g. - David Osumi-Sutherland + x 'cell expresses' y iff: cell(x) AND gene(y) @@ -1427,7 +1427,7 @@ AND t has_input y x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - David Osumi-Sutherland + regulates in other organism @@ -1441,7 +1441,7 @@ AND t has_input y A relationship that holds between a process that regulates a transport process and the entity transported by that process. - David Osumi-Sutherland + regulates transport of @@ -1685,7 +1685,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + @@ -1697,7 +1697,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + di Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. encompasses @@ -1720,7 +1720,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + @@ -1757,7 +1757,7 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure that its soma is part of. - David Osumi-Sutherland + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -1774,7 +1774,7 @@ Examples include: the relationship between two channels collected simultaneously relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - David Osumi-Sutherland + fasciculates with (forall (?x ?y) (iff @@ -1813,9 +1813,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure its axon forms (chemical) synapses in. - Chris Mungall - David Osumi-Sutherland - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -1834,8 +1833,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -1851,9 +1850,9 @@ Examples include: the relationship between two channels collected simultaneously Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - Alexander Diehl - Chris Mungall - Lindsay Cowell + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) @@ -1869,8 +1868,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -1887,8 +1886,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -1905,8 +1904,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) @@ -1921,8 +1920,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1939,8 +1938,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1961,8 +1960,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - Chris Mungall - David Osumi-Sutherland + + synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( @@ -1990,8 +1989,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -2057,8 +2056,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -2086,8 +2085,8 @@ N1 SubclassOf ( Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -2109,7 +2108,7 @@ N1 SubclassOf ( A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - David Osumi-Sutherland + has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) @@ -2167,7 +2166,7 @@ N1 SubclassOf ( The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - David Osumi-Sutherland + has fasciculating component (forall (?x ?y) (iff @@ -2210,7 +2209,7 @@ N1 SubclassOf ( Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - David Osumi-Sutherland + <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -2226,7 +2225,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. X continuous_with Y if and only if X and Y share a fiat boundary. - David Osumi-Sutherland + connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) @@ -2327,7 +2326,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria - Chris Mungall + only in taxon @@ -2378,8 +2377,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - Chris Mungall - Jennifer Deegan + + @@ -2397,7 +2396,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - Chris Mungall + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) @@ -2516,7 +2515,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - Chris Mungall + has phenotype @@ -2529,7 +2528,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of has phenotype - Chris Mungall + phenotype of @@ -2545,10 +2544,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - Terry Meehan + + + + This is the transitive form of the develops from relation develops from @@ -2564,9 +2563,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of develops from - Chris Mungall - David Osumi-Sutherland - Terry Meehan + + + develops into @@ -2585,7 +2584,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x" We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g. - Chris Mungall + gene product of @@ -2603,7 +2602,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y - Chris Mungall + has gene product @@ -2621,7 +2620,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.'neural crest cell' SubClassOf expresses some 'Wnt1 gene' x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process - Chris Mungall + expressed in @@ -2634,11 +2633,11 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - Chris Mungall - David Osumi-Sutherland - has developmental precursor + + FBbt + has developmental precursor TODO - add child relations from DOS directly develops from @@ -2699,9 +2698,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - Chris Mungall - David Hill - Tanya Berardini + + + GO Regulation precludes parthood; the regulatory process may not be within the regulated process. @@ -2726,7 +2725,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - Chris Mungall + negatively regulates (process to process) @@ -2754,7 +2753,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - Chris Mungall + positively regulates (process to process) @@ -2776,7 +2775,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) TODO: add homeomorphy axiom This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. - Chris Mungall + has prototype @@ -2789,7 +2788,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - Chris Mungall + has function realized in @@ -2810,7 +2809,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - Chris Mungall + has function in capable of part of @@ -2831,7 +2830,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role - Chris Mungall + agent in Obsoleted as the inverse property was obsoleted. @@ -2845,7 +2844,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. OBSOLETE x has participant y if and only if x realizes some active role that inheres in y - Chris Mungall + has agent obsolete has active participant @@ -2861,7 +2860,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - Chris Mungall + surrounded by @@ -2879,7 +2878,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - Chris Mungall + @@ -2901,7 +2900,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of surrounded by - Chris Mungall + surrounds @@ -2912,7 +2911,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 @@ -2924,7 +2923,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Chris Mungall + @@ -2934,7 +2933,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Chris Mungall + @@ -2950,7 +2949,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - Chris Mungall + develops from part of @@ -2966,7 +2965,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x develops_in y if x is located in y whilst x is developing - Chris Mungall + EHDAA2 Jonathan Bard, EHDAA2 develops in @@ -2998,7 +2997,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Chris Mungall + @@ -3008,7 +3007,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Chris Mungall + @@ -3024,7 +3023,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - Chris Mungall + starts with process that occurs in has start location @@ -3042,7 +3041,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - Chris Mungall + ends with process that occurs in has end location @@ -3060,7 +3059,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + consumes @@ -3081,7 +3080,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - Chris Mungall + produces @@ -3126,7 +3125,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - Bill Duncan (https://orcid.org/0000-0001-9625-1899) + This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. @@ -3274,7 +3273,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y - Chris Mungall + has developmental contribution from @@ -3291,7 +3290,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho inverse of has developmental contribution from - Chris Mungall + developmentally contributes to @@ -3305,9 +3304,9 @@ If you need an axiom that says 'has_participant min 2 object', you sho t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - Chris Mungall - David Osumi-Sutherland - Melissa Haendel + + + induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) @@ -3325,7 +3324,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally induced by - Chris Mungall + developmentally induces @@ -3339,7 +3338,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - Chris Mungall + In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by @@ -3389,7 +3388,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - Chris Mungall + replaces developmentally replaces @@ -3402,7 +3401,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally preceded by - Chris Mungall + developmentally succeeded by @@ -3418,7 +3417,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - Chris Mungall + part of developmental precursor of @@ -3432,7 +3431,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part. - Chris Mungall + ubiquitously expressed in @@ -3444,7 +3443,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of 'expressed in' - Chris Mungall + expresses @@ -3456,7 +3455,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho inverse of ubiquiotously expressed in - Chris Mungall + ubiquitously expresses @@ -3470,7 +3469,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - Chris Mungall + results in developmental progression of @@ -3485,7 +3484,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - Chris Mungall + http://www.geneontology.org/GO.doc.development.shtml @@ -3504,7 +3503,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - Chris Mungall + GOC:mtg_berkeley_2013 @@ -3523,7 +3522,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - Chris Mungall + GOC:mtg_berkeley_2013 @@ -3542,7 +3541,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - Chris Mungall + GOC:mtg_berkeley_2013 @@ -3558,7 +3557,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho foramen ovale closure SubClassOf results in disappearance of foramen ovale - Chris Mungall + May be merged into parent relation results in disappearance of @@ -3571,7 +3570,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) - Chris Mungall + May be merged into parent relation results in developmental regression of @@ -3584,7 +3583,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of 'is substance that treats' - cjm + is treated by substance @@ -3600,7 +3599,7 @@ where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. - Pier Buttigieg + adapted for living in A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. @@ -3616,7 +3615,7 @@ where p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - cjm + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y @@ -3632,7 +3631,7 @@ where p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - cjm + causally upstream of, negative effect @@ -3645,10 +3644,10 @@ where A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. - Austin Meier - Chris Mungall - Marie Angelique Laporte - cjm + + + + 2017-06-05T17:35:04Z has exposure stimulus @@ -3659,7 +3658,7 @@ where - Chris Mungall + evolutionary variant of @@ -3671,7 +3670,7 @@ where Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. - Chris Mungall + regulates localization of @@ -3691,7 +3690,7 @@ where q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of - Chris Mungall + inheres in part of @@ -3708,7 +3707,7 @@ where an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - Chris Mungall + GOC:mtg_berkeley_2013 @@ -3722,7 +3721,7 @@ where A relationship that holds via some environmental process - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to @@ -3734,7 +3733,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions ecologically related to @@ -3747,7 +3746,7 @@ where An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. - Chris Mungall + adapted for confers advantage in @@ -3759,7 +3758,7 @@ where A mereological relationship or a topological relationship - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to @@ -3771,7 +3770,7 @@ where A relationship that holds between entities participating in some developmental process (GO:0032502) - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to @@ -3784,9 +3783,8 @@ where Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. - Chris Mungall + In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - Gene Ontology Consortium colocalizes with @@ -3812,7 +3810,7 @@ then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. - Chris Mungall + In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. contributes to @@ -3835,7 +3833,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - Chris Mungall + catalyzes executes has @@ -3852,7 +3850,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to @@ -3868,7 +3866,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati this relation holds between c and p when c is part of some c', and c' is capable of p. - Chris Mungall + false part of structure that is capable of @@ -3888,7 +3886,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism genomically related to @@ -3908,7 +3906,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati c involved_in p if and only if c enables some process p', and p' is part of p - Chris Mungall + actively involved in enables part of involved in @@ -3923,7 +3921,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - Chris Mungall + regulates levels of (process to entity) regulates levels of @@ -3936,7 +3934,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables - Chris Mungall + enabled by @@ -3949,7 +3947,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of regulates - Chris Mungall + regulated by (processual) regulated by @@ -3962,7 +3960,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of negatively regulates - Chris Mungall + negatively regulated by @@ -3974,7 +3972,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of positively regulates - Chris Mungall + positively regulated by @@ -3985,7 +3983,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds via some process of localization - Chris Mungall + Do not use this relation directly. It is a grouping relation. related via localization to @@ -4001,7 +3999,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - Chris Mungall + @@ -4019,7 +4017,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - Chris Mungall + @@ -4033,7 +4031,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. - Chris Mungall + imports @@ -4045,7 +4043,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - Chris Mungall + results in transport along @@ -4057,7 +4055,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - Chris Mungall + results in transport across @@ -4070,7 +4068,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'pollen tube growth' results_in growth_of some 'pollen tube' - Chris Mungall + results in growth of @@ -4081,7 +4079,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - Chris Mungall + results in transport to from or in @@ -4092,7 +4090,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. - Chris Mungall + exports @@ -4105,7 +4103,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - Chris Mungall + @@ -4119,7 +4117,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - Chris Mungall + @@ -4133,7 +4131,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has input - Chris Mungall + input of @@ -4146,7 +4144,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has output - Chris Mungall + output of @@ -4158,7 +4156,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + formed as result of @@ -4170,7 +4168,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. - Chris Mungall + results in structural organization of @@ -4181,7 +4179,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - Chris Mungall + @@ -4195,7 +4193,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. - Chris Mungall + results in developmental induction of @@ -4205,7 +4203,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + http://neurolex.org/wiki/Property:DendriteLocation has dendrite location @@ -4219,7 +4217,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - Chris Mungall + attached to (anatomical structure to anatomical structure) attached to @@ -4233,7 +4231,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - Chris Mungall + Wikipedia:Insertion_(anatomy) has muscle origin @@ -4247,7 +4245,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - Chris Mungall + Wikipedia:Insertion_(anatomy) has muscle insertion @@ -4262,8 +4260,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati false x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat - Chris Mungall - Chris Mungall + has fused element A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. @@ -4278,7 +4275,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) @@ -4298,7 +4295,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - Chris Mungall + drains into drains to tributary channel of @@ -4321,7 +4318,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Deschutes River distributary_of Little Lava Lake x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - Chris Mungall + branch of distributary channel of http://en.wikipedia.org/wiki/Distributary @@ -4345,7 +4342,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. - Chris Mungall + anastomoses with anabranch of @@ -4365,7 +4362,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - Chris Mungall + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with @@ -4384,7 +4381,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - Chris Mungall + branching part of @@ -4401,7 +4398,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. - Chris Mungall + main stem of @@ -4415,7 +4412,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_distributary_of y iff x distributary_of y and x does not flow back into y - Chris Mungall + proper distributary of @@ -4428,7 +4425,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_tributary_of y iff x tributary_of y and x does not originate from y - Chris Mungall + proper tributary of @@ -4441,7 +4438,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - Chris Mungall + has developmental potential involving @@ -4453,7 +4450,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - Chris Mungall + has potential to developmentally contribute to @@ -4465,7 +4462,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - Chris Mungall + has potential to developmentally induce @@ -4477,7 +4474,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has the potential to develop into y iff x develops into y or if x is capable of developing into y - Chris Mungall + has potential to develop into @@ -4489,7 +4486,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - Chris Mungall + has potential to directly develop into @@ -4506,7 +4503,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' has direct input @@ -4518,7 +4515,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit obsolete has indirect input @@ -4533,7 +4530,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ translation SubClassOf has_direct_output some protein p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. - Chris Mungall + directly produces obsolete has direct output true @@ -4549,7 +4546,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - Chris Mungall + Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit obsolete has indirect output @@ -4566,7 +4563,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ inverse of upstream of - Chris Mungall + causally downstream of @@ -4578,7 +4575,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - Chris Mungall + immediately causally downstream of @@ -4618,7 +4615,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - Chris Mungall + indirectly activates indirectly positively regulates @@ -4656,7 +4653,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - Chris Mungall + indirectly inhibits indirectly negatively regulates @@ -4683,7 +4680,7 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to @@ -4703,7 +4700,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - Chris Mungall + causally upstream of @@ -4717,7 +4714,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - Chris Mungall + immediately causally upstream of @@ -4735,7 +4732,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit - Chris Mungall + directly provides input for directly provides input for (process to process) @@ -4751,7 +4748,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different transitive form of directly_provides_input_for - Chris Mungall + This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. transitively provides input for (process to process) transitively provides input for @@ -4767,7 +4764,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall + influences (processual) affects causally upstream of or within @@ -4779,7 +4776,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different false - Chris Mungall + This is an exploratory relation differs in https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions @@ -4791,7 +4788,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + differs in attribute of @@ -4801,7 +4798,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + differs in attribute @@ -4813,7 +4810,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - Chris Mungall + causally downstream of or within @@ -4835,7 +4832,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - Chris Mungall + involved in regulation of @@ -4854,7 +4851,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - Chris Mungall + involved in positive regulation of @@ -4874,7 +4871,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - Chris Mungall + involved in negative regulation of @@ -4889,7 +4886,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - Chris Mungall + involved in or reguates involved in or involved in regulation of @@ -4907,7 +4904,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall + executes activity in enables activity in @@ -4937,7 +4934,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - Chris Mungall + contributes to morphology of @@ -4950,7 +4947,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. - Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with @@ -4967,7 +4964,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) - Chris Mungall + genetically interacts with http://purl.obolibrary.org/obo/MI_0208 @@ -4981,7 +4978,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - Chris Mungall + binds molecularly binds with molecularly interacts with @@ -4998,7 +4995,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - Chris Mungall + interacts with on organism level biotically interacts with @@ -5013,7 +5010,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the partners are related via a feeding relationship. - Chris Mungall + trophically interacts with @@ -5029,9 +5026,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] Baleen whale preys on krill An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - Chris Mungall - Jorrit Poelen - Katja Shulz + + + is subject of predation interaction with preys upon @@ -5055,7 +5052,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A biotic interaction in which the two organisms live together in more or less intimate association. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism @@ -5076,7 +5073,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 commensually interacts with @@ -5096,7 +5093,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 mutualistically interacts with @@ -5116,7 +5113,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 This relation groups a pair of inverse relations, parasite of and parasitized by @@ -5139,7 +5136,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human - Chris Mungall + parasitizes direct parasite of @@ -5154,7 +5151,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + has parasite parasitised by directly parasitized by @@ -5171,7 +5168,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - Chris Mungall + semibiotically interacts with participates in a abiotic-biotic interaction with @@ -5190,7 +5187,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates @@ -5210,8 +5207,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - Chris Mungall - Vasundra Touré + + molecularly controls directly regulates activity of @@ -5229,8 +5226,8 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly inhibits molecularly decreases activity of directly negatively regulates activity of @@ -5249,8 +5246,8 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly activates molecularly increases activity of directly positively regulates activity of @@ -5265,7 +5262,7 @@ For example, A and B may be gene products and binding of B by A positively regul all dengue disease transmitted by some mosquito A relationship that holds between a disease and organism Add domain and range constraints - Chris Mungall + transmitted by @@ -5276,7 +5273,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between a disease or an organism and a phenotype - Chris Mungall + has symptom @@ -5286,7 +5283,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) host of @@ -5299,7 +5296,7 @@ For example, A and B may be gene products and binding of B by A positively regul X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y - Chris Mungall + has host http://eol.org/schema/terms/hasHost @@ -5314,7 +5311,7 @@ For example, A and B may be gene products and binding of B by A positively regul Bees pollinate Flowers This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - Chris Mungall + is subject of pollination interaction with pollinates @@ -5327,7 +5324,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + has polinator is target of pollination interaction with @@ -5342,7 +5339,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. acquires nutrients from @@ -5355,7 +5352,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of preys on - Chris Mungall + has predator is target of predation interaction with @@ -5373,7 +5370,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anopheles is a vector for Plasmodium - Chris Mungall + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism is vector for @@ -5385,7 +5382,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + has vector @@ -5395,7 +5392,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target partner in @@ -5406,7 +5403,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. subject participant in @@ -5417,7 +5414,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. target participant in @@ -5427,7 +5424,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) @@ -5438,7 +5435,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is symbiosis @@ -5448,7 +5445,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is commensalism @@ -5458,7 +5455,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is mutualism @@ -5468,7 +5465,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is parasitism @@ -5478,7 +5475,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + provides nutrients for @@ -5489,7 +5486,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is subject of eating interaction with eats @@ -5501,7 +5498,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + eaten by is target of eating interaction with @@ -5517,7 +5514,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and the a supports either the existence of b, or the truth value of b. - Chris Mungall + is evidence for @@ -5530,7 +5527,7 @@ the a supports either the existence of b, or the truth value of b. 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - Chris Mungall + @@ -5545,7 +5542,7 @@ the a supports either the existence of b, or the truth value of b. ABal nucleus child nucleus of ABa nucleus (in C elegans) c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d - Chris Mungall + This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. child nucleus of @@ -5557,7 +5554,7 @@ the a supports either the existence of b, or the truth value of b. A child nucleus relationship in which the cells are part of a hermaphroditic organism - Chris Mungall + child nucleus of in hermaphrodite @@ -5568,7 +5565,7 @@ the a supports either the existence of b, or the truth value of b. A child nucleus relationship in which the cells are part of a male organism - Chris Mungall + child nucleus of in male @@ -5582,7 +5579,7 @@ the a supports either the existence of b, or the truth value of b. p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall + has part that occurs in @@ -5609,7 +5606,7 @@ the a supports either the existence of b, or the truth value of b. An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y Axiomatization to GO to be added later - Chris Mungall + ubiquitinates @@ -5619,7 +5616,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + is kinase activity @@ -5629,7 +5626,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + is ubiquitination @@ -5641,7 +5638,7 @@ the a supports either the existence of b, or the truth value of b. See notes for inverse relation - Chris Mungall + receives input from @@ -5652,7 +5649,7 @@ the a supports either the existence of b, or the truth value of b. This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - Chris Mungall + sends output to @@ -5661,7 +5658,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. relation between physical entity and a process or stage @@ -5682,7 +5679,7 @@ the a supports either the existence of b, or the truth value of b. x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). - Chris Mungall + existence starts during @@ -5693,7 +5690,7 @@ the a supports either the existence of b, or the truth value of b. x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). - Chris Mungall + existence starts with @@ -5704,7 +5701,7 @@ the a supports either the existence of b, or the truth value of b. x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) - Chris Mungall + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps @@ -5717,7 +5714,7 @@ the a supports either the existence of b, or the truth value of b. x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) - Chris Mungall + exists during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts and ends during @@ -5739,7 +5736,7 @@ the a supports either the existence of b, or the truth value of b. x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). - Chris Mungall + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during @@ -5751,7 +5748,7 @@ the a supports either the existence of b, or the truth value of b. x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). - Chris Mungall + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with @@ -5764,7 +5761,7 @@ the a supports either the existence of b, or the truth value of b. x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - Chris Mungall + transformation of @@ -5776,7 +5773,7 @@ the a supports either the existence of b, or the truth value of b. x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - Chris Mungall + immediate transformation of @@ -5815,7 +5812,7 @@ the a supports either the existence of b, or the truth value of b. x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). - Chris Mungall + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after @@ -5854,7 +5851,7 @@ the a supports either the existence of b, or the truth value of b. x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. - Chris Mungall + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before @@ -5878,7 +5875,7 @@ the a supports either the existence of b, or the truth value of b. p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes @@ -5889,7 +5886,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + depends on @@ -5902,7 +5899,7 @@ the a supports either the existence of b, or the truth value of b. q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. - Chris Mungall + towards @@ -5914,7 +5911,7 @@ the a supports either the existence of b, or the truth value of b. 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c - Chris Mungall + has intermediate product has intermediate @@ -5927,7 +5924,7 @@ the a supports either the existence of b, or the truth value of b. The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities @@ -5945,11 +5942,11 @@ the a supports either the existence of b, or the truth value of b.A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future - Chris Mungall + determined by (system to material entity) - Chris Mungall - Pier Buttigieg + + determined by @@ -5961,7 +5958,7 @@ the a supports either the existence of b, or the truth value of b. inverse of determined by - Chris Mungall + determines (material entity to system) @@ -5980,7 +5977,7 @@ the a supports either the existence of b, or the truth value of b. s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. - Chris Mungall + determined by part of @@ -6002,7 +5999,7 @@ the a supports either the existence of b, or the truth value of b. x is transcribed from y if and only if x is synthesized from template y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 transcribed from @@ -6014,7 +6011,7 @@ the a supports either the existence of b, or the truth value of b. inverse of transcribed from - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 transcribed to @@ -6028,7 +6025,7 @@ the a supports either the existence of b, or the truth value of b. x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 ribosomal translation of @@ -6040,7 +6037,7 @@ the a supports either the existence of b, or the truth value of b. inverse of ribosomal translation of - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 ribosomally translates to @@ -6051,7 +6048,7 @@ the a supports either the existence of b, or the truth value of b. A relation that holds between two entities that have the property of being sequences or having sequences. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. @@ -6069,7 +6066,7 @@ the a supports either the existence of b, or the truth value of b.Two consecutive DNA residues are sequentially adjacent Two exons on a processed transcript that were previously connected by an intron are adjacent x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 sequentially adjacent to @@ -6085,7 +6082,7 @@ the a supports either the existence of b, or the truth value of b. Every CDS has as a start sequence the start codon for that transcript x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence - Chris Mungall + started by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6100,7 +6097,7 @@ the a supports either the existence of b, or the truth value of b. inverse of has start sequence - Chris Mungall + starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6118,7 +6115,7 @@ the a supports either the existence of b, or the truth value of b. Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence - Chris Mungall + ended by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6133,7 +6130,7 @@ the a supports either the existence of b, or the truth value of b. inverse of has end sequence - Chris Mungall + ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6149,7 +6146,7 @@ the a supports either the existence of b, or the truth value of b. x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. In the SO paper, this was defined as an instance-type relation - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 is consecutive sequence of @@ -6164,7 +6161,7 @@ the a supports either the existence of b, or the truth value of b. Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering - Chris Mungall + is sequentially aligned with @@ -6179,7 +6176,7 @@ the a supports either the existence of b, or the truth value of b. The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y - Chris Mungall + bounds sequence of @@ -6192,7 +6189,7 @@ the a supports either the existence of b, or the truth value of b. inverse of bounds sequence of - Chris Mungall + is bound by sequence of @@ -6208,8 +6205,8 @@ the a supports either the existence of b, or the truth value of b. - x has subsequence y iff all of the sequence parts of x are sequence parts of y - Chris Mungall + x has subsequence y iff all of the sequence parts of y are sequence parts of x + contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6226,7 +6223,7 @@ the a supports either the existence of b, or the truth value of b. inverse of has subsequence - Chris Mungall + contained by @@ -6245,8 +6242,8 @@ the a supports either the existence of b, or the truth value of b. - x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. - Chris Mungall + x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. + overlaps sequence of @@ -6258,8 +6255,8 @@ the a supports either the existence of b, or the truth value of b. - x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. - Chris Mungall + x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + disconnected from does not overlap sequence of @@ -6273,7 +6270,7 @@ the a supports either the existence of b, or the truth value of b. inverse of downstream of sequence of - Chris Mungall + is upstream of sequence of @@ -6287,7 +6284,7 @@ the a supports either the existence of b, or the truth value of b. x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. - Chris Mungall + is downstream of sequence of @@ -6301,7 +6298,7 @@ the a supports either the existence of b, or the truth value of b. A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y - Chris Mungall + is immediately downstream of sequence of @@ -6316,7 +6313,7 @@ the a supports either the existence of b, or the truth value of b. A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript inverse of immediately downstream of - Chris Mungall + is immediately upstream of sequence of @@ -6332,7 +6329,7 @@ the a supports either the existence of b, or the truth value of b. Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - Chris Mungall + has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). has skeleton @@ -6346,7 +6343,7 @@ the a supports either the existence of b, or the truth value of b. p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. - Chris Mungall + results in ending of @@ -6363,7 +6360,7 @@ the a supports either the existence of b, or the truth value of b. x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - Chris Mungall + http://eol.org/schema/terms/hyperparasitoidOf https://en.wikipedia.org/wiki/Hyperparasite hyperparasitoid of @@ -6383,7 +6380,7 @@ the a supports either the existence of b, or the truth value of b. inverse of hyperparasite of - Chris Mungall + has epiparasite has hyperparasite hyperparasitoidized by @@ -6398,7 +6395,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + http://en.wikipedia.org/wiki/Allelopathy allelopath of @@ -6413,7 +6410,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + pathogen of @@ -6424,7 +6421,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + has pathogen @@ -6436,7 +6433,7 @@ the a supports either the existence of b, or the truth value of b. inverse of is evidence for - Chris Mungall + @@ -6451,7 +6448,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + causally influenced by (entity-centric) causally influenced by @@ -6463,7 +6460,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ @@ -6475,7 +6472,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + molecular interaction relation helper property @@ -6486,7 +6483,7 @@ the a supports either the existence of b, or the truth value of b. Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - Chris Mungall + @@ -6511,8 +6508,8 @@ the a supports either the existence of b, or the truth value of b. The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - Chris Mungall - Vasundra Touré + + causally influences (entity-centric) causally influences @@ -6525,7 +6522,7 @@ the a supports either the existence of b, or the truth value of b. A relation that holds between elements of a musculoskeletal system or its analogs. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. biomechanically related to @@ -6537,7 +6534,7 @@ the a supports either the existence of b, or the truth value of b. m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - Chris Mungall + Wikipedia:Antagonist_(muscle) has muscle antagonist @@ -6551,7 +6548,7 @@ the a supports either the existence of b, or the truth value of b. inverse of branching part of - Chris Mungall + has branching part @@ -6564,7 +6561,7 @@ the a supports either the existence of b, or the truth value of b. x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - Chris Mungall + UBERON:cjm This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. @@ -6578,7 +6575,7 @@ the a supports either the existence of b, or the truth value of b. x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - Chris Mungall + GOC:cjm lumen of @@ -6591,7 +6588,7 @@ the a supports either the existence of b, or the truth value of b. s is luminal space of x iff s is lumen_of x and s is an immaterial entity - Chris Mungall + luminal space of @@ -6602,7 +6599,7 @@ the a supports either the existence of b, or the truth value of b. A relation that holds between an attribute or a qualifier and another attribute. - Chris Mungall + This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. @@ -6615,7 +6612,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + participates in a biotic-biotic interaction with @@ -6628,7 +6625,7 @@ the a supports either the existence of b, or the truth value of b. inverse of has skeleton - Chris Mungall + skeleton of @@ -6641,7 +6638,7 @@ the a supports either the existence of b, or the truth value of b. p directly regulates q iff p is immediately causally upstream of q and p regulates q. - Chris Mungall + directly regulates (processual) @@ -6674,7 +6671,7 @@ the a supports either the existence of b, or the truth value of b. gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - Chris Mungall + has part structure that is capable of @@ -6779,7 +6776,7 @@ the a supports either the existence of b, or the truth value of b. A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall + causal relation between material entity and a process @@ -7204,7 +7201,7 @@ the a supports either the existence of b, or the truth value of b. a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. - Melissa Haendel + Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces @@ -7217,7 +7214,7 @@ the a supports either the existence of b, or the truth value of b. a produced_by b iff some process that occurs_in b has_output a. - Melissa Haendel + produced by @@ -7229,7 +7226,7 @@ the a supports either the existence of b, or the truth value of b. Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. - Vasundra Touré + represses expression of @@ -7240,7 +7237,7 @@ the a supports either the existence of b, or the truth value of b. Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. - Vasundra Touré + increases expression of @@ -7252,7 +7249,7 @@ the a supports either the existence of b, or the truth value of b. A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. - Matthew Brush + is used to study The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate. has role in modeling @@ -7379,7 +7376,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:38:20Z condition has genetic basis in @@ -7391,7 +7388,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:20Z has material basis in gain of function germline mutation in @@ -7405,7 +7402,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:37Z has material basis in loss of function germline mutation in @@ -7417,7 +7414,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:54Z has material basis in germline mutation in @@ -7430,7 +7427,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:07Z has material basis in somatic mutation in @@ -7443,7 +7440,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:26Z has major susceptibility factor @@ -7455,7 +7452,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:57Z has partial material basis in germline mutation in @@ -7466,7 +7463,7 @@ Environmental exposures include those imposed by natural environments, experimen p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - cjm + 2018-12-13T11:26:17Z has primary input or output @@ -7480,7 +7477,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - cjm + 2018-12-13T11:26:32Z has primary output @@ -7504,7 +7501,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - cjm + 2018-12-13T11:26:56Z has primary input @@ -7527,7 +7524,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:53:08Z is genetic basis for condition @@ -7539,7 +7536,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:55:51Z is causal gain of function germline mutation of in @@ -7552,7 +7549,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:06Z is causal loss of function germline mutation of in @@ -7566,7 +7563,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:40Z is causal germline mutation in @@ -7580,7 +7577,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:57:07Z is causal somatic mutation in @@ -7593,7 +7590,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. - cjm + 2017-11-05T02:57:43Z is causal susceptibility factor for @@ -7607,7 +7604,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. - cjm + 2017-11-05T02:58:43Z is causal germline mutation partially giving rise to @@ -7620,7 +7617,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:01Z realizable has basis in @@ -7631,7 +7628,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:29Z is basis for realizable @@ -7643,7 +7640,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:26:47Z disease has basis in @@ -7656,7 +7653,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) - cjm + 2017-11-05T03:29:32Z disease has basis in dysfunction of @@ -7669,7 +7666,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. disease has basis in disruption of (disease to process) - cjm + 2017-11-05T03:37:52Z disease has basis in disruption of @@ -7682,7 +7679,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. - cjm + 2017-11-05T03:46:07Z disease has basis in feature @@ -7695,7 +7692,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. - cjm + 2017-11-05T03:50:54Z causal relationship with disease as subject @@ -7716,7 +7713,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and a process where the disease process disrupts the execution of the process. disease causes disruption of (disease to process) - cjm + 2017-11-05T03:51:09Z disease causes disruption of @@ -7732,7 +7729,7 @@ Environmental exposures include those imposed by natural environments, experimen disease causes dysfunction of (disease to anatomical entity) - cjm + 2017-11-05T03:58:20Z disease causes dysfunction of @@ -7746,7 +7743,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. - cjm + 2017-11-05T04:06:02Z disease has location @@ -7758,7 +7755,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity - cjm + 2017-12-26T19:37:31Z disease has inflammation site @@ -7774,7 +7771,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - cjm + 2017-12-26T19:45:49Z realized in response to stimulus @@ -7786,7 +7783,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. - cjm + 2017-12-26T19:50:53Z disease has feature @@ -7798,7 +7795,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. - cjm + 2017-12-26T19:58:44Z disease arises from alteration in structure @@ -7814,7 +7811,7 @@ Environmental exposures include those imposed by natural environments, experimen Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - cjm + 2018-01-25T23:20:13Z enables subfunction @@ -7830,7 +7827,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:30Z acts upstream of or within, positive effect @@ -7848,7 +7845,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:51Z acts upstream of or within, negative effect @@ -7867,7 +7864,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - cjm + 2018-01-26T23:53:14Z acts upstream of, positive effect @@ -7887,7 +7884,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - cjm + 2018-01-26T23:53:22Z acts upstream of, negative effect @@ -7901,7 +7898,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:05Z causally upstream of or within, negative effect @@ -7913,7 +7910,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:19Z causally upstream of or within, positive effect @@ -8039,7 +8036,7 @@ Environmental exposures include those imposed by natural environments, experimen "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. - Damion Dooley + has substance added @@ -8052,7 +8049,7 @@ Environmental exposures include those imposed by natural environments, experimen 'egg white' 'has substance removed' some 'egg yolk' "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. - Damion Dooley + has substance removed @@ -8065,7 +8062,7 @@ Environmental exposures include those imposed by natural environments, experimen sardines 'immersed in' some 'oil and mustard' "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. - Damion Dooley + immersed in @@ -8077,7 +8074,7 @@ Environmental exposures include those imposed by natural environments, experimen sardine has consumer some homo sapiens 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. - Damion Dooley + has consumer @@ -8091,7 +8088,7 @@ Environmental exposures include those imposed by natural environments, experimen bread 'has primary substance added' some 'flour' 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance. - Damion Dooley + has primary substance added @@ -8105,10 +8102,10 @@ Environmental exposures include those imposed by natural environments, experimen An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - Austin Meier - Chris Mungall - David Osumi-Sutherland - Marie Angelique Laporte + + + + triggered by process realized in response to https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit @@ -8157,7 +8154,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - Vasundra Touré + regulates activity of @@ -8168,7 +8165,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. - Vasundra Touré + regulates quantity of @@ -8179,7 +8176,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. - Vasundra Touré + indirectly regulates activity of @@ -8192,7 +8189,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + decreases by repression quantity of @@ -8205,7 +8202,7 @@ For example, protein A (transcription factor) indirectly decreases by repression The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + increases by expression quantity of @@ -8216,7 +8213,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly positively regulates the quantity of B. - Vasundra Touré + directly positively regulates quantity of @@ -8227,7 +8224,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly negatively regulates the quantity of B. - Vasundra Touré + directly negatively regulates quantity of @@ -8238,7 +8235,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. - Vasundra Touré + indirectly activates indirectly positively regulates activity of @@ -8251,7 +8248,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. - Vasundra Touré + destabilizes quantity of @@ -8263,7 +8260,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. - Vasundra Touré + stabilizes quantity of @@ -8274,7 +8271,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. - Vasundra Touré + indirectly inhibits indirectly negatively regulates activity of @@ -8286,7 +8283,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. - Vasundra Touré + directly regulates quantity of @@ -8297,7 +8294,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. - Vasundra Touré + indirectly regulates quantity of @@ -8308,7 +8305,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. - Vasundra Touré + indirectly negatively regulates quantity of @@ -8319,7 +8316,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. - Vasundra Touré + indirectly positively regulates quantity of @@ -8650,7 +8647,7 @@ For example, protein A (transcription factor) indirectly increases by expression transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data]) A relation between a material entity and some data in which the data is taken as exemplifying the material entity. C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C. - Patrick Ray + This relation is not meant to capture the relation between occurrents and data. has exemplar data @@ -8660,7 +8657,7 @@ For example, protein A (transcription factor) indirectly increases by expression - Patrick Ray + exemplar data of @@ -8673,7 +8670,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relation between a group and another group it is part of but does not fully constitute. X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. - Shawn Tan + This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. subcluster of @@ -8855,7 +8852,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - http://orcid.org/0000-0002-7463-6306 + 2021-11-05T17:30:44Z has disease https://github.com/oborel/obo-relations/issues/478 @@ -8885,8 +8882,8 @@ For example, protein A (transcription factor) indirectly increases by expression A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - https://orcid.org/0000-0001-9625-1899 - https://orcid.org/0000-0003-2620-0345 + + A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z @@ -9039,7 +9036,7 @@ For example, protein A (transcription factor) indirectly increases by expression This relation groups relations between diseases and any other kind of entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. - cjm + 2018-09-26T00:00:32Z disease relationship @@ -9050,7 +9047,7 @@ For example, protein A (transcription factor) indirectly increases by expression p has anatomical participant c iff p has participant c, and c is an anatomical entity - cjm + 2018-09-26T01:08:58Z results in changes to anatomical or cellular structure diff --git a/src/ontology/subsets/ro-interaction.obo b/src/ontology/subsets/ro-interaction.obo index 31f6972d..521beb78 100644 --- a/src/ontology/subsets/ro-interaction.obo +++ b/src/ontology/subsets/ro-interaction.obo @@ -13,7 +13,7 @@ id: acquires_nutrients_from name: acquires nutrients from subset: ro-eco xref: RO:0002457 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for @@ -58,7 +58,7 @@ property_value: RO:0004050 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:22Z [Typedef] @@ -71,7 +71,7 @@ property_value: RO:0004049 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:14Z [Typedef] @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z [Typedef] @@ -103,7 +103,7 @@ xref: RO:0004032 property_value: RO:0004049 RO:0002264 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z [Typedef] @@ -120,7 +120,7 @@ property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cy property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 domain: BFO:0000004 range: BFO:0000004 @@ -131,7 +131,7 @@ id: allelopath_of name: allelopath of subset: ro-eco xref: RO:0002555 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string @@ -153,7 +153,7 @@ def: "x anabranch_of y if x is a distributary of y (i.e. it channels a from a la subset: ro-eco xref: RO:0002378 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "anastomoses with" xsd:string is_a: distributary_of ! distributary of disjoint_from: proper_distributary_of ! proper distributary of @@ -165,7 +165,7 @@ name: attached to def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] subset: ro-eco xref: RO:0002371 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: attached_to_part_of ! attached to part of @@ -189,9 +189,8 @@ def: "Relation between a neuron and some structure its axon forms (chemical) syn xref: RO:0002102 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in @@ -202,7 +201,7 @@ id: biomechanically_related_to name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] xref: RO:0002567 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: CARO:0000003 range: CARO:0000003 @@ -214,7 +213,7 @@ name: biotically interacts with def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] subset: ro-eco xref: RO:0002437 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string @@ -231,7 +230,7 @@ def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\ comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco xref: RO:0002007 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 is_a: part_of @@ -242,7 +241,7 @@ def: "x bounds the sequence of y iff the upstream-most part of x is upstream of xref: RO:0002522 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to inverse_of: is_bound_by_sequence_of ! is bound by sequence of @@ -254,7 +253,7 @@ def: "x is a branching part of y if and only if x is part of y and x is connecte subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso FMA:85994 xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with @@ -269,7 +268,7 @@ subset: ro-eco xref: RO:0002215 property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 @@ -302,7 +301,7 @@ id: capable_of_part_of name: capable of part of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ is_a: causal_agent_in_process ! causal agent in process @@ -350,7 +349,7 @@ id: causal_relation_between_entities name: causal relation between entities xref: RO:0002506 property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000002 @@ -363,7 +362,7 @@ name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] xref: RO:0002595 property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 range: BFO:0000015 @@ -374,7 +373,7 @@ id: causal_relation_between_processes name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 @@ -389,7 +388,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: OGMS:0000031 is_a: causally_related_to ! causally related to is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:50:54Z [Typedef] @@ -398,7 +397,7 @@ name: causally downstream of def: "inverse of upstream of" [] xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within is_a: preceded_by inverse_of: causally_upstream_of ! causally upstream of @@ -409,7 +408,7 @@ name: causally downstream of or within def: "inverse of causally upstream of or within" [] subset: RO:0002259 xref: RO:0002427 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -418,7 +417,7 @@ is_a: causal_relation_between_processes ! causal relation between processes id: causally_influenced_by name: causally influenced by xref: RO:0002559 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: causal_relation_between_entities ! causal relation between entities @@ -429,8 +428,8 @@ id: causally_influences name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] xref: RO:0002566 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 @@ -443,7 +442,7 @@ name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] @@ -453,7 +452,7 @@ def: "p is causally upstream of q iff p is causally related to q, the end of p p subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes @@ -465,7 +464,7 @@ def: "p is causally upstream of, negative effect q iff p is casually upstream of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -478,7 +477,7 @@ comment: holds between x and y if and only if x is causally upstream of y and th subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -490,7 +489,7 @@ def: "p is 'causally upstream or within' q iff p is causally related to q, and t synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -502,7 +501,7 @@ name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -511,7 +510,7 @@ name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -537,7 +536,7 @@ name: child nucleus of def: "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" [] xref: RO:0002476 property_value: IAO:0000112 "ABal nucleus child nucleus of ABa nucleus (in C elegans)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." xsd:string domain: GO:0005634 range: GO:0005634 @@ -548,7 +547,7 @@ id: child_nucleus_of_in_hermaphrodite name: child nucleus of in hermaphrodite def: "A child nucleus relationship in which the cells are part of a hermaphroditic organism" [] xref: RO:0002477 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -556,7 +555,7 @@ id: child_nucleus_of_in_male name: child nucleus of in male def: "A child nucleus relationship in which the cells are part of a male organism" [] xref: RO:0002478 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -576,7 +575,7 @@ comment: Example: if we define region of chromosome as any subdivision of a chro subset: ro-eco xref: RO:0002008 property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -585,9 +584,8 @@ name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 -property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -599,7 +597,7 @@ name: commensually interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] subset: ro-eco xref: RO:0002441 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -610,7 +608,7 @@ def: "x composed_primarily_of y if and only if more than half of the mass of x i subset: ro-eco xref: RO:0002473 property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 @@ -639,7 +637,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: BFO:0000017 is_a: causally_related_to ! causally related to inverse_of: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:38:20Z [Typedef] @@ -648,7 +646,7 @@ name: conduit for def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] subset: ro-eco xref: RO:0002570 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 UBERON:cjm xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 @@ -661,7 +659,7 @@ name: confers advantage in subset: ro-eco xref: RO:0002322 property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "adapted for" xsd:string range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -727,7 +725,7 @@ name: continuous with def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 @@ -746,7 +744,7 @@ property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a het property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -771,7 +769,7 @@ id: contributes_to_morphology_of name: contributes to morphology of def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] xref: RO:0002433 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -796,7 +794,7 @@ id: decreases_by_repression_quantity_of name: decreases by repression quantity of def: "The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011007 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_negatively_regulates_quantity_of ! indirectly negatively regulates quantity of @@ -808,8 +806,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in wh xref: RO:0002121 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in @@ -821,7 +819,7 @@ name: destabilizes quantity of def: "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." [] xref: RO:0011014 property_value: IAO:0000112 "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_quantity_of ! directly negatively regulates quantity of @@ -832,11 +830,11 @@ name: determined by def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] subset: ro-eco xref: RO:0002507 -property_value: http://purl.org/dc/terms/creator "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/creator "Pier Buttigieg" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-4366-3088 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "A coral reef environment is determined by a particular coral reef" xsd:string property_value: IAO:0000116 "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602 property_value: IAO:0000589 "determined by (system to material entity)" xsd:string domain: RO:0002577 @@ -852,7 +850,7 @@ name: determined by part of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] subset: ro-eco xref: RO:0002509 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 range: BFO:0000040 is_a: causal_relation_between_entities ! causal relation between entities @@ -865,7 +863,7 @@ def: "inverse of determined by" [] subset: ro-eco subset: RO:0002259 xref: RO:0002508 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "determines (material entity to system)" xsd:string is_a: causally_influences ! causally influences @@ -876,7 +874,7 @@ def: "inverse of has developmental contribution from" [] subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to @@ -886,9 +884,9 @@ name: developmentally induced by def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] xref: RO:0002256 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string property_value: IAO:0000119 GO:0001759 xsd:string @@ -905,7 +903,7 @@ name: developmentally induces def: "Inverse of developmentally induced by" [] xref: RO:0002257 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_induce ! has potential to developmentally induce @@ -917,7 +915,7 @@ comment: This relation groups together various other developmental relations. It xref: RO:0002258 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string domain: BFO:0000002 range: BFO:0000002 @@ -929,7 +927,7 @@ id: developmentally_related_to name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] xref: RO:0002324 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] @@ -939,7 +937,7 @@ def: "x developmentally replaces y if and only if there is some developmental pr xref: RO:0002285 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "replaces" xsd:string is_a: developmentally_preceded_by ! developmentally preceded by @@ -949,7 +947,7 @@ name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] xref: RO:0002286 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -959,10 +957,10 @@ def: "x develops from y if and only if either (a) x directly develops from y or comment: This is the transitive form of the develops from relation xref: RO:0002202 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 domain: BFO:0000004 range: BFO:0000004 is_transitive: true @@ -975,7 +973,7 @@ name: develops from part of def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] xref: RO:0002225 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: develops_from ! develops from [Typedef] @@ -984,7 +982,7 @@ name: develops in def: "x develops_in y if x is located in y whilst x is developing" [] xref: RO:0002226 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string domain: CARO:0000000 @@ -997,9 +995,9 @@ def: "inverse of develops from" [] subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 is_transitive: true is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into @@ -1010,11 +1008,11 @@ id: directly_develops_from name: directly develops from def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] xref: RO:0002207 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "has developmental precursor" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000119 "FBbt" xsd:string property_value: RO:0002575 RO:0002202 is_a: develops_from ! develops from @@ -1060,8 +1058,8 @@ name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] xref: RO:0002449 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1072,7 +1070,7 @@ id: directly_negatively_regulates_quantity_of name: directly negatively regulates quantity of def: "The entity A has an activity that directly negatively regulates the quantity of B." [] xref: RO:0011010 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1107,8 +1105,8 @@ name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] xref: RO:0002450 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1119,7 +1117,7 @@ id: directly_positively_regulates_quantity_of name: directly positively regulates quantity of def: "The entity A has an activity that directly positively regulates the quantity of B." [] xref: RO:0011009 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1142,7 +1140,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002578 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string property_value: RO:0002575 RO:0002211 @@ -1155,8 +1153,8 @@ name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] xref: RO:0002448 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: molecularly_interacts_with ! molecularly interacts with @@ -1167,7 +1165,7 @@ id: directly_regulates_quantity_of name: directly regulates quantity of def: "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B." [] xref: RO:0011021 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -1177,7 +1175,7 @@ def: "A relationship between a disease and an anatomical structure where the mat xref: RO:0004030 range: CARO:0000003 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z [Typedef] @@ -1189,7 +1187,7 @@ property_value: IAO:0000589 "disease causes disruption of (disease to process)" domain: OGMS:0000031 range: BFO:0000015 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:51:09Z [Typedef] @@ -1200,7 +1198,7 @@ property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomica domain: OGMS:0000031 range: CARO:0000006 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z [Typedef] @@ -1210,7 +1208,7 @@ xref: RO:0004019 domain: OGMS:0000031 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject is_a: realizable_has_basis_in ! realizable has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:26:47Z [Typedef] @@ -1221,7 +1219,7 @@ xref: RO:0004021 property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:37:52Z [Typedef] @@ -1232,7 +1230,7 @@ xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string range: CARO:0000006 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z [Typedef] @@ -1243,7 +1241,7 @@ xref: RO:0004022 domain: OGMS:0000031 is_a: disease_has_basis_in ! disease has basis in is_a: has_phenotype ! has phenotype -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:46:07Z [Typedef] @@ -1253,7 +1251,7 @@ def: "A relationship between a disease and some feature of that disease, where t xref: RO:0004029 domain: OGMS:0000031 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:50:53Z [Typedef] @@ -1272,7 +1270,7 @@ xref: RO:0004027 domain: OGMS:0000031 range: BFO:0000004 is_a: disease_has_location ! disease has location -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:37:31Z [Typedef] @@ -1285,7 +1283,7 @@ property_value: IAO:0000232 "This relation is intentionally very general, and co domain: OGMS:0000031 range: BFO:0000004 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T04:06:02Z [Typedef] @@ -1294,7 +1292,7 @@ name: disease relationship def: "This relation groups relations between diseases and any other kind of entity." [] xref: RO:0040035 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z [Typedef] @@ -1306,7 +1304,7 @@ subset: ro-eco xref: RO:0002377 property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string @@ -1316,10 +1314,10 @@ is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: does_not_overlap_sequence_of name: does not overlap sequence of -def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] xref: RO:0002527 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "disconnected from" xsd:string is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -1338,7 +1336,7 @@ id: eats name: eats subset: ro-eco xref: RO:0002470 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -1359,7 +1357,7 @@ def: "A relationship that is mediated in some way by the environment or environm subset: ro-eco xref: RO:0002321 property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string [Typedef] @@ -1377,7 +1375,7 @@ name: electrically_synapsed_to def: "A relation that holds between two neurons that are electrically coupled via gap junctions." [] xref: RO:0002003 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: connected_to ! connected to [Typedef] @@ -1386,7 +1384,7 @@ name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: has_participant @@ -1397,7 +1395,7 @@ def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string property_value: IAO:0000118 "has" xsd:string @@ -1413,7 +1411,7 @@ name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] xref: RO:0004031 is_a: functionally_related_to ! functionally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z [Typedef] @@ -1430,14 +1428,14 @@ inverse_of: has_endoparasite ! has endoparasite id: ends subset: ro-eco xref: RO:0002229 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: ends_with subset: ro-eco xref: RO:0002230 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -1462,7 +1460,7 @@ name: exports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002345 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -1479,7 +1477,7 @@ def: "relationship between a neuron and a neuron projection bundle (e.g.- tract xref: RO:0002101 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 @@ -1492,7 +1490,7 @@ inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron proje id: formed_as_result_of name: formed as result of xref: RO:0002354 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of [Typedef] @@ -1500,7 +1498,7 @@ id: functionally_related_to name: functionally related to def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] xref: RO:0002328 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string [Typedef] @@ -1509,7 +1507,7 @@ name: genetically interacts with xref: RO:0002435 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with @@ -1517,7 +1515,7 @@ is_a: interacts_with ! interacts with [Typedef] id: has_2D_boundary xref: RO:0002002 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1557,7 +1555,7 @@ def: "inverse of branching part of" [] subset: ro-eco subset: RO:0002259 xref: RO:0002569 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: has_part is_a: in_branching_relationship_with ! in branching relationship with @@ -1593,7 +1591,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 "Bill Duncan (https://orcid.org/0000-0001-9625-1899)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant @@ -1622,7 +1620,7 @@ id: has_dendrite_location name: has dendrite location xref: RO:0002360 property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -1632,7 +1630,7 @@ def: "x has developmental contribution from y iff x has some part z such that z xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by @@ -1644,7 +1642,7 @@ name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to @@ -1656,7 +1654,7 @@ def: "p has direct input c iff c is a participant in p, c is present at the star xref: RO:0002400 property_value: IAO:0000112 "'protein catabolic process' SubClassOf has_direct_input some protein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly consumes" xsd:string property_value: IAO:0000232 "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" xsd:string is_a: has_input ! has input @@ -1666,7 +1664,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1711,7 +1709,7 @@ def: "x 'has end location' y if and only if there exists some process z such tha subset: ro-eco xref: RO:0002232 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -1724,7 +1722,7 @@ def: "x has end sequence y if the end of x is identical to the end of y, and x h xref: RO:0002518 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -1776,11 +1774,11 @@ id: has_exposure_stimulus name: has exposure stimulus def: "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002309 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 is_a: related_via_exposure_to ! related via exposure to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:35:04Z [Typedef] @@ -1806,7 +1804,7 @@ def: "The relation between a neuron projection bundle and a neuron projection th xref: RO:0002132 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 @@ -1828,7 +1826,7 @@ subset: ro-eco xref: RO:0002303 property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Pier Buttigieg" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string domain: CARO:0001010 range: ENVO:01000254 @@ -1851,7 +1849,7 @@ name: has host def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] subset: ro-eco xref: RO:0002454 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -1865,7 +1863,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 is_a: has_participant @@ -1886,7 +1884,7 @@ def: "p has intermediate c if and only if p has parts p1, p2 and p1 has output c subset: ro-eco xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string is_a: has_participant @@ -1924,7 +1922,7 @@ name: has major susceptibility factor xref: RO:0004005 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_susceptibility_factor_for ! is causal susceptibility factor for -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:26Z [Typedef] @@ -1935,7 +1933,7 @@ property_value: seeAlso Orphanet:410295 property_value: seeAlso Orphanet:410296 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_gain_of_function_germline_mutation_of_in ! is causal gain of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:20Z [Typedef] @@ -1945,7 +1943,7 @@ xref: RO:0004003 property_value: seeAlso Orphanet:317343 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_in ! is causal germline mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:54Z [Typedef] @@ -1954,7 +1952,7 @@ name: has material basis in loss of function germline mutation in xref: RO:0004002 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_loss_of_function_germline_mutation_of_in ! is causal loss of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:37Z [Typedef] @@ -1964,7 +1962,7 @@ xref: RO:0004004 property_value: seeAlso Orphanet:317344 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z [Typedef] @@ -1980,7 +1978,7 @@ id: has_muscle_antagonist name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string is_a: biomechanically_related_to ! biomechanically related to @@ -1989,7 +1987,7 @@ id: has_muscle_insertion name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} @@ -2001,7 +1999,7 @@ id: has_muscle_origin name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} @@ -2039,7 +2037,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string is_a: has_participant inverse_of: output_of ! output of @@ -2066,7 +2064,7 @@ name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] xref: RO:0002584 property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causal_relation_between_material_entity_and_a_process ! causal relation between material entity and a process is_a: functionally_related_to ! functionally related to @@ -2076,7 +2074,7 @@ name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco xref: RO:0002479 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 range: BFO:0000004 @@ -2086,7 +2084,7 @@ name: has partial material basis in germline mutation in xref: RO:0004006 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_partially_giving_rise_to ! is causal germline mutation partially giving rise to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:57Z [Typedef] @@ -2098,7 +2096,7 @@ id: has_pathogen name: has pathogen subset: ro-eco xref: RO:0002557 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2108,7 +2106,7 @@ def: "A relationship that holds between a biological entity and a phenotype. Her subset: ro-eco xref: RO:0002200 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: UPHENO:0001001 is_a: has_phenotype_or_disease ! has phenotype or disease inverse_of: phenotype_of ! phenotype of @@ -2129,9 +2127,9 @@ def: "Holds between a cell c and a protein complex or protein p if and only if t xref: RO:0002104 property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Alexander Diehl" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 @@ -2157,8 +2155,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in whi xref: RO:0002110 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "synapsed in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2172,7 +2170,7 @@ name: has potential to develop into def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] xref: RO:0002387 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2181,7 +2179,7 @@ name: has potential to developmentally contribute to def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] xref: RO:0002385 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2190,7 +2188,7 @@ name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] xref: RO:0002386 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2199,7 +2197,7 @@ name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] xref: RO:0002388 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_potential_to_develop_into ! has potential to develop into [Typedef] @@ -2223,7 +2221,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -2233,7 +2231,7 @@ def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c o subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -2244,7 +2242,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -2276,7 +2274,7 @@ name: has skeleton def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] xref: RO:0002551 property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 @@ -2321,7 +2319,7 @@ name: has soma location def: "Relation between a neuron and an anatomical structure that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 range: CARO:0000003 @@ -2335,7 +2333,7 @@ def: "x 'has starts location' y if and only if there exists some process z such subset: ro-eco xref: RO:0002231 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -2348,7 +2346,7 @@ def: "x has start sequence y if the start of x is identical to the start of y, a xref: RO:0002516 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2358,10 +2356,10 @@ inverse_of: is_start_sequence_of ! is start sequence of [Typedef] id: has_subsequence name: has subsequence -def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2375,7 +2373,7 @@ id: has_symptom name: has symptom def: "A relation that holds between a disease or an organism and a phenotype" [] xref: RO:0002452 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: OGMS:0000031 is_a: has_phenotype ! has phenotype @@ -2405,7 +2403,7 @@ def: "A general relation between a neuron and some structure in which it either xref: RO:0002130 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has synapse in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2417,7 +2415,7 @@ id: has_synaptic_terminal_of name: has synaptic terminal of xref: RO:0002006 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: overlaps ! overlaps inverse_of: has_synaptic_terminal_in ! has synaptic terminal in @@ -2429,7 +2427,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002339 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2440,7 +2438,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002338 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2448,7 +2446,7 @@ id: has_vector name: has vector subset: ro-eco xref: RO:0002460 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with [Typedef] @@ -2463,7 +2461,7 @@ id: host_of name: host of subset: ro-eco xref: RO:0002453 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2476,7 +2474,7 @@ synonym: "epiparasite of" RELATED [] synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string is_a: has_host ! has host @@ -2492,7 +2490,7 @@ synonym: "has epiparasite" RELATED [] synonym: "has hyperparasite" RELATED [] synonym: "hyperparasitoidized by" RELATED [] xref: RO:0002554 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2500,7 +2498,7 @@ id: immediate_transformation_of name: immediate transformation of def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] xref: RO:0002495 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002494 is_a: directly_develops_from ! directly develops from is_a: transformation_of ! transformation of @@ -2510,7 +2508,7 @@ id: immediately_causally_downstream_of name: immediately causally downstream of xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of is_a: immediately_preceded_by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of @@ -2520,7 +2518,7 @@ id: immediately_causally_upstream_of name: immediately causally upstream of def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: immediately_precedes @@ -2533,7 +2531,7 @@ xref: RO:0002087 id: immediately_precedes subset: ro-eco xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0002575 BFO:0000063 [Typedef] @@ -2542,7 +2540,7 @@ name: imports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002340 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -2551,7 +2549,7 @@ name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] xref: RO:0002375 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 @@ -2577,7 +2575,7 @@ id: increases_by_expression_quantity_of name: increases by expression quantity of def: "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011008 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_positively_regulates_quantity_of ! indirectly positively regulates quantity of @@ -2587,7 +2585,7 @@ id: increases_expression_of name: increases expression of def: "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." [] xref: RO:0003003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -2606,7 +2604,7 @@ id: indirectly_negatively_regulates name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true @@ -2618,7 +2616,7 @@ id: indirectly_negatively_regulates_activity_of name: indirectly negatively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B." [] xref: RO:0011016 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly inhibits" xsd:string is_a: indirectly_regulates_activity_of ! indirectly regulates activity of @@ -2627,7 +2625,7 @@ id: indirectly_negatively_regulates_quantity_of name: indirectly negatively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B." [] xref: RO:0011023 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2635,7 +2633,7 @@ id: indirectly_positively_regulates name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 is_transitive: true @@ -2647,7 +2645,7 @@ id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." [] xref: RO:0011013 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -2658,7 +2656,7 @@ id: indirectly_positively_regulates_quantity_of name: indirectly positively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B." [] xref: RO:0011024 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2676,7 +2674,7 @@ id: indirectly_regulates_activity_of name: indirectly regulates activity of def: "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." [] xref: RO:0011004 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: regulates_activity_of ! regulates activity of @@ -2686,7 +2684,7 @@ id: indirectly_regulates_quantity_of name: indirectly regulates quantity of def: "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B." [] xref: RO:0011022 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -2696,7 +2694,7 @@ def: "inverse of has input" [] subset: ro-eco subset: RO:0002259 xref: RO:0002352 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -2710,7 +2708,7 @@ xref: RO:0002434 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI domain: BFO:0000040 @@ -2723,7 +2721,7 @@ name: interacts with via parasite-host interaction def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] subset: ro-eco xref: RO:0002443 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2751,7 +2749,7 @@ id: involved_in name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] xref: RO:0002331 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in @@ -2763,7 +2761,7 @@ id: involved_in_negative_regulation_of name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] xref: RO:0002430 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2773,7 +2771,7 @@ name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in_process ! causal agent in process @@ -2784,7 +2782,7 @@ id: involved_in_positive_regulation_of name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] xref: RO:0002429 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2793,7 +2791,7 @@ id: involved_in_regulation_of name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] xref: RO:0002428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of @@ -2804,7 +2802,7 @@ def: "c executes activity in d if and only if c enables p and p occurs_in d. As synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -2853,7 +2851,7 @@ id: is_basis_for_realizable name: is basis for realizable xref: RO:0004018 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:29Z [Typedef] @@ -2863,7 +2861,7 @@ def: "inverse of bounds sequence of" [] subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to @@ -2874,7 +2872,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004011 property_value: seeAlso Orphanet:410296 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:55:51Z [Typedef] @@ -2885,7 +2883,7 @@ xref: RO:0004013 property_value: seeAlso Orphanet:317343 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:40Z [Typedef] @@ -2896,7 +2894,7 @@ xref: RO:0004016 property_value: seeAlso Orphanet:317346 is_a: contributes_to_condition ! contributes to condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:58:43Z [Typedef] @@ -2906,7 +2904,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004012 property_value: seeAlso Orphanet:410295 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:06Z [Typedef] @@ -2917,7 +2915,7 @@ xref: RO:0004014 property_value: seeAlso Orphanet:317344 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:07Z [Typedef] @@ -2927,7 +2925,7 @@ def: "Relates a gene to condition, such that a mutation in this gene predisposes xref: RO:0004015 property_value: seeAlso Orphanet:317345 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:43Z [Typedef] @@ -2937,7 +2935,7 @@ def: "x is a consecutive sequence of y iff x has subsequence y, and all the part xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: has_subsequence ! has subsequence @@ -2947,7 +2945,7 @@ name: is downstream of sequence of def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] xref: RO:0002529 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of @@ -2957,7 +2955,7 @@ id: is_eaten_by name: is eaten by subset: ro-eco xref: RO:0002471 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -2969,7 +2967,7 @@ def: "inverse of has end sequence" [] subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2982,7 +2980,7 @@ xref: RO:0004010 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string range: BFO:0000017 is_a: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:53:08Z [Typedef] @@ -2992,7 +2990,7 @@ def: "x is immediately downstream of the sequence of y iff either (1) x and y ha xref: RO:0002530 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002529 is_a: is_downstream_of_sequence_of ! is downstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3004,7 +3002,7 @@ def: "inverse of immediately downstream of" [] xref: RO:0002531 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: is_upstream_of_sequence_of ! is upstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3031,7 +3029,7 @@ def: "x is sequentially aligned with if a significant portion bases of x and y c xref: RO:0002521 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -3071,7 +3069,7 @@ def: "inverse of has start sequence" [] subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3084,7 +3082,7 @@ def: "inverse of has subsequence" [] subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of @@ -3107,7 +3105,7 @@ name: is treated by substance def: "Inverse of 'is substance that treats'" [] subset: RO:0002259 xref: RO:0002302 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 is_a: causally_related_to ! causally related to inverse_of: is_substance_that_treats ! is substance that treats @@ -3117,7 +3115,7 @@ name: is upstream of sequence of def: "inverse of downstream of sequence of" [] xref: RO:0002528 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -3127,7 +3125,7 @@ name: is vector for subset: ro-eco xref: RO:0002459 property_value: IAO:0000112 "Anopheles is a vector for Plasmodium" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: has_vector ! has vector @@ -3179,7 +3177,7 @@ name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco xref: RO:0002571 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:cjm xsd:string range: BFO:0000040 is_a: part_of @@ -3190,7 +3188,7 @@ name: luminal space of def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] subset: ro-eco xref: RO:0002572 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000141 is_a: lumen_of ! lumen of @@ -3202,7 +3200,7 @@ subset: ro-eco xref: RO:0002381 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with is_a: part_of @@ -3212,7 +3210,7 @@ id: mereotopologically_related_to name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] xref: RO:0002323 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string property_value: RO:0001900 RO:0001901 @@ -3230,7 +3228,7 @@ name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 @@ -3243,7 +3241,7 @@ name: mutualistically interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] subset: ro-eco xref: RO:0002442 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -3270,7 +3268,7 @@ name: negatively regulated by def: "inverse of negatively regulates" [] subset: RO:0002259 xref: RO:0002335 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3281,7 +3279,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 @@ -3330,7 +3328,7 @@ def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -3351,10 +3349,10 @@ expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://p [Typedef] id: overlaps_sequence_of name: overlaps sequence of -def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] xref: RO:0002526 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: overlaps ! overlaps is_a: sequentially_related_to ! sequentially related to @@ -3366,7 +3364,7 @@ subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string is_a: has_host ! has host @@ -3379,7 +3377,7 @@ name: parasitized by subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string @@ -3418,7 +3416,7 @@ name: part of developmental precursor of xref: RO:0002287 property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by [Typedef] @@ -3426,7 +3424,7 @@ id: part_of_structure_that_is_capable_of name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] xref: RO:0002329 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean is_a: functionally_related_to ! functionally related to @@ -3455,7 +3453,7 @@ subset: ro-eco synonym: "semibiotically interacts with" RELATED [] xref: RO:0002446 property_value: IAO:0000112 "Porifiera attaches to substrate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: biotically_interacts_with ! biotically interacts with @@ -3464,7 +3462,7 @@ id: participates_in_a_biotic-biotic_interaction_with name: participates in a biotic-biotic interaction with subset: ro-eco xref: RO:0002574 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 domain: CARO:0001010 range: CARO:0001010 @@ -3474,7 +3472,7 @@ is_a: biotically_interacts_with ! biotically interacts with id: partner_in name: partner in xref: RO:0002461 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string is_a: participates_in @@ -3483,7 +3481,7 @@ id: pathogen_of name: pathogen of subset: ro-eco xref: RO:0002556 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_host ! has host inverse_of: has_pathogen ! has pathogen @@ -3495,7 +3493,7 @@ subset: ro-eco subset: RO:0002259 xref: RO:0002201 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_functional: true [Typedef] @@ -3503,7 +3501,7 @@ id: phosphorylates name: phosphorylates xref: RO:0002447 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: molecularly_interacts_with ! molecularly interacts with @@ -3512,7 +3510,7 @@ id: pollinated_by name: pollinated by subset: ro-eco xref: RO:0002456 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string @@ -3525,7 +3523,7 @@ subset: ro-eco xref: RO:0002455 property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with @@ -3537,7 +3535,7 @@ name: positively regulated by def: "inverse of positively regulates" [] subset: RO:0002259 xref: RO:0002336 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3548,7 +3546,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002211 @@ -3583,7 +3581,7 @@ def: "inverse of preys on" [] subset: ro-eco subset: RO:0002259 xref: RO:0002458 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string @@ -3598,9 +3596,9 @@ subset: ro-eco xref: RO:0002439 property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Jorrit Poelen" xsd:string -property_value: IAO:0000117 "Katja Shulz" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7134-3324 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string @@ -3623,7 +3621,7 @@ def: "x proper_distributary_of y iff x distributary_of y and x does not flow bac subset: ro-eco xref: RO:0002382 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: distributary_of ! distributary of [Typedef] @@ -3633,7 +3631,7 @@ def: "x proper_tributary_of y iff x tributary_of y and x does not originate from subset: ro-eco xref: RO:0002383 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: tributary_of ! tributary of [Typedef] @@ -3642,7 +3640,7 @@ name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string @@ -3654,7 +3652,7 @@ id: provides_nutrients_for name: provides nutrients for subset: ro-eco xref: RO:0002469 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3663,7 +3661,7 @@ name: realizable has basis in xref: RO:0004017 is_a: causally_related_to ! causally related to inverse_of: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:01Z [Typedef] @@ -3672,10 +3670,10 @@ name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] synonym: "triggered by process" EXACT [RO:cjm] xref: RO:0009501 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "David Osumi-Sutherland" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string @@ -3692,7 +3690,7 @@ xref: RO:0004028 domain: BFO:0000017 range: BFO:0000040 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:45:49Z [Typedef] @@ -3700,7 +3698,7 @@ id: receives_input_from name: receives input from xref: RO:0002485 property_value: IAO:0000116 "See notes for inverse relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to inverse_of: sends_output_to ! sends output to @@ -3740,7 +3738,7 @@ name: regulated by def: "inverse of regulates" [] subset: RO:0002259 xref: RO:0002334 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 range: BFO:0000015 @@ -3755,9 +3753,9 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Hill" xsd:string -property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 +property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string @@ -3774,7 +3772,7 @@ id: regulates_activity_of name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] xref: RO:0011002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3794,7 +3792,7 @@ id: regulates_in_other_organism name: regulates in other organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] xref: RO:0002010 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 range: BFO:0000015 is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -3805,7 +3803,7 @@ name: regulates levels of def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] xref: RO:0002332 property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 @@ -3817,7 +3815,7 @@ id: regulates_quantity_of name: regulates quantity of def: "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." [] xref: RO:0011003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3836,7 +3834,7 @@ id: related_via_localization_to name: related via localization to def: "A relationship that holds via some process of localization" [] xref: RO:0002337 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 range: BFO:0000002 @@ -3857,7 +3855,7 @@ id: represses_expression_of name: represses expression of def: "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." [] xref: RO:0003002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3871,7 +3869,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -3916,7 +3914,7 @@ name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] @@ -3936,7 +3934,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002348 property_value: IAO:0000112 "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3948,7 +3946,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002349 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3962,7 +3960,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3972,7 +3970,7 @@ id: results_in_developmental_induction_of name: results in developmental induction of def: "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." [] xref: RO:0002357 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3982,7 +3980,7 @@ def: "p results in the developmental progression of s iff p is a developmental p xref: RO:0002295 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 range: CARO:0000000 @@ -3994,7 +3992,7 @@ name: results in developmental regression of xref: RO:0002301 property_value: IAO:0000112 "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4004,7 +4002,7 @@ name: results in disappearance of xref: RO:0002300 property_value: IAO:0000112 "foramen ovale closure SubClassOf results in disappearance of foramen ovale" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4020,7 +4018,7 @@ id: results_in_ending_of name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4034,7 +4032,7 @@ xref: RO:0002297 property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4056,7 +4054,7 @@ id: results_in_growth_of name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4071,7 +4069,7 @@ xref: RO:0002299 property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4087,7 +4085,7 @@ xref: RO:0002298 property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4100,7 +4098,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002565 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4126,7 +4124,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002356 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4135,7 +4133,7 @@ id: results_in_structural_organization_of name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4151,7 +4149,7 @@ name: results in transport across def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002342 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: occurs_across ! occurs across is_a: results_in_transport_to_from_or_in ! results in transport to from or in @@ -4160,7 +4158,7 @@ id: results_in_transport_along name: results in transport along def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] xref: RO:0002341 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4168,7 +4166,7 @@ id: results_in_transport_to_from_or_in name: results in transport to from or in xref: RO:0002344 property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4183,7 +4181,7 @@ id: sends_output_to name: sends output to xref: RO:0002486 property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to [Typedef] @@ -4225,7 +4223,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcript" xsd:string property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -4235,7 +4233,7 @@ name: sequentially related to def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string @@ -4248,7 +4246,7 @@ name: skeleton of def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 is_a: part_of @@ -4259,7 +4257,7 @@ name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] xref: RO:0002379 property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: overlaps ! overlaps @@ -4271,7 +4269,7 @@ subset: ro-eco xref: RO:0002163 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 @@ -4285,7 +4283,7 @@ name: stabilizes quantity of def: "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." [] xref: RO:0011015 property_value: IAO:0000112 "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_quantity_of ! directly positively regulates quantity of @@ -4294,14 +4292,14 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates id: starts subset: ro-eco xref: RO:0002223 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: starts_with subset: ro-eco xref: RO:0002224 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -4317,7 +4315,7 @@ name: subcluster of def: "A relation between a group and another group it is part of but does not fully constitute." [] xref: RO:0015003 property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." xsd:string -property_value: IAO:0000117 "Shawn Tan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true is_a: part_of @@ -4326,7 +4324,7 @@ is_a: part_of id: subject_participant_in name: subject participant in xref: RO:0002462 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4345,7 +4343,7 @@ name: surrounded by def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] xref: RO:0002219 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to inverse_of: surrounds ! surrounds @@ -4357,7 +4355,7 @@ def: "inverse of surrounded by" [] subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to @@ -4367,7 +4365,7 @@ name: symbiotically interacts with def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] subset: ro-eco xref: RO:0002440 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true @@ -4380,8 +4378,8 @@ def: "Relation between an anatomical structure (including cells) and a neuron th xref: RO:0002103 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: receives_input_from ! receives input from inverse_of: synapsed_to ! synapsed to @@ -4406,8 +4404,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002108 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" [] @@ -4420,8 +4418,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002109 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4434,8 +4432,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002112 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4448,8 +4446,8 @@ comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part som xref: RO:0002120 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: sends_output_to ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -4473,8 +4471,8 @@ def: "A relation between a motor neuron and a muscle that it synapses to via a t comment: Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) xref: RO:0002107 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_II_bouton ! synapsed_by_via_type_II_bouton @@ -4488,8 +4486,8 @@ comment: Expands to: has_part some ('type Ib terminal button' that has_part some xref: RO:0002105 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Ib_bouton ! synapsed_by_via_type_Ib_bouton @@ -4503,8 +4501,8 @@ comment: Expands to: has_part some ('type Is terminal button' that has_part some xref: RO:0002106 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Is_bouton ! synapsed_by_via_type_Is_bouton @@ -4514,7 +4512,7 @@ expand_expression_to: "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that id: target_participant_in name: target participant in xref: RO:0002463 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4523,7 +4521,7 @@ id: temporally_related_to subset: ro-eco xref: RO:0002222 property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string [Typedef] @@ -4531,7 +4529,7 @@ id: transformation_of name: transformation of def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] xref: RO:0002494 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: develops_from ! develops from @@ -4541,7 +4539,7 @@ name: transitively provides input for def: "transitive form of directly_provides_input_for" [] xref: RO:0002414 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." xsd:string property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string domain: BFO:0000015 @@ -4556,7 +4554,7 @@ def: "A relationship that holds between a disease and organism" [] xref: RO:0002451 property_value: IAO:0000112 "all dengue disease transmitted by some mosquito" xsd:string property_value: IAO:0000116 "Add domain and range constraints" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -4576,7 +4574,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002313 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "regulates localization of" xsd:string is_a: related_via_localization_to ! related via localization to is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4590,7 +4588,7 @@ xref: RO:0002376 property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string @@ -4608,7 +4606,7 @@ name: trophically interacts with def: "An interaction relationship in which the partners are related via a feeding relationship." [] subset: ro-eco xref: RO:0002438 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4618,7 +4616,7 @@ name: ubiquitinates def: "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" [] xref: RO:0002480 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with [Typedef] diff --git a/src/ontology/subsets/ro-interaction.owl b/src/ontology/subsets/ro-interaction.owl index 717d6903..1f7b268f 100644 --- a/src/ontology/subsets/ro-interaction.owl +++ b/src/ontology/subsets/ro-interaction.owl @@ -409,7 +409,7 @@ - David Osumi-Sutherland + RO:0002002 has_2D_boundary @@ -421,7 +421,7 @@ A relation that holds between two neurons that are electrically coupled via gap junctions. - David Osumi-Sutherland + RO:0002003 electrically_synapsed_to @@ -435,7 +435,7 @@ - David Osumi-Sutherland + RO:0002006 has_synaptic_terminal_of @@ -469,7 +469,7 @@ has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland + RO:0002007 bounding_layer_of @@ -505,9 +505,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. + A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. Note from NCEAS meeting: consider changing primary label - David Osumi-Sutherland + RO:0002008 coincident_with @@ -524,7 +524,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - David Osumi-Sutherland + RO:0002010 regulates_in_other_organism regulates in other organism @@ -553,7 +553,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + dos 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -568,7 +568,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + dos 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -584,7 +584,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + dos 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -599,7 +599,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -613,7 +613,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -630,7 +630,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + dos 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -644,7 +644,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + dos 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -658,7 +658,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + dos 2017-07-20T17:11:08Z RO:0002020 transports @@ -672,7 +672,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + dos 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -686,7 +686,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -697,7 +697,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + GOC:dos @@ -708,7 +708,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + dos 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -718,7 +718,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + GOC:dos @@ -729,7 +729,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + dos 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -739,7 +739,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + GOC:dos @@ -750,7 +750,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + dos 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -761,7 +761,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + GOC:dos @@ -780,7 +780,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + dos 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -797,7 +797,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + GOC:dos @@ -814,7 +814,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + RO:0002090 @@ -831,7 +831,7 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure that its soma is part of. - David Osumi-Sutherland + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -852,9 +852,9 @@ Examples include: the relationship between two channels collected simultaneously relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - David Osumi-Sutherland + fasciculates with - (forall (?x ?y) + (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) @@ -890,9 +890,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure its axon forms (chemical) synapses in. - Chris Mungall - David Osumi-Sutherland - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -924,8 +923,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -945,9 +944,9 @@ Examples include: the relationship between two channels collected simultaneously Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - Alexander Diehl - Chris Mungall - Lindsay Cowell + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) @@ -965,8 +964,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -985,8 +984,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -1005,8 +1004,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) RO:0002107 @@ -1023,8 +1022,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1043,8 +1042,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1064,8 +1063,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - Chris Mungall - David Osumi-Sutherland + + synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( @@ -1085,8 +1084,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1168,8 +1167,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -1196,8 +1195,8 @@ N1 SubclassOf ( Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -1218,7 +1217,7 @@ N1 SubclassOf ( A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - David Osumi-Sutherland + has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) @@ -1267,9 +1266,9 @@ N1 SubclassOf ( The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - David Osumi-Sutherland + has fasciculating component - (forall (?x ?y) + (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) @@ -1309,8 +1308,8 @@ N1 SubclassOf ( - X continuous_with Y if and only if X and Y share a fiat boundary. - David Osumi-Sutherland + X continuous_with Y if and only if X and Y share a fiat boundary. + connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) @@ -1329,8 +1328,8 @@ N1 SubclassOf ( x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom - proper overlaps - (forall (?x ?y) + proper overlaps + (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and @@ -1353,7 +1352,7 @@ N1 SubclassOf ( A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - Chris Mungall + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) @@ -1361,7 +1360,7 @@ N1 SubclassOf ( RO:0002163 spatially_disjoint_from - spatially disjoint from + spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern @@ -1498,7 +1497,7 @@ N1 SubclassOf ( A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - Chris Mungall + RO:0002200 has_phenotype @@ -1513,7 +1512,7 @@ N1 SubclassOf ( inverse of has phenotype - Chris Mungall + RO:0002201 @@ -1533,10 +1532,10 @@ N1 SubclassOf ( x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - Terry Meehan + + + + RO:0002202 develops_from This is the transitive form of the develops from relation @@ -1554,9 +1553,9 @@ N1 SubclassOf ( inverse of develops from - Chris Mungall - David Osumi-Sutherland - Terry Meehan + + + RO:0002203 develops_into @@ -1588,12 +1587,12 @@ N1 SubclassOf ( Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - Chris Mungall - David Osumi-Sutherland - has developmental precursor + + FBbt RO:0002207 + has developmental precursor directly_develops_from TODO - add child relations from DOS directly develops from @@ -1651,9 +1650,9 @@ N1 SubclassOf ( p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - Chris Mungall - David Hill - Tanya Berardini + + + GO Regulation precludes parthood; the regulatory process may not be within the regulated process. @@ -1676,7 +1675,7 @@ N1 SubclassOf ( p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - Chris Mungall + negatively regulates (process to process) @@ -1698,7 +1697,7 @@ N1 SubclassOf ( p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - Chris Mungall + positively regulates (process to process) @@ -1721,7 +1720,7 @@ N1 SubclassOf ( mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - Chris Mungall + has function realized in @@ -1740,7 +1739,7 @@ N1 SubclassOf ( c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - Chris Mungall + has function in RO:0002216 capable_of_part_of @@ -1757,7 +1756,7 @@ N1 SubclassOf ( x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - Chris Mungall + RO:0002219 surrounded_by @@ -1779,7 +1778,7 @@ N1 SubclassOf ( x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - Chris Mungall + RO:0002220 @@ -1803,7 +1802,7 @@ N1 SubclassOf ( inverse of surrounded by - Chris Mungall + RO:0002221 @@ -1816,7 +1815,7 @@ N1 SubclassOf ( - Chris Mungall + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 @@ -1830,7 +1829,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002223 starts @@ -1842,7 +1841,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002224 starts_with @@ -1856,7 +1855,7 @@ N1 SubclassOf ( x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - Chris Mungall + RO:0002225 develops_from_part_of develops from part of @@ -1871,7 +1870,7 @@ N1 SubclassOf ( x develops_in y if x is located in y whilst x is developing - Chris Mungall + EHDAA2 Jonathan Bard, EHDAA2 RO:0002226 @@ -1909,7 +1908,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002229 ends @@ -1921,7 +1920,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002230 ends_with @@ -1937,7 +1936,7 @@ N1 SubclassOf ( x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - Chris Mungall + starts with process that occurs in RO:0002231 @@ -1955,7 +1954,7 @@ N1 SubclassOf ( x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - Chris Mungall + ends with process that occurs in RO:0002232 @@ -1973,7 +1972,7 @@ N1 SubclassOf ( p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + consumes RO:0002233 @@ -1993,7 +1992,7 @@ N1 SubclassOf ( p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - Chris Mungall + produces RO:0002234 @@ -2047,7 +2046,7 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - Bill Duncan (https://orcid.org/0000-0001-9625-1899) + This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. @@ -2196,7 +2195,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y - Chris Mungall + RO:0002254 has_developmental_contribution_from has developmental contribution from @@ -2211,7 +2210,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho inverse of has developmental contribution from - Chris Mungall + RO:0002255 developmentally_contributes_to @@ -2229,9 +2228,9 @@ If you need an axiom that says 'has_participant min 2 object', you sho t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - Chris Mungall - David Osumi-Sutherland - Melissa Haendel + + + induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) @@ -2251,7 +2250,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally induced by - Chris Mungall + RO:0002257 developmentally_induces developmentally induces @@ -2269,7 +2268,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - Chris Mungall + In general you should not use this relation to make assertions - use one of the more specific relations below this one RO:0002258 developmentally_preceded_by @@ -2317,7 +2316,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - Chris Mungall + replaces RO:0002285 developmentally_replaces @@ -2332,7 +2331,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally preceded by - Chris Mungall + RO:0002286 developmentally_succeeded_by developmentally succeeded by @@ -2346,7 +2345,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - Chris Mungall + RO:0002287 part_of_developmental_precursor_of part of developmental precursor of @@ -2363,7 +2362,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - Chris Mungall + RO:0002295 results_in_developmental_progression_of results in developmental progression of @@ -2380,7 +2379,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - Chris Mungall + http://www.geneontology.org/GO.doc.development.shtml RO:0002296 @@ -2401,7 +2400,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002297 @@ -2422,7 +2421,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002298 @@ -2443,7 +2442,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002299 @@ -2461,7 +2460,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho foramen ovale closure SubClassOf results in disappearance of foramen ovale - Chris Mungall + May be merged into parent relation RO:0002300 results_in_disappearance_of @@ -2476,7 +2475,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) - Chris Mungall + May be merged into parent relation RO:0002301 results_in_developmental_regression_of @@ -2491,7 +2490,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of 'is substance that treats' - cjm + RO:0002302 is_treated_by_substance @@ -2511,7 +2510,7 @@ where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. - Pier Buttigieg + adapted for living in RO:0002303 @@ -2529,7 +2528,7 @@ where p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - cjm + RO:0002304 @@ -2547,7 +2546,7 @@ where p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - cjm + RO:0002305 @@ -2562,10 +2561,10 @@ where A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. - Austin Meier - Chris Mungall - Marie Angelique Laporte - cjm + + + + 2017-06-05T17:35:04Z RO:0002309 has_exposure_stimulus @@ -2580,7 +2579,7 @@ where Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. - Chris Mungall + regulates localization of RO:0002313 @@ -2600,7 +2599,7 @@ where an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002315 @@ -2617,7 +2616,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions RO:0002321 @@ -2633,7 +2632,7 @@ where An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. - Chris Mungall + adapted for RO:0002322 @@ -2647,7 +2646,7 @@ where A mereological relationship or a topological relationship - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships RO:0002323 @@ -2661,7 +2660,7 @@ where A relationship that holds between entities participating in some developmental process (GO:0032502) - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development RO:0002324 developmentally_related_to @@ -2678,9 +2677,8 @@ where Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. - Chris Mungall + In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - Gene Ontology Consortium RO:0002325 colocalizes_with @@ -2708,7 +2706,7 @@ then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. - Chris Mungall + In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 @@ -2725,7 +2723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - Chris Mungall + catalyzes executes has @@ -2744,7 +2742,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 functionally_related_to @@ -2758,7 +2756,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati this relation holds between c and p when c is part of some c', and c' is capable of p. - Chris Mungall + false RO:0002329 part_of_structure_that_is_capable_of @@ -2773,7 +2771,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati c involved_in p if and only if c enables some process p', and p' is part of p - Chris Mungall + actively involved in enables part of RO:0002331 @@ -2792,7 +2790,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - Chris Mungall + regulates levels of (process to entity) RO:0002332 @@ -2808,7 +2806,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables - Chris Mungall + RO:0002333 enabled_by @@ -2825,7 +2823,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of regulates - Chris Mungall + regulated by (processual) RO:0002334 @@ -2840,7 +2838,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of negatively regulates - Chris Mungall + RO:0002335 negatively_regulated_by @@ -2854,7 +2852,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of positively regulates - Chris Mungall + RO:0002336 positively_regulated_by @@ -2869,7 +2867,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds via some process of localization - Chris Mungall + Do not use this relation directly. It is a grouping relation. RO:0002337 related_via_localization_to @@ -2883,7 +2881,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - Chris Mungall + RO:0002338 @@ -2899,7 +2897,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - Chris Mungall + RO:0002339 @@ -2915,7 +2913,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. - Chris Mungall + RO:0002340 imports @@ -2929,7 +2927,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - Chris Mungall + RO:0002341 results_in_transport_along results in transport along @@ -2943,7 +2941,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - Chris Mungall + RO:0002342 results_in_transport_across @@ -2958,7 +2956,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'pollen tube growth' results_in growth_of some 'pollen tube' - Chris Mungall + RO:0002343 results_in_growth_of results in growth of @@ -2971,7 +2969,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - Chris Mungall + RO:0002344 results_in_transport_to_from_or_in results in transport to from or in @@ -2983,8 +2981,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. - Chris Mungall + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. + RO:0002345 exports @@ -3000,7 +2998,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - Chris Mungall + RO:0002348 @@ -3017,7 +3015,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - Chris Mungall + RO:0002349 @@ -3034,7 +3032,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has input - Chris Mungall + RO:0002352 @@ -3050,7 +3048,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has output - Chris Mungall + RO:0002353 @@ -3064,7 +3062,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002354 formed_as_result_of formed as result of @@ -3078,7 +3076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. - Chris Mungall + RO:0002355 results_in_structural_organization_of results in structural organization of @@ -3092,7 +3090,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - Chris Mungall + RO:0002356 @@ -3108,7 +3106,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. - Chris Mungall + RO:0002357 results_in_developmental_induction_of results in developmental induction of @@ -3120,7 +3118,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + http://neurolex.org/wiki/Property:DendriteLocation RO:0002360 has_dendrite_location @@ -3136,7 +3134,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - Chris Mungall + attached to (anatomical structure to anatomical structure) RO:0002371 @@ -3153,7 +3151,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002372 has_muscle_origin @@ -3176,7 +3174,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002373 has_muscle_insertion @@ -3200,7 +3198,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) @@ -3222,7 +3220,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - Chris Mungall + drains into drains to tributary channel of @@ -3247,7 +3245,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Deschutes River distributary_of Little Lava Lake x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - Chris Mungall + branch of distributary channel of http://en.wikipedia.org/wiki/Distributary @@ -3273,7 +3271,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. - Chris Mungall + anastomoses with RO:0002378 @@ -3289,7 +3287,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - Chris Mungall + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios RO:0002379 spatially_coextensive_with @@ -3312,7 +3310,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - Chris Mungall + RO:0002380 branching_part_of @@ -3331,7 +3329,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. - Chris Mungall + RO:0002381 main_stem_of @@ -3347,7 +3345,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_distributary_of y iff x distributary_of y and x does not flow back into y - Chris Mungall + RO:0002382 proper_distributary_of @@ -3362,7 +3360,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_tributary_of y iff x tributary_of y and x does not originate from y - Chris Mungall + RO:0002383 proper_tributary_of @@ -3379,7 +3377,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - Chris Mungall + RO:0002384 has_developmental_potential_involving has developmental potential involving @@ -3393,7 +3391,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - Chris Mungall + RO:0002385 has_potential_to_developmentally_contribute_to has potential to developmentally contribute to @@ -3407,7 +3405,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - Chris Mungall + RO:0002386 has_potential_to_developmentally_induce has potential to developmentally induce @@ -3421,7 +3419,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has the potential to develop into y iff x develops into y or if x is capable of developing into y - Chris Mungall + RO:0002387 has_potential_to_develop_into has potential to develop into @@ -3435,7 +3433,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - Chris Mungall + RO:0002388 has_potential_to_directly_develop_into has potential to directly develop into @@ -3450,7 +3448,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' RO:0002400 @@ -3468,7 +3466,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of upstream of - Chris Mungall + RO:0002404 causally_downstream_of causally downstream of @@ -3483,7 +3481,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002405 immediately_causally_downstream_of immediately causally downstream of @@ -3498,7 +3496,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - Chris Mungall + indirectly activates RO:0002407 @@ -3515,7 +3513,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - Chris Mungall + indirectly inhibits RO:0002409 @@ -3544,7 +3542,7 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002410 causally_related_to @@ -3566,7 +3564,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - Chris Mungall + RO:0002411 @@ -3582,7 +3580,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - Chris Mungall + RO:0002412 immediately_causally_upstream_of @@ -3598,7 +3596,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit - Chris Mungall + directly provides input for directly provides input for (process to process) @@ -3618,7 +3616,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different transitive form of directly_provides_input_for - Chris Mungall + This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. transitively provides input for (process to process) RO:0002414 @@ -3636,7 +3634,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall + influences (processual) RO:0002418 affects @@ -3652,7 +3650,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - Chris Mungall + RO:0002427 @@ -3668,7 +3666,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - Chris Mungall + RO:0002428 involved_in_regulation_of involved in regulation of @@ -3681,7 +3679,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - Chris Mungall + RO:0002429 involved_in_positive_regulation_of @@ -3695,7 +3693,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - Chris Mungall + RO:0002430 involved_in_negative_regulation_of @@ -3712,7 +3710,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - Chris Mungall + involved in or reguates RO:0002431 involved_in_or_involved_in_regulation_of @@ -3728,7 +3726,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall + executes activity in RO:0002432 enables activity in @@ -3740,8 +3738,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + GOC:cjm + GOC:dos @@ -3751,7 +3749,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - Chris Mungall + RO:0002433 contributes_to_morphology_of contributes to morphology of @@ -3768,7 +3766,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. - Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. RO:0002434 in pairwise interaction with @@ -3787,7 +3785,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) - Chris Mungall + RO:0002435 genetically_interacts_with genetically interacts with @@ -3803,7 +3801,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - Chris Mungall + binds molecularly binds with RO:0002436 @@ -3824,7 +3822,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - Chris Mungall + interacts with on organism level RO:0002437 @@ -3841,7 +3839,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the partners are related via a feeding relationship. - Chris Mungall + RO:0002438 trophically_interacts_with @@ -3859,9 +3857,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] Baleen whale preys on krill An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - Chris Mungall - Jorrit Poelen - Katja Shulz + + + is subject of predation interaction with preys upon RO:0002439 @@ -3880,7 +3878,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A biotic interaction in which the two organisms live together in more or less intimate association. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism RO:0002440 @@ -3896,7 +3894,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002441 @@ -3911,7 +3909,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002442 @@ -3926,7 +3924,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 This relation groups a pair of inverse relations, parasite of and parasitized by RO:0002443 @@ -3944,7 +3942,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human - Chris Mungall + parasitizes RO:0002444 direct parasite of @@ -3961,7 +3959,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + has parasite parasitised by RO:0002445 @@ -3980,7 +3978,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - Chris Mungall + RO:0002446 semibiotically interacts with @@ -3996,7 +3994,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. RO:0002447 phosphorylates @@ -4015,8 +4013,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - Chris Mungall - Vasundra Touré + + RO:0002448 molecularly controls directly_regulates_activity_of @@ -4033,8 +4031,8 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly inhibits RO:0002449 molecularly decreases activity of @@ -4052,8 +4050,8 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly activates RO:0002450 molecularly increases activity of @@ -4070,7 +4068,7 @@ For example, A and B may be gene products and binding of B by A positively regul all dengue disease transmitted by some mosquito A relationship that holds between a disease and organism Add domain and range constraints - Chris Mungall + RO:0002451 transmitted_by transmitted by @@ -4084,7 +4082,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between a disease or an organism and a phenotype - Chris Mungall + RO:0002452 has_symptom has symptom @@ -4096,7 +4094,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) RO:0002453 @@ -4111,7 +4109,7 @@ For example, A and B may be gene products and binding of B by A positively regul X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y - Chris Mungall + RO:0002454 has_host @@ -4128,7 +4126,7 @@ For example, A and B may be gene products and binding of B by A positively regul Bees pollinate Flowers This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - Chris Mungall + is subject of pollination interaction with RO:0002455 @@ -4143,7 +4141,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + has polinator is target of pollination interaction with RO:0002456 @@ -4160,7 +4158,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4175,7 +4173,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of preys on - Chris Mungall + has predator is target of predation interaction with RO:0002458 @@ -4195,7 +4193,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anopheles is a vector for Plasmodium - Chris Mungall + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism RO:0002459 @@ -4209,7 +4207,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002460 has_vector @@ -4222,7 +4220,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target RO:0002461 partner_in @@ -4235,7 +4233,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002462 subject_participant_in @@ -4248,7 +4246,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002463 target_participant_in @@ -4261,7 +4259,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002469 provides_nutrients_for @@ -4274,7 +4272,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is subject of eating interaction with RO:0002470 @@ -4288,7 +4286,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + eaten by is target of eating interaction with RO:0002471 @@ -4307,7 +4305,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - Chris Mungall + RO:0002473 @@ -4326,7 +4324,7 @@ For example, A and B may be gene products and binding of B by A positively regul ABal nucleus child nucleus of ABa nucleus (in C elegans) c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d - Chris Mungall + This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. RO:0002476 child_nucleus_of @@ -4340,7 +4338,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a hermaphroditic organism - Chris Mungall + RO:0002477 child_nucleus_of_in_hermaphrodite child nucleus of in hermaphrodite @@ -4353,7 +4351,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a male organism - Chris Mungall + RO:0002478 child_nucleus_of_in_male child nucleus of in male @@ -4367,7 +4365,7 @@ For example, A and B may be gene products and binding of B by A positively regul p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall + RO:0002479 has_part_that_occurs_in @@ -4382,7 +4380,7 @@ For example, A and B may be gene products and binding of B by A positively regul An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y Axiomatization to GO to be added later - Chris Mungall + RO:0002480 ubiquitinates ubiquitinates @@ -4396,7 +4394,7 @@ For example, A and B may be gene products and binding of B by A positively regul See notes for inverse relation - Chris Mungall + RO:0002485 receives_input_from receives input from @@ -4409,7 +4407,7 @@ For example, A and B may be gene products and binding of B by A positively regul This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - Chris Mungall + RO:0002486 sends_output_to sends output to @@ -4423,7 +4421,7 @@ For example, A and B may be gene products and binding of B by A positively regul x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - Chris Mungall + RO:0002494 transformation_of transformation of @@ -4437,7 +4435,7 @@ For example, A and B may be gene products and binding of B by A positively regul x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - Chris Mungall + RO:0002495 immediate_transformation_of @@ -4467,7 +4465,7 @@ For example, A and B may be gene products and binding of B by A positively regul p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002501 @@ -4483,7 +4481,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c - Chris Mungall + has intermediate product RO:0002505 @@ -4500,7 +4498,7 @@ For example, A and B may be gene products and binding of B by A positively regul The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002506 @@ -4522,11 +4520,11 @@ For example, A and B may be gene products and binding of B by A positively regul A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future - Chris Mungall + determined by (system to material entity) - Chris Mungall - Pier Buttigieg + + RO:0002507 determined_by @@ -4540,7 +4538,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of determined by - Chris Mungall + determines (material entity to system) RO:0002508 @@ -4559,7 +4557,7 @@ For example, A and B may be gene products and binding of B by A positively regul s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. - Chris Mungall + RO:0002509 determined_by_part_of @@ -4574,7 +4572,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between two entities that have the property of being sequences or having sequences. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. @@ -4594,7 +4592,7 @@ For example, A and B may be gene products and binding of B by A positively regul Two consecutive DNA residues are sequentially adjacent Two exons on a processed transcript that were previously connected by an intron are adjacent x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002515 @@ -4612,7 +4610,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as a start sequence the start codon for that transcript x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence - Chris Mungall + started by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4629,7 +4627,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has start sequence - Chris Mungall + starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4649,7 +4647,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence - Chris Mungall + ended by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4666,7 +4664,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has end sequence - Chris Mungall + ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4684,7 +4682,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. In the SO paper, this was defined as an instance-type relation - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002520 @@ -4701,7 +4699,7 @@ For example, A and B may be gene products and binding of B by A positively regul Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering - Chris Mungall + RO:0002521 is_sequentially_aligned_with @@ -4718,7 +4716,7 @@ For example, A and B may be gene products and binding of B by A positively regul The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y - Chris Mungall + RO:0002522 bounds_sequence_of @@ -4733,7 +4731,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of bounds sequence of - Chris Mungall + RO:0002523 @@ -4751,8 +4749,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x has subsequence y iff all of the sequence parts of x are sequence parts of y - Chris Mungall + x has subsequence y iff all of the sequence parts of y are sequence parts of x + contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4771,7 +4769,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has subsequence - Chris Mungall + contained by RO:0002525 @@ -4788,8 +4786,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. - Chris Mungall + x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. + RO:0002526 overlaps_sequence_of @@ -4803,8 +4801,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. - Chris Mungall + x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + disconnected from RO:0002527 @@ -4820,7 +4818,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of downstream of sequence of - Chris Mungall + RO:0002528 is_upstream_of_sequence_of @@ -4836,7 +4834,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. - Chris Mungall + RO:0002529 is_downstream_of_sequence_of @@ -4852,7 +4850,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y - Chris Mungall + RO:0002530 @@ -4869,7 +4867,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript inverse of immediately downstream of - Chris Mungall + RO:0002531 is_immediately_upstream_of_sequence_of @@ -4889,7 +4887,7 @@ For example, A and B may be gene products and binding of B by A positively regul Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - Chris Mungall + has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). RO:0002551 @@ -4911,7 +4909,7 @@ For example, A and B may be gene products and binding of B by A positively regul p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. - Chris Mungall + RO:0002552 results_in_ending_of results in ending of @@ -4926,7 +4924,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - Chris Mungall + http://eol.org/schema/terms/hyperparasitoidOf https://en.wikipedia.org/wiki/Hyperparasite RO:0002553 @@ -4944,7 +4942,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of hyperparasite of - Chris Mungall + RO:0002554 has epiparasite has hyperparasite @@ -4961,7 +4959,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + http://en.wikipedia.org/wiki/Allelopathy RO:0002555 @@ -4978,7 +4976,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002556 pathogen_of @@ -4991,7 +4989,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002557 has_pathogen @@ -5005,7 +5003,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + causally influenced by (entity-centric) RO:0002559 @@ -5020,7 +5018,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - Chris Mungall + RO:0002565 @@ -5039,8 +5037,8 @@ For example, A and B may be gene products and binding of B by A positively regul The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - Chris Mungall - Vasundra Touré + + causally influences (entity-centric) RO:0002566 @@ -5057,7 +5055,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between elements of a musculoskeletal system or its analogs. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. RO:0002567 biomechanically_related_to @@ -5071,7 +5069,7 @@ For example, A and B may be gene products and binding of B by A positively regul m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - Chris Mungall + Wikipedia:Antagonist_(muscle) RO:0002568 has_muscle_antagonist @@ -5087,7 +5085,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of branching part of - Chris Mungall + RO:0002569 @@ -5104,7 +5102,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - Chris Mungall + UBERON:cjm This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. RO:0002570 @@ -5121,7 +5119,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - Chris Mungall + GOC:cjm RO:0002571 @@ -5137,7 +5135,7 @@ For example, A and B may be gene products and binding of B by A positively regul s is luminal space of x iff s is lumen_of x and s is an immaterial entity - Chris Mungall + RO:0002572 luminal_space_of @@ -5152,7 +5150,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002574 participates_in_a_biotic-biotic_interaction_with @@ -5169,7 +5167,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has skeleton - Chris Mungall + RO:0002576 skeleton_of @@ -5184,7 +5182,7 @@ For example, A and B may be gene products and binding of B by A positively regul p directly regulates q iff p is immediately causally upstream of q and p regulates q. - Chris Mungall + directly regulates (processual) @@ -5205,7 +5203,7 @@ For example, A and B may be gene products and binding of B by A positively regul gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - Chris Mungall + RO:0002584 has_part_structure_that_is_capable_of has part structure that is capable of @@ -5320,7 +5318,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall + RO:0002595 causal_relation_between_material_entity_and_a_process @@ -5723,7 +5721,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. - Vasundra Touré + RO:0003002 represses_expression_of represses expression of @@ -5738,7 +5736,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. - Vasundra Touré + RO:0003003 increases_expression_of increases expression of @@ -5883,7 +5881,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:38:20Z RO:0004000 condition_has_genetic_basis_in @@ -5897,7 +5895,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:20Z RO:0004001 has_material_basis_in_gain_of_function_germline_mutation_in @@ -5913,7 +5911,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:37Z RO:0004002 has_material_basis_in_loss_of_function_germline_mutation_in @@ -5927,7 +5925,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:54Z RO:0004003 has_material_basis_in_germline_mutation_in @@ -5942,7 +5940,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:07Z RO:0004004 has_material_basis_in_somatic_mutation_in @@ -5957,7 +5955,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:26Z RO:0004005 has_major_susceptibility_factor @@ -5971,7 +5969,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:57Z RO:0004006 has_partial_material_basis_in_germline_mutation_in @@ -5985,7 +5983,7 @@ Environmental exposures include those imposed by natural environments, experimen p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - cjm + 2018-12-13T11:26:17Z RO:0004007 @@ -6001,7 +5999,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - cjm + 2018-12-13T11:26:32Z RO:0004008 @@ -6012,8 +6010,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6027,7 +6025,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - cjm + 2018-12-13T11:26:56Z RO:0004009 @@ -6038,8 +6036,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6053,7 +6051,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:53:08Z RO:0004010 is_genetic_basis_for_condition @@ -6067,7 +6065,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:55:51Z RO:0004011 is_causal_gain_of_function_germline_mutation_of_in @@ -6082,7 +6080,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:06Z RO:0004012 is_causal_loss_of_function_germline_mutation_of_in @@ -6098,7 +6096,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:40Z RO:0004013 is_causal_germline_mutation_in @@ -6114,7 +6112,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:57:07Z RO:0004014 is_causal_somatic_mutation_in @@ -6129,7 +6127,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. - cjm + 2017-11-05T02:57:43Z RO:0004015 is_causal_susceptibility_factor_for @@ -6145,7 +6143,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. - cjm + 2017-11-05T02:58:43Z RO:0004016 is_causal_germline_mutation_partially_giving_rise_to @@ -6160,7 +6158,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:01Z RO:0004017 realizable_has_basis_in @@ -6173,7 +6171,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:29Z RO:0004018 is_basis_for_realizable @@ -6188,7 +6186,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:26:47Z RO:0004019 disease_has_basis_in @@ -6204,7 +6202,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) - cjm + 2017-11-05T03:29:32Z RO:0004020 disease_has_basis_in_dysfunction_of @@ -6220,7 +6218,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. disease has basis in disruption of (disease to process) - cjm + 2017-11-05T03:37:52Z RO:0004021 disease_has_basis_in_disruption_of @@ -6244,7 +6242,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. - cjm + 2017-11-05T03:46:07Z RO:0004022 disease_has_basis_in_feature @@ -6260,7 +6258,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. - cjm + 2017-11-05T03:50:54Z RO:0004023 causal_relationship_with_disease_as_subject @@ -6277,7 +6275,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and a process where the disease process disrupts the execution of the process. disease causes disruption of (disease to process) - cjm + 2017-11-05T03:51:09Z RO:0004024 disease_causes_disruption_of @@ -6293,7 +6291,7 @@ Environmental exposures include those imposed by natural environments, experimen disease causes dysfunction of (disease to anatomical entity) - cjm + 2017-11-05T03:58:20Z RO:0004025 disease_causes_dysfunction_of @@ -6319,7 +6317,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. - cjm + 2017-11-05T04:06:02Z RO:0004026 disease_has_location @@ -6343,7 +6341,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity - cjm + 2017-12-26T19:37:31Z RO:0004027 disease_has_inflammation_site @@ -6359,7 +6357,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - cjm + 2017-12-26T19:45:49Z RO:0004028 realized_in_response_to_stimulus @@ -6382,7 +6380,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. - cjm + 2017-12-26T19:50:53Z RO:0004029 disease_has_feature @@ -6397,7 +6395,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. - cjm + 2017-12-26T19:58:44Z RO:0004030 disease_arises_from_alteration_in_structure @@ -6411,7 +6409,7 @@ Environmental exposures include those imposed by natural environments, experimen Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - cjm + 2018-01-25T23:20:13Z RO:0004031 enables_subfunction @@ -6425,7 +6423,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:30Z RO:0004032 @@ -6441,7 +6439,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:51Z RO:0004033 @@ -6458,7 +6456,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - cjm + 2018-01-26T23:53:14Z RO:0004034 @@ -6476,7 +6474,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - cjm + 2018-01-26T23:53:22Z RO:0004035 @@ -6492,7 +6490,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:05Z RO:0004046 causally_upstream_of_or_within,_negative_effect @@ -6506,7 +6504,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:19Z RO:0004047 causally_upstream_of_or_within,_positive_effect @@ -6633,10 +6631,10 @@ Environmental exposures include those imposed by natural environments, experimen An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - Austin Meier - Chris Mungall - David Osumi-Sutherland - Marie Angelique Laporte + + + + RO:0009501 triggered by process realized_in_response_to @@ -6659,7 +6657,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - Vasundra Touré + RO:0011002 regulates_activity_of regulates activity of @@ -6674,7 +6672,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. - Vasundra Touré + RO:0011003 regulates_quantity_of regulates quantity of @@ -6689,7 +6687,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. - Vasundra Touré + RO:0011004 indirectly_regulates_activity_of indirectly regulates activity of @@ -6706,7 +6704,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011007 decreases_by_repression_quantity_of decreases by repression quantity of @@ -6723,7 +6721,7 @@ For example, protein A (transcription factor) indirectly decreases by repression The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011008 increases_by_expression_quantity_of increases by expression quantity of @@ -6738,7 +6736,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly positively regulates the quantity of B. - Vasundra Touré + RO:0011009 directly_positively_regulates_quantity_of directly positively regulates quantity of @@ -6753,7 +6751,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly negatively regulates the quantity of B. - Vasundra Touré + RO:0011010 directly_negatively_regulates_quantity_of directly negatively regulates quantity of @@ -6768,7 +6766,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. - Vasundra Touré + indirectly activates RO:0011013 indirectly_positively_regulates_activity_of @@ -6785,7 +6783,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. - Vasundra Touré + RO:0011014 destabilizes_quantity_of destabilizes quantity of @@ -6801,7 +6799,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. - Vasundra Touré + RO:0011015 stabilizes_quantity_of stabilizes quantity of @@ -6814,7 +6812,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. - Vasundra Touré + indirectly inhibits RO:0011016 indirectly_negatively_regulates_activity_of @@ -6828,7 +6826,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. - Vasundra Touré + RO:0011021 directly_regulates_quantity_of directly regulates quantity of @@ -6841,7 +6839,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011022 indirectly_regulates_quantity_of indirectly regulates quantity of @@ -6854,7 +6852,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011023 indirectly_negatively_regulates_quantity_of indirectly negatively regulates quantity of @@ -6867,7 +6865,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011024 indirectly_positively_regulates_quantity_of indirectly positively regulates quantity of @@ -6880,8 +6878,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is regulated by the small molecule continuant + pg 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -6895,8 +6893,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is activated by the small molecule continuant + pg 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -6910,8 +6908,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant + pg 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -6924,8 +6922,8 @@ For example, protein A (transcription factor) indirectly increases by expression - p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + p acts on population of c iff c' is a collection, has members of type c, and p has participant c + pg 2020-06-08T17:21:33Z RO:0012003 @@ -6941,8 +6939,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process + pg 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -6956,8 +6954,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process + pg 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of @@ -6971,8 +6969,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process + pg 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of @@ -6985,8 +6983,8 @@ For example, protein A (transcription factor) indirectly increases by expression - The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. + pg 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -6999,7 +6997,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + pg 2021-02-26T07:28:29Z RO:0012008 @@ -7016,7 +7014,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + pg 2022-09-26T06:01:01Z RO:0012009 @@ -7032,7 +7030,7 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + pg 2022-09-26T06:06:20Z RO:0012010 @@ -7048,7 +7046,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + pg 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7063,7 +7061,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + pg 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7229,7 +7227,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relation between a group and another group it is part of but does not fully constitute. X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. - Shawn Tan + This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. RO:0015003 subcluster_of @@ -7301,7 +7299,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - http://orcid.org/0000-0002-7463-6306 + 2021-11-05T17:30:44Z RO:0016002 has_disease @@ -7457,7 +7455,7 @@ For example, protein A (transcription factor) indirectly increases by expression This relation groups relations between diseases and any other kind of entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. - cjm + 2018-09-26T00:00:32Z RO:0040035 disease_relationship @@ -7471,7 +7469,7 @@ For example, protein A (transcription factor) indirectly increases by expression p has anatomical participant c iff p has participant c, and c is an anatomical entity - cjm + 2018-09-26T01:08:58Z RO:0040036 results_in_changes_to_anatomical_or_cellular_structure diff --git a/src/ontology/subsets/ro-mereotopology.obo b/src/ontology/subsets/ro-mereotopology.obo index 7945191a..33d6e97a 100644 --- a/src/ontology/subsets/ro-mereotopology.obo +++ b/src/ontology/subsets/ro-mereotopology.obo @@ -13,7 +13,7 @@ id: acquires_nutrients_from name: acquires nutrients from subset: ro-eco xref: RO:0002457 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for @@ -58,7 +58,7 @@ property_value: RO:0004050 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:22Z [Typedef] @@ -71,7 +71,7 @@ property_value: RO:0004049 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:14Z [Typedef] @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z [Typedef] @@ -103,7 +103,7 @@ xref: RO:0004032 property_value: RO:0004049 RO:0002264 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z [Typedef] @@ -120,7 +120,7 @@ property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cy property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 domain: BFO:0000004 range: BFO:0000004 @@ -131,7 +131,7 @@ id: allelopath_of name: allelopath of subset: ro-eco xref: RO:0002555 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string @@ -153,7 +153,7 @@ def: "x anabranch_of y if x is a distributary of y (i.e. it channels a from a la subset: ro-eco xref: RO:0002378 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "anastomoses with" xsd:string is_a: distributary_of ! distributary of disjoint_from: proper_distributary_of ! proper distributary of @@ -165,7 +165,7 @@ name: attached to def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] subset: ro-eco xref: RO:0002371 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: attached_to_part_of ! attached to part of @@ -189,9 +189,8 @@ def: "Relation between a neuron and some structure its axon forms (chemical) syn xref: RO:0002102 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in @@ -202,7 +201,7 @@ id: biomechanically_related_to name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] xref: RO:0002567 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: CARO:0000003 range: CARO:0000003 @@ -214,7 +213,7 @@ name: biotically interacts with def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] subset: ro-eco xref: RO:0002437 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string @@ -231,7 +230,7 @@ def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\ comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco xref: RO:0002007 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 is_a: part_of @@ -242,7 +241,7 @@ def: "x bounds the sequence of y iff the upstream-most part of x is upstream of xref: RO:0002522 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to inverse_of: is_bound_by_sequence_of ! is bound by sequence of @@ -254,7 +253,7 @@ def: "x is a branching part of y if and only if x is part of y and x is connecte subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso FMA:85994 xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with @@ -269,7 +268,7 @@ subset: ro-eco xref: RO:0002215 property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 @@ -302,7 +301,7 @@ id: capable_of_part_of name: capable of part of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ is_a: causal_agent_in_process ! causal agent in process @@ -350,7 +349,7 @@ id: causal_relation_between_entities name: causal relation between entities xref: RO:0002506 property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000002 @@ -363,7 +362,7 @@ name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] xref: RO:0002595 property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 range: BFO:0000015 @@ -374,7 +373,7 @@ id: causal_relation_between_processes name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 @@ -389,7 +388,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: OGMS:0000031 is_a: causally_related_to ! causally related to is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:50:54Z [Typedef] @@ -398,7 +397,7 @@ name: causally downstream of def: "inverse of upstream of" [] xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within is_a: preceded_by inverse_of: causally_upstream_of ! causally upstream of @@ -409,7 +408,7 @@ name: causally downstream of or within def: "inverse of causally upstream of or within" [] subset: RO:0002259 xref: RO:0002427 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -418,7 +417,7 @@ is_a: causal_relation_between_processes ! causal relation between processes id: causally_influenced_by name: causally influenced by xref: RO:0002559 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: causal_relation_between_entities ! causal relation between entities @@ -429,8 +428,8 @@ id: causally_influences name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] xref: RO:0002566 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 @@ -443,7 +442,7 @@ name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] @@ -453,7 +452,7 @@ def: "p is causally upstream of q iff p is causally related to q, the end of p p subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes @@ -465,7 +464,7 @@ def: "p is causally upstream of, negative effect q iff p is casually upstream of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -478,7 +477,7 @@ comment: holds between x and y if and only if x is causally upstream of y and th subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -490,7 +489,7 @@ def: "p is 'causally upstream or within' q iff p is causally related to q, and t synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -502,7 +501,7 @@ name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -511,7 +510,7 @@ name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -537,7 +536,7 @@ name: child nucleus of def: "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" [] xref: RO:0002476 property_value: IAO:0000112 "ABal nucleus child nucleus of ABa nucleus (in C elegans)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." xsd:string domain: GO:0005634 range: GO:0005634 @@ -548,7 +547,7 @@ id: child_nucleus_of_in_hermaphrodite name: child nucleus of in hermaphrodite def: "A child nucleus relationship in which the cells are part of a hermaphroditic organism" [] xref: RO:0002477 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -556,7 +555,7 @@ id: child_nucleus_of_in_male name: child nucleus of in male def: "A child nucleus relationship in which the cells are part of a male organism" [] xref: RO:0002478 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -576,7 +575,7 @@ comment: Example: if we define region of chromosome as any subdivision of a chro subset: ro-eco xref: RO:0002008 property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -585,9 +584,8 @@ name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 -property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -599,7 +597,7 @@ name: commensually interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] subset: ro-eco xref: RO:0002441 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -610,7 +608,7 @@ def: "x composed_primarily_of y if and only if more than half of the mass of x i subset: ro-eco xref: RO:0002473 property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 @@ -639,7 +637,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: BFO:0000017 is_a: causally_related_to ! causally related to inverse_of: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:38:20Z [Typedef] @@ -648,7 +646,7 @@ name: conduit for def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] subset: ro-eco xref: RO:0002570 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 UBERON:cjm xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 @@ -661,7 +659,7 @@ name: confers advantage in subset: ro-eco xref: RO:0002322 property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "adapted for" xsd:string range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -727,7 +725,7 @@ name: continuous with def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 @@ -746,7 +744,7 @@ property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a het property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -771,7 +769,7 @@ id: contributes_to_morphology_of name: contributes to morphology of def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] xref: RO:0002433 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -796,7 +794,7 @@ id: decreases_by_repression_quantity_of name: decreases by repression quantity of def: "The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011007 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_negatively_regulates_quantity_of ! indirectly negatively regulates quantity of @@ -808,8 +806,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in wh xref: RO:0002121 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in @@ -821,7 +819,7 @@ name: destabilizes quantity of def: "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." [] xref: RO:0011014 property_value: IAO:0000112 "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_quantity_of ! directly negatively regulates quantity of @@ -832,11 +830,11 @@ name: determined by def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] subset: ro-eco xref: RO:0002507 -property_value: http://purl.org/dc/terms/creator "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/creator "Pier Buttigieg" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-4366-3088 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "A coral reef environment is determined by a particular coral reef" xsd:string property_value: IAO:0000116 "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602 property_value: IAO:0000589 "determined by (system to material entity)" xsd:string domain: RO:0002577 @@ -852,7 +850,7 @@ name: determined by part of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] subset: ro-eco xref: RO:0002509 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 range: BFO:0000040 is_a: causal_relation_between_entities ! causal relation between entities @@ -865,7 +863,7 @@ def: "inverse of determined by" [] subset: ro-eco subset: RO:0002259 xref: RO:0002508 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "determines (material entity to system)" xsd:string is_a: causally_influences ! causally influences @@ -876,7 +874,7 @@ def: "inverse of has developmental contribution from" [] subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to @@ -886,9 +884,9 @@ name: developmentally induced by def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] xref: RO:0002256 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string property_value: IAO:0000119 GO:0001759 xsd:string @@ -905,7 +903,7 @@ name: developmentally induces def: "Inverse of developmentally induced by" [] xref: RO:0002257 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_induce ! has potential to developmentally induce @@ -917,7 +915,7 @@ comment: This relation groups together various other developmental relations. It xref: RO:0002258 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string domain: BFO:0000002 range: BFO:0000002 @@ -929,7 +927,7 @@ id: developmentally_related_to name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] xref: RO:0002324 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] @@ -939,7 +937,7 @@ def: "x developmentally replaces y if and only if there is some developmental pr xref: RO:0002285 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "replaces" xsd:string is_a: developmentally_preceded_by ! developmentally preceded by @@ -949,7 +947,7 @@ name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] xref: RO:0002286 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -959,10 +957,10 @@ def: "x develops from y if and only if either (a) x directly develops from y or comment: This is the transitive form of the develops from relation xref: RO:0002202 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 domain: BFO:0000004 range: BFO:0000004 is_transitive: true @@ -975,7 +973,7 @@ name: develops from part of def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] xref: RO:0002225 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: develops_from ! develops from [Typedef] @@ -984,7 +982,7 @@ name: develops in def: "x develops_in y if x is located in y whilst x is developing" [] xref: RO:0002226 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string domain: CARO:0000000 @@ -997,9 +995,9 @@ def: "inverse of develops from" [] subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 is_transitive: true is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into @@ -1010,11 +1008,11 @@ id: directly_develops_from name: directly develops from def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] xref: RO:0002207 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "has developmental precursor" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000119 "FBbt" xsd:string property_value: RO:0002575 RO:0002202 is_a: develops_from ! develops from @@ -1060,8 +1058,8 @@ name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] xref: RO:0002449 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1072,7 +1070,7 @@ id: directly_negatively_regulates_quantity_of name: directly negatively regulates quantity of def: "The entity A has an activity that directly negatively regulates the quantity of B." [] xref: RO:0011010 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1107,8 +1105,8 @@ name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] xref: RO:0002450 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1119,7 +1117,7 @@ id: directly_positively_regulates_quantity_of name: directly positively regulates quantity of def: "The entity A has an activity that directly positively regulates the quantity of B." [] xref: RO:0011009 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1142,7 +1140,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002578 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string property_value: RO:0002575 RO:0002211 @@ -1155,8 +1153,8 @@ name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] xref: RO:0002448 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: molecularly_interacts_with ! molecularly interacts with @@ -1167,7 +1165,7 @@ id: directly_regulates_quantity_of name: directly regulates quantity of def: "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B." [] xref: RO:0011021 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -1177,7 +1175,7 @@ def: "A relationship between a disease and an anatomical structure where the mat xref: RO:0004030 range: CARO:0000003 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z [Typedef] @@ -1189,7 +1187,7 @@ property_value: IAO:0000589 "disease causes disruption of (disease to process)" domain: OGMS:0000031 range: BFO:0000015 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:51:09Z [Typedef] @@ -1200,7 +1198,7 @@ property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomica domain: OGMS:0000031 range: CARO:0000006 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z [Typedef] @@ -1210,7 +1208,7 @@ xref: RO:0004019 domain: OGMS:0000031 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject is_a: realizable_has_basis_in ! realizable has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:26:47Z [Typedef] @@ -1221,7 +1219,7 @@ xref: RO:0004021 property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:37:52Z [Typedef] @@ -1232,7 +1230,7 @@ xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string range: CARO:0000006 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z [Typedef] @@ -1243,7 +1241,7 @@ xref: RO:0004022 domain: OGMS:0000031 is_a: disease_has_basis_in ! disease has basis in is_a: has_phenotype ! has phenotype -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:46:07Z [Typedef] @@ -1253,7 +1251,7 @@ def: "A relationship between a disease and some feature of that disease, where t xref: RO:0004029 domain: OGMS:0000031 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:50:53Z [Typedef] @@ -1272,7 +1270,7 @@ xref: RO:0004027 domain: OGMS:0000031 range: BFO:0000004 is_a: disease_has_location ! disease has location -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:37:31Z [Typedef] @@ -1285,7 +1283,7 @@ property_value: IAO:0000232 "This relation is intentionally very general, and co domain: OGMS:0000031 range: BFO:0000004 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T04:06:02Z [Typedef] @@ -1294,7 +1292,7 @@ name: disease relationship def: "This relation groups relations between diseases and any other kind of entity." [] xref: RO:0040035 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z [Typedef] @@ -1306,7 +1304,7 @@ subset: ro-eco xref: RO:0002377 property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string @@ -1316,10 +1314,10 @@ is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: does_not_overlap_sequence_of name: does not overlap sequence of -def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] xref: RO:0002527 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "disconnected from" xsd:string is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -1338,7 +1336,7 @@ id: eats name: eats subset: ro-eco xref: RO:0002470 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -1359,7 +1357,7 @@ def: "A relationship that is mediated in some way by the environment or environm subset: ro-eco xref: RO:0002321 property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string [Typedef] @@ -1377,7 +1375,7 @@ name: electrically_synapsed_to def: "A relation that holds between two neurons that are electrically coupled via gap junctions." [] xref: RO:0002003 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: connected_to ! connected to [Typedef] @@ -1386,7 +1384,7 @@ name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: has_participant @@ -1397,7 +1395,7 @@ def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string property_value: IAO:0000118 "has" xsd:string @@ -1413,7 +1411,7 @@ name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] xref: RO:0004031 is_a: functionally_related_to ! functionally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z [Typedef] @@ -1430,14 +1428,14 @@ inverse_of: has_endoparasite ! has endoparasite id: ends subset: ro-eco xref: RO:0002229 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: ends_with subset: ro-eco xref: RO:0002230 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -1462,7 +1460,7 @@ name: exports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002345 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -1479,7 +1477,7 @@ def: "relationship between a neuron and a neuron projection bundle (e.g.- tract xref: RO:0002101 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 @@ -1492,7 +1490,7 @@ inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron proje id: formed_as_result_of name: formed as result of xref: RO:0002354 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of [Typedef] @@ -1500,7 +1498,7 @@ id: functionally_related_to name: functionally related to def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] xref: RO:0002328 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string [Typedef] @@ -1509,7 +1507,7 @@ name: genetically interacts with xref: RO:0002435 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with @@ -1517,7 +1515,7 @@ is_a: interacts_with ! interacts with [Typedef] id: has_2D_boundary xref: RO:0002002 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1557,7 +1555,7 @@ def: "inverse of branching part of" [] subset: ro-eco subset: RO:0002259 xref: RO:0002569 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: has_part is_a: in_branching_relationship_with ! in branching relationship with @@ -1593,7 +1591,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 "Bill Duncan (https://orcid.org/0000-0001-9625-1899)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant @@ -1622,7 +1620,7 @@ id: has_dendrite_location name: has dendrite location xref: RO:0002360 property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -1632,7 +1630,7 @@ def: "x has developmental contribution from y iff x has some part z such that z xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by @@ -1644,7 +1642,7 @@ name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to @@ -1656,7 +1654,7 @@ def: "p has direct input c iff c is a participant in p, c is present at the star xref: RO:0002400 property_value: IAO:0000112 "'protein catabolic process' SubClassOf has_direct_input some protein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly consumes" xsd:string property_value: IAO:0000232 "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" xsd:string is_a: has_input ! has input @@ -1666,7 +1664,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1711,7 +1709,7 @@ def: "x 'has end location' y if and only if there exists some process z such tha subset: ro-eco xref: RO:0002232 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -1724,7 +1722,7 @@ def: "x has end sequence y if the end of x is identical to the end of y, and x h xref: RO:0002518 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -1776,11 +1774,11 @@ id: has_exposure_stimulus name: has exposure stimulus def: "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002309 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 is_a: related_via_exposure_to ! related via exposure to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:35:04Z [Typedef] @@ -1806,7 +1804,7 @@ def: "The relation between a neuron projection bundle and a neuron projection th xref: RO:0002132 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 @@ -1828,7 +1826,7 @@ subset: ro-eco xref: RO:0002303 property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Pier Buttigieg" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string domain: CARO:0001010 range: ENVO:01000254 @@ -1851,7 +1849,7 @@ name: has host def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] subset: ro-eco xref: RO:0002454 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -1865,7 +1863,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 is_a: has_participant @@ -1886,7 +1884,7 @@ def: "p has intermediate c if and only if p has parts p1, p2 and p1 has output c subset: ro-eco xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string is_a: has_participant @@ -1924,7 +1922,7 @@ name: has major susceptibility factor xref: RO:0004005 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_susceptibility_factor_for ! is causal susceptibility factor for -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:26Z [Typedef] @@ -1935,7 +1933,7 @@ property_value: seeAlso Orphanet:410295 property_value: seeAlso Orphanet:410296 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_gain_of_function_germline_mutation_of_in ! is causal gain of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:20Z [Typedef] @@ -1945,7 +1943,7 @@ xref: RO:0004003 property_value: seeAlso Orphanet:317343 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_in ! is causal germline mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:54Z [Typedef] @@ -1954,7 +1952,7 @@ name: has material basis in loss of function germline mutation in xref: RO:0004002 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_loss_of_function_germline_mutation_of_in ! is causal loss of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:37Z [Typedef] @@ -1964,7 +1962,7 @@ xref: RO:0004004 property_value: seeAlso Orphanet:317344 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z [Typedef] @@ -1980,7 +1978,7 @@ id: has_muscle_antagonist name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string is_a: biomechanically_related_to ! biomechanically related to @@ -1989,7 +1987,7 @@ id: has_muscle_insertion name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} @@ -2001,7 +1999,7 @@ id: has_muscle_origin name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} @@ -2039,7 +2037,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string is_a: has_participant inverse_of: output_of ! output of @@ -2066,7 +2064,7 @@ name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] xref: RO:0002584 property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causal_relation_between_material_entity_and_a_process ! causal relation between material entity and a process is_a: functionally_related_to ! functionally related to @@ -2076,7 +2074,7 @@ name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco xref: RO:0002479 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 range: BFO:0000004 @@ -2086,7 +2084,7 @@ name: has partial material basis in germline mutation in xref: RO:0004006 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_partially_giving_rise_to ! is causal germline mutation partially giving rise to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:57Z [Typedef] @@ -2098,7 +2096,7 @@ id: has_pathogen name: has pathogen subset: ro-eco xref: RO:0002557 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2108,7 +2106,7 @@ def: "A relationship that holds between a biological entity and a phenotype. Her subset: ro-eco xref: RO:0002200 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: UPHENO:0001001 is_a: has_phenotype_or_disease ! has phenotype or disease inverse_of: phenotype_of ! phenotype of @@ -2129,9 +2127,9 @@ def: "Holds between a cell c and a protein complex or protein p if and only if t xref: RO:0002104 property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Alexander Diehl" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 @@ -2157,8 +2155,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in whi xref: RO:0002110 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "synapsed in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2172,7 +2170,7 @@ name: has potential to develop into def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] xref: RO:0002387 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2181,7 +2179,7 @@ name: has potential to developmentally contribute to def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] xref: RO:0002385 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2190,7 +2188,7 @@ name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] xref: RO:0002386 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2199,7 +2197,7 @@ name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] xref: RO:0002388 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_potential_to_develop_into ! has potential to develop into [Typedef] @@ -2223,7 +2221,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -2233,7 +2231,7 @@ def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c o subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -2244,7 +2242,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -2276,7 +2274,7 @@ name: has skeleton def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] xref: RO:0002551 property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 @@ -2321,7 +2319,7 @@ name: has soma location def: "Relation between a neuron and an anatomical structure that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 range: CARO:0000003 @@ -2335,7 +2333,7 @@ def: "x 'has starts location' y if and only if there exists some process z such subset: ro-eco xref: RO:0002231 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -2348,7 +2346,7 @@ def: "x has start sequence y if the start of x is identical to the start of y, a xref: RO:0002516 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2358,10 +2356,10 @@ inverse_of: is_start_sequence_of ! is start sequence of [Typedef] id: has_subsequence name: has subsequence -def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2375,7 +2373,7 @@ id: has_symptom name: has symptom def: "A relation that holds between a disease or an organism and a phenotype" [] xref: RO:0002452 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: OGMS:0000031 is_a: has_phenotype ! has phenotype @@ -2405,7 +2403,7 @@ def: "A general relation between a neuron and some structure in which it either xref: RO:0002130 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has synapse in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2417,7 +2415,7 @@ id: has_synaptic_terminal_of name: has synaptic terminal of xref: RO:0002006 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: overlaps ! overlaps inverse_of: has_synaptic_terminal_in ! has synaptic terminal in @@ -2429,7 +2427,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002339 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2440,7 +2438,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002338 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2448,7 +2446,7 @@ id: has_vector name: has vector subset: ro-eco xref: RO:0002460 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with [Typedef] @@ -2463,7 +2461,7 @@ id: host_of name: host of subset: ro-eco xref: RO:0002453 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2476,7 +2474,7 @@ synonym: "epiparasite of" RELATED [] synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string is_a: has_host ! has host @@ -2492,7 +2490,7 @@ synonym: "has epiparasite" RELATED [] synonym: "has hyperparasite" RELATED [] synonym: "hyperparasitoidized by" RELATED [] xref: RO:0002554 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2500,7 +2498,7 @@ id: immediate_transformation_of name: immediate transformation of def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] xref: RO:0002495 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002494 is_a: directly_develops_from ! directly develops from is_a: transformation_of ! transformation of @@ -2510,7 +2508,7 @@ id: immediately_causally_downstream_of name: immediately causally downstream of xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of is_a: immediately_preceded_by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of @@ -2520,7 +2518,7 @@ id: immediately_causally_upstream_of name: immediately causally upstream of def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: immediately_precedes @@ -2533,7 +2531,7 @@ xref: RO:0002087 id: immediately_precedes subset: ro-eco xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0002575 BFO:0000063 [Typedef] @@ -2542,7 +2540,7 @@ name: imports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002340 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -2551,7 +2549,7 @@ name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] xref: RO:0002375 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 @@ -2577,7 +2575,7 @@ id: increases_by_expression_quantity_of name: increases by expression quantity of def: "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011008 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_positively_regulates_quantity_of ! indirectly positively regulates quantity of @@ -2587,7 +2585,7 @@ id: increases_expression_of name: increases expression of def: "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." [] xref: RO:0003003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -2606,7 +2604,7 @@ id: indirectly_negatively_regulates name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true @@ -2618,7 +2616,7 @@ id: indirectly_negatively_regulates_activity_of name: indirectly negatively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B." [] xref: RO:0011016 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly inhibits" xsd:string is_a: indirectly_regulates_activity_of ! indirectly regulates activity of @@ -2627,7 +2625,7 @@ id: indirectly_negatively_regulates_quantity_of name: indirectly negatively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B." [] xref: RO:0011023 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2635,7 +2633,7 @@ id: indirectly_positively_regulates name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 is_transitive: true @@ -2647,7 +2645,7 @@ id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." [] xref: RO:0011013 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -2658,7 +2656,7 @@ id: indirectly_positively_regulates_quantity_of name: indirectly positively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B." [] xref: RO:0011024 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2676,7 +2674,7 @@ id: indirectly_regulates_activity_of name: indirectly regulates activity of def: "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." [] xref: RO:0011004 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: regulates_activity_of ! regulates activity of @@ -2686,7 +2684,7 @@ id: indirectly_regulates_quantity_of name: indirectly regulates quantity of def: "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B." [] xref: RO:0011022 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -2696,7 +2694,7 @@ def: "inverse of has input" [] subset: ro-eco subset: RO:0002259 xref: RO:0002352 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -2710,7 +2708,7 @@ xref: RO:0002434 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI domain: BFO:0000040 @@ -2723,7 +2721,7 @@ name: interacts with via parasite-host interaction def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] subset: ro-eco xref: RO:0002443 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2751,7 +2749,7 @@ id: involved_in name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] xref: RO:0002331 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in @@ -2763,7 +2761,7 @@ id: involved_in_negative_regulation_of name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] xref: RO:0002430 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2773,7 +2771,7 @@ name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in_process ! causal agent in process @@ -2784,7 +2782,7 @@ id: involved_in_positive_regulation_of name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] xref: RO:0002429 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2793,7 +2791,7 @@ id: involved_in_regulation_of name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] xref: RO:0002428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of @@ -2804,7 +2802,7 @@ def: "c executes activity in d if and only if c enables p and p occurs_in d. As synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -2853,7 +2851,7 @@ id: is_basis_for_realizable name: is basis for realizable xref: RO:0004018 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:29Z [Typedef] @@ -2863,7 +2861,7 @@ def: "inverse of bounds sequence of" [] subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to @@ -2874,7 +2872,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004011 property_value: seeAlso Orphanet:410296 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:55:51Z [Typedef] @@ -2885,7 +2883,7 @@ xref: RO:0004013 property_value: seeAlso Orphanet:317343 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:40Z [Typedef] @@ -2896,7 +2894,7 @@ xref: RO:0004016 property_value: seeAlso Orphanet:317346 is_a: contributes_to_condition ! contributes to condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:58:43Z [Typedef] @@ -2906,7 +2904,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004012 property_value: seeAlso Orphanet:410295 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:06Z [Typedef] @@ -2917,7 +2915,7 @@ xref: RO:0004014 property_value: seeAlso Orphanet:317344 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:07Z [Typedef] @@ -2927,7 +2925,7 @@ def: "Relates a gene to condition, such that a mutation in this gene predisposes xref: RO:0004015 property_value: seeAlso Orphanet:317345 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:43Z [Typedef] @@ -2937,7 +2935,7 @@ def: "x is a consecutive sequence of y iff x has subsequence y, and all the part xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: has_subsequence ! has subsequence @@ -2947,7 +2945,7 @@ name: is downstream of sequence of def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] xref: RO:0002529 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of @@ -2957,7 +2955,7 @@ id: is_eaten_by name: is eaten by subset: ro-eco xref: RO:0002471 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -2969,7 +2967,7 @@ def: "inverse of has end sequence" [] subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2982,7 +2980,7 @@ xref: RO:0004010 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string range: BFO:0000017 is_a: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:53:08Z [Typedef] @@ -2992,7 +2990,7 @@ def: "x is immediately downstream of the sequence of y iff either (1) x and y ha xref: RO:0002530 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002529 is_a: is_downstream_of_sequence_of ! is downstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3004,7 +3002,7 @@ def: "inverse of immediately downstream of" [] xref: RO:0002531 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: is_upstream_of_sequence_of ! is upstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3031,7 +3029,7 @@ def: "x is sequentially aligned with if a significant portion bases of x and y c xref: RO:0002521 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -3071,7 +3069,7 @@ def: "inverse of has start sequence" [] subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3084,7 +3082,7 @@ def: "inverse of has subsequence" [] subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of @@ -3107,7 +3105,7 @@ name: is treated by substance def: "Inverse of 'is substance that treats'" [] subset: RO:0002259 xref: RO:0002302 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 is_a: causally_related_to ! causally related to inverse_of: is_substance_that_treats ! is substance that treats @@ -3117,7 +3115,7 @@ name: is upstream of sequence of def: "inverse of downstream of sequence of" [] xref: RO:0002528 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -3127,7 +3125,7 @@ name: is vector for subset: ro-eco xref: RO:0002459 property_value: IAO:0000112 "Anopheles is a vector for Plasmodium" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: has_vector ! has vector @@ -3179,7 +3177,7 @@ name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco xref: RO:0002571 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:cjm xsd:string range: BFO:0000040 is_a: part_of @@ -3190,7 +3188,7 @@ name: luminal space of def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] subset: ro-eco xref: RO:0002572 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000141 is_a: lumen_of ! lumen of @@ -3202,7 +3200,7 @@ subset: ro-eco xref: RO:0002381 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with is_a: part_of @@ -3212,7 +3210,7 @@ id: mereotopologically_related_to name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] xref: RO:0002323 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string property_value: RO:0001900 RO:0001901 @@ -3230,7 +3228,7 @@ name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 @@ -3243,7 +3241,7 @@ name: mutualistically interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] subset: ro-eco xref: RO:0002442 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -3270,7 +3268,7 @@ name: negatively regulated by def: "inverse of negatively regulates" [] subset: RO:0002259 xref: RO:0002335 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3281,7 +3279,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 @@ -3330,7 +3328,7 @@ def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -3351,10 +3349,10 @@ expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://p [Typedef] id: overlaps_sequence_of name: overlaps sequence of -def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] xref: RO:0002526 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: overlaps ! overlaps is_a: sequentially_related_to ! sequentially related to @@ -3366,7 +3364,7 @@ subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string is_a: has_host ! has host @@ -3379,7 +3377,7 @@ name: parasitized by subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string @@ -3418,7 +3416,7 @@ name: part of developmental precursor of xref: RO:0002287 property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by [Typedef] @@ -3426,7 +3424,7 @@ id: part_of_structure_that_is_capable_of name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] xref: RO:0002329 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean is_a: functionally_related_to ! functionally related to @@ -3455,7 +3453,7 @@ subset: ro-eco synonym: "semibiotically interacts with" RELATED [] xref: RO:0002446 property_value: IAO:0000112 "Porifiera attaches to substrate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: biotically_interacts_with ! biotically interacts with @@ -3464,7 +3462,7 @@ id: participates_in_a_biotic-biotic_interaction_with name: participates in a biotic-biotic interaction with subset: ro-eco xref: RO:0002574 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 domain: CARO:0001010 range: CARO:0001010 @@ -3474,7 +3472,7 @@ is_a: biotically_interacts_with ! biotically interacts with id: partner_in name: partner in xref: RO:0002461 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string is_a: participates_in @@ -3483,7 +3481,7 @@ id: pathogen_of name: pathogen of subset: ro-eco xref: RO:0002556 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_host ! has host inverse_of: has_pathogen ! has pathogen @@ -3495,7 +3493,7 @@ subset: ro-eco subset: RO:0002259 xref: RO:0002201 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_functional: true [Typedef] @@ -3503,7 +3501,7 @@ id: phosphorylates name: phosphorylates xref: RO:0002447 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: molecularly_interacts_with ! molecularly interacts with @@ -3512,7 +3510,7 @@ id: pollinated_by name: pollinated by subset: ro-eco xref: RO:0002456 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string @@ -3525,7 +3523,7 @@ subset: ro-eco xref: RO:0002455 property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with @@ -3537,7 +3535,7 @@ name: positively regulated by def: "inverse of positively regulates" [] subset: RO:0002259 xref: RO:0002336 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3548,7 +3546,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002211 @@ -3583,7 +3581,7 @@ def: "inverse of preys on" [] subset: ro-eco subset: RO:0002259 xref: RO:0002458 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string @@ -3598,9 +3596,9 @@ subset: ro-eco xref: RO:0002439 property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Jorrit Poelen" xsd:string -property_value: IAO:0000117 "Katja Shulz" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7134-3324 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string @@ -3623,7 +3621,7 @@ def: "x proper_distributary_of y iff x distributary_of y and x does not flow bac subset: ro-eco xref: RO:0002382 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: distributary_of ! distributary of [Typedef] @@ -3633,7 +3631,7 @@ def: "x proper_tributary_of y iff x tributary_of y and x does not originate from subset: ro-eco xref: RO:0002383 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: tributary_of ! tributary of [Typedef] @@ -3642,7 +3640,7 @@ name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string @@ -3654,7 +3652,7 @@ id: provides_nutrients_for name: provides nutrients for subset: ro-eco xref: RO:0002469 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3663,7 +3661,7 @@ name: realizable has basis in xref: RO:0004017 is_a: causally_related_to ! causally related to inverse_of: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:01Z [Typedef] @@ -3672,10 +3670,10 @@ name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] synonym: "triggered by process" EXACT [RO:cjm] xref: RO:0009501 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "David Osumi-Sutherland" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string @@ -3692,7 +3690,7 @@ xref: RO:0004028 domain: BFO:0000017 range: BFO:0000040 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:45:49Z [Typedef] @@ -3700,7 +3698,7 @@ id: receives_input_from name: receives input from xref: RO:0002485 property_value: IAO:0000116 "See notes for inverse relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to inverse_of: sends_output_to ! sends output to @@ -3740,7 +3738,7 @@ name: regulated by def: "inverse of regulates" [] subset: RO:0002259 xref: RO:0002334 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 range: BFO:0000015 @@ -3755,9 +3753,9 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Hill" xsd:string -property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 +property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string @@ -3774,7 +3772,7 @@ id: regulates_activity_of name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] xref: RO:0011002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3794,7 +3792,7 @@ id: regulates_in_other_organism name: regulates in other organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] xref: RO:0002010 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 range: BFO:0000015 is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -3805,7 +3803,7 @@ name: regulates levels of def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] xref: RO:0002332 property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 @@ -3817,7 +3815,7 @@ id: regulates_quantity_of name: regulates quantity of def: "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." [] xref: RO:0011003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3836,7 +3834,7 @@ id: related_via_localization_to name: related via localization to def: "A relationship that holds via some process of localization" [] xref: RO:0002337 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 range: BFO:0000002 @@ -3857,7 +3855,7 @@ id: represses_expression_of name: represses expression of def: "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." [] xref: RO:0003002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3871,7 +3869,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -3916,7 +3914,7 @@ name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] @@ -3936,7 +3934,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002348 property_value: IAO:0000112 "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3948,7 +3946,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002349 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3962,7 +3960,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3972,7 +3970,7 @@ id: results_in_developmental_induction_of name: results in developmental induction of def: "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." [] xref: RO:0002357 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3982,7 +3980,7 @@ def: "p results in the developmental progression of s iff p is a developmental p xref: RO:0002295 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 range: CARO:0000000 @@ -3994,7 +3992,7 @@ name: results in developmental regression of xref: RO:0002301 property_value: IAO:0000112 "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4004,7 +4002,7 @@ name: results in disappearance of xref: RO:0002300 property_value: IAO:0000112 "foramen ovale closure SubClassOf results in disappearance of foramen ovale" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4020,7 +4018,7 @@ id: results_in_ending_of name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4034,7 +4032,7 @@ xref: RO:0002297 property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4056,7 +4054,7 @@ id: results_in_growth_of name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4071,7 +4069,7 @@ xref: RO:0002299 property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4087,7 +4085,7 @@ xref: RO:0002298 property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4100,7 +4098,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002565 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4126,7 +4124,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002356 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4135,7 +4133,7 @@ id: results_in_structural_organization_of name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4151,7 +4149,7 @@ name: results in transport across def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002342 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: occurs_across ! occurs across is_a: results_in_transport_to_from_or_in ! results in transport to from or in @@ -4160,7 +4158,7 @@ id: results_in_transport_along name: results in transport along def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] xref: RO:0002341 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4168,7 +4166,7 @@ id: results_in_transport_to_from_or_in name: results in transport to from or in xref: RO:0002344 property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4183,7 +4181,7 @@ id: sends_output_to name: sends output to xref: RO:0002486 property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to [Typedef] @@ -4225,7 +4223,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcript" xsd:string property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -4235,7 +4233,7 @@ name: sequentially related to def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string @@ -4248,7 +4246,7 @@ name: skeleton of def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 is_a: part_of @@ -4259,7 +4257,7 @@ name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] xref: RO:0002379 property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: overlaps ! overlaps @@ -4271,7 +4269,7 @@ subset: ro-eco xref: RO:0002163 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 @@ -4285,7 +4283,7 @@ name: stabilizes quantity of def: "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." [] xref: RO:0011015 property_value: IAO:0000112 "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_quantity_of ! directly positively regulates quantity of @@ -4294,14 +4292,14 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates id: starts subset: ro-eco xref: RO:0002223 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: starts_with subset: ro-eco xref: RO:0002224 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -4317,7 +4315,7 @@ name: subcluster of def: "A relation between a group and another group it is part of but does not fully constitute." [] xref: RO:0015003 property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." xsd:string -property_value: IAO:0000117 "Shawn Tan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true is_a: part_of @@ -4326,7 +4324,7 @@ is_a: part_of id: subject_participant_in name: subject participant in xref: RO:0002462 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4345,7 +4343,7 @@ name: surrounded by def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] xref: RO:0002219 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to inverse_of: surrounds ! surrounds @@ -4357,7 +4355,7 @@ def: "inverse of surrounded by" [] subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to @@ -4367,7 +4365,7 @@ name: symbiotically interacts with def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] subset: ro-eco xref: RO:0002440 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true @@ -4380,8 +4378,8 @@ def: "Relation between an anatomical structure (including cells) and a neuron th xref: RO:0002103 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: receives_input_from ! receives input from inverse_of: synapsed_to ! synapsed to @@ -4406,8 +4404,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002108 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" [] @@ -4420,8 +4418,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002109 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4434,8 +4432,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002112 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4448,8 +4446,8 @@ comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part som xref: RO:0002120 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: sends_output_to ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -4473,8 +4471,8 @@ def: "A relation between a motor neuron and a muscle that it synapses to via a t comment: Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) xref: RO:0002107 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_II_bouton ! synapsed_by_via_type_II_bouton @@ -4488,8 +4486,8 @@ comment: Expands to: has_part some ('type Ib terminal button' that has_part some xref: RO:0002105 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Ib_bouton ! synapsed_by_via_type_Ib_bouton @@ -4503,8 +4501,8 @@ comment: Expands to: has_part some ('type Is terminal button' that has_part some xref: RO:0002106 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Is_bouton ! synapsed_by_via_type_Is_bouton @@ -4514,7 +4512,7 @@ expand_expression_to: "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that id: target_participant_in name: target participant in xref: RO:0002463 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4523,7 +4521,7 @@ id: temporally_related_to subset: ro-eco xref: RO:0002222 property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string [Typedef] @@ -4531,7 +4529,7 @@ id: transformation_of name: transformation of def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] xref: RO:0002494 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: develops_from ! develops from @@ -4541,7 +4539,7 @@ name: transitively provides input for def: "transitive form of directly_provides_input_for" [] xref: RO:0002414 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." xsd:string property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string domain: BFO:0000015 @@ -4556,7 +4554,7 @@ def: "A relationship that holds between a disease and organism" [] xref: RO:0002451 property_value: IAO:0000112 "all dengue disease transmitted by some mosquito" xsd:string property_value: IAO:0000116 "Add domain and range constraints" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -4576,7 +4574,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002313 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "regulates localization of" xsd:string is_a: related_via_localization_to ! related via localization to is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4590,7 +4588,7 @@ xref: RO:0002376 property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string @@ -4608,7 +4606,7 @@ name: trophically interacts with def: "An interaction relationship in which the partners are related via a feeding relationship." [] subset: ro-eco xref: RO:0002438 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4618,7 +4616,7 @@ name: ubiquitinates def: "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" [] xref: RO:0002480 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with [Typedef] diff --git a/src/ontology/subsets/ro-mereotopology.owl b/src/ontology/subsets/ro-mereotopology.owl index 3c0480b9..55296922 100644 --- a/src/ontology/subsets/ro-mereotopology.owl +++ b/src/ontology/subsets/ro-mereotopology.owl @@ -409,7 +409,7 @@ - David Osumi-Sutherland + RO:0002002 has_2D_boundary @@ -421,7 +421,7 @@ A relation that holds between two neurons that are electrically coupled via gap junctions. - David Osumi-Sutherland + RO:0002003 electrically_synapsed_to @@ -435,7 +435,7 @@ - David Osumi-Sutherland + RO:0002006 has_synaptic_terminal_of @@ -469,7 +469,7 @@ has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland + RO:0002007 bounding_layer_of @@ -505,9 +505,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. + A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. Note from NCEAS meeting: consider changing primary label - David Osumi-Sutherland + RO:0002008 coincident_with @@ -524,7 +524,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - David Osumi-Sutherland + RO:0002010 regulates_in_other_organism regulates in other organism @@ -553,7 +553,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + dos 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -568,7 +568,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + dos 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -584,7 +584,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + dos 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -599,7 +599,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -613,7 +613,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -630,7 +630,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + dos 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -644,7 +644,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + dos 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -658,7 +658,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + dos 2017-07-20T17:11:08Z RO:0002020 transports @@ -672,7 +672,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + dos 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -686,7 +686,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -697,7 +697,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + GOC:dos @@ -708,7 +708,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + dos 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -718,7 +718,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + GOC:dos @@ -729,7 +729,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + dos 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -739,7 +739,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + GOC:dos @@ -750,7 +750,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + dos 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -761,7 +761,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + GOC:dos @@ -780,7 +780,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + dos 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -797,7 +797,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + GOC:dos @@ -814,7 +814,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + RO:0002090 @@ -831,7 +831,7 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure that its soma is part of. - David Osumi-Sutherland + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -852,9 +852,9 @@ Examples include: the relationship between two channels collected simultaneously relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - David Osumi-Sutherland + fasciculates with - (forall (?x ?y) + (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) @@ -890,9 +890,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure its axon forms (chemical) synapses in. - Chris Mungall - David Osumi-Sutherland - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -924,8 +923,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -945,9 +944,9 @@ Examples include: the relationship between two channels collected simultaneously Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - Alexander Diehl - Chris Mungall - Lindsay Cowell + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) @@ -965,8 +964,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -985,8 +984,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -1005,8 +1004,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) RO:0002107 @@ -1023,8 +1022,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1043,8 +1042,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1064,8 +1063,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - Chris Mungall - David Osumi-Sutherland + + synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( @@ -1085,8 +1084,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1168,8 +1167,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -1196,8 +1195,8 @@ N1 SubclassOf ( Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -1218,7 +1217,7 @@ N1 SubclassOf ( A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - David Osumi-Sutherland + has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) @@ -1267,9 +1266,9 @@ N1 SubclassOf ( The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - David Osumi-Sutherland + has fasciculating component - (forall (?x ?y) + (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) @@ -1309,8 +1308,8 @@ N1 SubclassOf ( - X continuous_with Y if and only if X and Y share a fiat boundary. - David Osumi-Sutherland + X continuous_with Y if and only if X and Y share a fiat boundary. + connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) @@ -1329,8 +1328,8 @@ N1 SubclassOf ( x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom - proper overlaps - (forall (?x ?y) + proper overlaps + (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and @@ -1353,7 +1352,7 @@ N1 SubclassOf ( A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - Chris Mungall + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) @@ -1361,7 +1360,7 @@ N1 SubclassOf ( RO:0002163 spatially_disjoint_from - spatially disjoint from + spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern @@ -1498,7 +1497,7 @@ N1 SubclassOf ( A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - Chris Mungall + RO:0002200 has_phenotype @@ -1513,7 +1512,7 @@ N1 SubclassOf ( inverse of has phenotype - Chris Mungall + RO:0002201 @@ -1533,10 +1532,10 @@ N1 SubclassOf ( x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - Terry Meehan + + + + RO:0002202 develops_from This is the transitive form of the develops from relation @@ -1554,9 +1553,9 @@ N1 SubclassOf ( inverse of develops from - Chris Mungall - David Osumi-Sutherland - Terry Meehan + + + RO:0002203 develops_into @@ -1588,12 +1587,12 @@ N1 SubclassOf ( Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - Chris Mungall - David Osumi-Sutherland - has developmental precursor + + FBbt RO:0002207 + has developmental precursor directly_develops_from TODO - add child relations from DOS directly develops from @@ -1651,9 +1650,9 @@ N1 SubclassOf ( p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - Chris Mungall - David Hill - Tanya Berardini + + + GO Regulation precludes parthood; the regulatory process may not be within the regulated process. @@ -1676,7 +1675,7 @@ N1 SubclassOf ( p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - Chris Mungall + negatively regulates (process to process) @@ -1698,7 +1697,7 @@ N1 SubclassOf ( p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - Chris Mungall + positively regulates (process to process) @@ -1721,7 +1720,7 @@ N1 SubclassOf ( mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - Chris Mungall + has function realized in @@ -1740,7 +1739,7 @@ N1 SubclassOf ( c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - Chris Mungall + has function in RO:0002216 capable_of_part_of @@ -1757,7 +1756,7 @@ N1 SubclassOf ( x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - Chris Mungall + RO:0002219 surrounded_by @@ -1779,7 +1778,7 @@ N1 SubclassOf ( x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - Chris Mungall + RO:0002220 @@ -1803,7 +1802,7 @@ N1 SubclassOf ( inverse of surrounded by - Chris Mungall + RO:0002221 @@ -1816,7 +1815,7 @@ N1 SubclassOf ( - Chris Mungall + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 @@ -1830,7 +1829,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002223 starts @@ -1842,7 +1841,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002224 starts_with @@ -1856,7 +1855,7 @@ N1 SubclassOf ( x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - Chris Mungall + RO:0002225 develops_from_part_of develops from part of @@ -1871,7 +1870,7 @@ N1 SubclassOf ( x develops_in y if x is located in y whilst x is developing - Chris Mungall + EHDAA2 Jonathan Bard, EHDAA2 RO:0002226 @@ -1909,7 +1908,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002229 ends @@ -1921,7 +1920,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002230 ends_with @@ -1937,7 +1936,7 @@ N1 SubclassOf ( x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - Chris Mungall + starts with process that occurs in RO:0002231 @@ -1955,7 +1954,7 @@ N1 SubclassOf ( x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - Chris Mungall + ends with process that occurs in RO:0002232 @@ -1973,7 +1972,7 @@ N1 SubclassOf ( p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + consumes RO:0002233 @@ -1993,7 +1992,7 @@ N1 SubclassOf ( p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - Chris Mungall + produces RO:0002234 @@ -2047,7 +2046,7 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - Bill Duncan (https://orcid.org/0000-0001-9625-1899) + This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. @@ -2196,7 +2195,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y - Chris Mungall + RO:0002254 has_developmental_contribution_from has developmental contribution from @@ -2211,7 +2210,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho inverse of has developmental contribution from - Chris Mungall + RO:0002255 developmentally_contributes_to @@ -2229,9 +2228,9 @@ If you need an axiom that says 'has_participant min 2 object', you sho t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - Chris Mungall - David Osumi-Sutherland - Melissa Haendel + + + induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) @@ -2251,7 +2250,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally induced by - Chris Mungall + RO:0002257 developmentally_induces developmentally induces @@ -2269,7 +2268,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - Chris Mungall + In general you should not use this relation to make assertions - use one of the more specific relations below this one RO:0002258 developmentally_preceded_by @@ -2317,7 +2316,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - Chris Mungall + replaces RO:0002285 developmentally_replaces @@ -2332,7 +2331,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally preceded by - Chris Mungall + RO:0002286 developmentally_succeeded_by developmentally succeeded by @@ -2346,7 +2345,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - Chris Mungall + RO:0002287 part_of_developmental_precursor_of part of developmental precursor of @@ -2363,7 +2362,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - Chris Mungall + RO:0002295 results_in_developmental_progression_of results in developmental progression of @@ -2380,7 +2379,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - Chris Mungall + http://www.geneontology.org/GO.doc.development.shtml RO:0002296 @@ -2401,7 +2400,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002297 @@ -2422,7 +2421,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002298 @@ -2443,7 +2442,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002299 @@ -2461,7 +2460,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho foramen ovale closure SubClassOf results in disappearance of foramen ovale - Chris Mungall + May be merged into parent relation RO:0002300 results_in_disappearance_of @@ -2476,7 +2475,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) - Chris Mungall + May be merged into parent relation RO:0002301 results_in_developmental_regression_of @@ -2491,7 +2490,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of 'is substance that treats' - cjm + RO:0002302 is_treated_by_substance @@ -2511,7 +2510,7 @@ where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. - Pier Buttigieg + adapted for living in RO:0002303 @@ -2529,7 +2528,7 @@ where p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - cjm + RO:0002304 @@ -2547,7 +2546,7 @@ where p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - cjm + RO:0002305 @@ -2562,10 +2561,10 @@ where A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. - Austin Meier - Chris Mungall - Marie Angelique Laporte - cjm + + + + 2017-06-05T17:35:04Z RO:0002309 has_exposure_stimulus @@ -2580,7 +2579,7 @@ where Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. - Chris Mungall + regulates localization of RO:0002313 @@ -2600,7 +2599,7 @@ where an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002315 @@ -2617,7 +2616,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions RO:0002321 @@ -2633,7 +2632,7 @@ where An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. - Chris Mungall + adapted for RO:0002322 @@ -2647,7 +2646,7 @@ where A mereological relationship or a topological relationship - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships RO:0002323 @@ -2661,7 +2660,7 @@ where A relationship that holds between entities participating in some developmental process (GO:0032502) - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development RO:0002324 developmentally_related_to @@ -2678,9 +2677,8 @@ where Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. - Chris Mungall + In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - Gene Ontology Consortium RO:0002325 colocalizes_with @@ -2708,7 +2706,7 @@ then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. - Chris Mungall + In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 @@ -2725,7 +2723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - Chris Mungall + catalyzes executes has @@ -2744,7 +2742,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 functionally_related_to @@ -2758,7 +2756,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati this relation holds between c and p when c is part of some c', and c' is capable of p. - Chris Mungall + false RO:0002329 part_of_structure_that_is_capable_of @@ -2773,7 +2771,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati c involved_in p if and only if c enables some process p', and p' is part of p - Chris Mungall + actively involved in enables part of RO:0002331 @@ -2792,7 +2790,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - Chris Mungall + regulates levels of (process to entity) RO:0002332 @@ -2808,7 +2806,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables - Chris Mungall + RO:0002333 enabled_by @@ -2825,7 +2823,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of regulates - Chris Mungall + regulated by (processual) RO:0002334 @@ -2840,7 +2838,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of negatively regulates - Chris Mungall + RO:0002335 negatively_regulated_by @@ -2854,7 +2852,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of positively regulates - Chris Mungall + RO:0002336 positively_regulated_by @@ -2869,7 +2867,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds via some process of localization - Chris Mungall + Do not use this relation directly. It is a grouping relation. RO:0002337 related_via_localization_to @@ -2883,7 +2881,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - Chris Mungall + RO:0002338 @@ -2899,7 +2897,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - Chris Mungall + RO:0002339 @@ -2915,7 +2913,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. - Chris Mungall + RO:0002340 imports @@ -2929,7 +2927,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - Chris Mungall + RO:0002341 results_in_transport_along results in transport along @@ -2943,7 +2941,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - Chris Mungall + RO:0002342 results_in_transport_across @@ -2958,7 +2956,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'pollen tube growth' results_in growth_of some 'pollen tube' - Chris Mungall + RO:0002343 results_in_growth_of results in growth of @@ -2971,7 +2969,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - Chris Mungall + RO:0002344 results_in_transport_to_from_or_in results in transport to from or in @@ -2983,8 +2981,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. - Chris Mungall + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. + RO:0002345 exports @@ -3000,7 +2998,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - Chris Mungall + RO:0002348 @@ -3017,7 +3015,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - Chris Mungall + RO:0002349 @@ -3034,7 +3032,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has input - Chris Mungall + RO:0002352 @@ -3050,7 +3048,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has output - Chris Mungall + RO:0002353 @@ -3064,7 +3062,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002354 formed_as_result_of formed as result of @@ -3078,7 +3076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. - Chris Mungall + RO:0002355 results_in_structural_organization_of results in structural organization of @@ -3092,7 +3090,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - Chris Mungall + RO:0002356 @@ -3108,7 +3106,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. - Chris Mungall + RO:0002357 results_in_developmental_induction_of results in developmental induction of @@ -3120,7 +3118,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + http://neurolex.org/wiki/Property:DendriteLocation RO:0002360 has_dendrite_location @@ -3136,7 +3134,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - Chris Mungall + attached to (anatomical structure to anatomical structure) RO:0002371 @@ -3153,7 +3151,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002372 has_muscle_origin @@ -3176,7 +3174,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002373 has_muscle_insertion @@ -3200,7 +3198,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) @@ -3222,7 +3220,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - Chris Mungall + drains into drains to tributary channel of @@ -3247,7 +3245,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Deschutes River distributary_of Little Lava Lake x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - Chris Mungall + branch of distributary channel of http://en.wikipedia.org/wiki/Distributary @@ -3273,7 +3271,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. - Chris Mungall + anastomoses with RO:0002378 @@ -3289,7 +3287,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - Chris Mungall + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios RO:0002379 spatially_coextensive_with @@ -3312,7 +3310,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - Chris Mungall + RO:0002380 branching_part_of @@ -3331,7 +3329,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. - Chris Mungall + RO:0002381 main_stem_of @@ -3347,7 +3345,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_distributary_of y iff x distributary_of y and x does not flow back into y - Chris Mungall + RO:0002382 proper_distributary_of @@ -3362,7 +3360,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_tributary_of y iff x tributary_of y and x does not originate from y - Chris Mungall + RO:0002383 proper_tributary_of @@ -3379,7 +3377,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - Chris Mungall + RO:0002384 has_developmental_potential_involving has developmental potential involving @@ -3393,7 +3391,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - Chris Mungall + RO:0002385 has_potential_to_developmentally_contribute_to has potential to developmentally contribute to @@ -3407,7 +3405,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - Chris Mungall + RO:0002386 has_potential_to_developmentally_induce has potential to developmentally induce @@ -3421,7 +3419,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has the potential to develop into y iff x develops into y or if x is capable of developing into y - Chris Mungall + RO:0002387 has_potential_to_develop_into has potential to develop into @@ -3435,7 +3433,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - Chris Mungall + RO:0002388 has_potential_to_directly_develop_into has potential to directly develop into @@ -3450,7 +3448,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' RO:0002400 @@ -3468,7 +3466,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of upstream of - Chris Mungall + RO:0002404 causally_downstream_of causally downstream of @@ -3483,7 +3481,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002405 immediately_causally_downstream_of immediately causally downstream of @@ -3498,7 +3496,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - Chris Mungall + indirectly activates RO:0002407 @@ -3515,7 +3513,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - Chris Mungall + indirectly inhibits RO:0002409 @@ -3544,7 +3542,7 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002410 causally_related_to @@ -3566,7 +3564,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - Chris Mungall + RO:0002411 @@ -3582,7 +3580,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - Chris Mungall + RO:0002412 immediately_causally_upstream_of @@ -3598,7 +3596,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit - Chris Mungall + directly provides input for directly provides input for (process to process) @@ -3618,7 +3616,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different transitive form of directly_provides_input_for - Chris Mungall + This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. transitively provides input for (process to process) RO:0002414 @@ -3636,7 +3634,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall + influences (processual) RO:0002418 affects @@ -3652,7 +3650,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - Chris Mungall + RO:0002427 @@ -3668,7 +3666,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - Chris Mungall + RO:0002428 involved_in_regulation_of involved in regulation of @@ -3681,7 +3679,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - Chris Mungall + RO:0002429 involved_in_positive_regulation_of @@ -3695,7 +3693,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - Chris Mungall + RO:0002430 involved_in_negative_regulation_of @@ -3712,7 +3710,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - Chris Mungall + involved in or reguates RO:0002431 involved_in_or_involved_in_regulation_of @@ -3728,7 +3726,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall + executes activity in RO:0002432 enables activity in @@ -3740,8 +3738,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + GOC:cjm + GOC:dos @@ -3751,7 +3749,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - Chris Mungall + RO:0002433 contributes_to_morphology_of contributes to morphology of @@ -3768,7 +3766,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. - Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. RO:0002434 in pairwise interaction with @@ -3787,7 +3785,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) - Chris Mungall + RO:0002435 genetically_interacts_with genetically interacts with @@ -3803,7 +3801,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - Chris Mungall + binds molecularly binds with RO:0002436 @@ -3824,7 +3822,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - Chris Mungall + interacts with on organism level RO:0002437 @@ -3841,7 +3839,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the partners are related via a feeding relationship. - Chris Mungall + RO:0002438 trophically_interacts_with @@ -3859,9 +3857,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] Baleen whale preys on krill An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - Chris Mungall - Jorrit Poelen - Katja Shulz + + + is subject of predation interaction with preys upon RO:0002439 @@ -3880,7 +3878,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A biotic interaction in which the two organisms live together in more or less intimate association. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism RO:0002440 @@ -3896,7 +3894,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002441 @@ -3911,7 +3909,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002442 @@ -3926,7 +3924,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 This relation groups a pair of inverse relations, parasite of and parasitized by RO:0002443 @@ -3944,7 +3942,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human - Chris Mungall + parasitizes RO:0002444 direct parasite of @@ -3961,7 +3959,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + has parasite parasitised by RO:0002445 @@ -3980,7 +3978,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - Chris Mungall + RO:0002446 semibiotically interacts with @@ -3996,7 +3994,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. RO:0002447 phosphorylates @@ -4015,8 +4013,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - Chris Mungall - Vasundra Touré + + RO:0002448 molecularly controls directly_regulates_activity_of @@ -4033,8 +4031,8 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly inhibits RO:0002449 molecularly decreases activity of @@ -4052,8 +4050,8 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly activates RO:0002450 molecularly increases activity of @@ -4070,7 +4068,7 @@ For example, A and B may be gene products and binding of B by A positively regul all dengue disease transmitted by some mosquito A relationship that holds between a disease and organism Add domain and range constraints - Chris Mungall + RO:0002451 transmitted_by transmitted by @@ -4084,7 +4082,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between a disease or an organism and a phenotype - Chris Mungall + RO:0002452 has_symptom has symptom @@ -4096,7 +4094,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) RO:0002453 @@ -4111,7 +4109,7 @@ For example, A and B may be gene products and binding of B by A positively regul X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y - Chris Mungall + RO:0002454 has_host @@ -4128,7 +4126,7 @@ For example, A and B may be gene products and binding of B by A positively regul Bees pollinate Flowers This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - Chris Mungall + is subject of pollination interaction with RO:0002455 @@ -4143,7 +4141,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + has polinator is target of pollination interaction with RO:0002456 @@ -4160,7 +4158,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4175,7 +4173,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of preys on - Chris Mungall + has predator is target of predation interaction with RO:0002458 @@ -4195,7 +4193,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anopheles is a vector for Plasmodium - Chris Mungall + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism RO:0002459 @@ -4209,7 +4207,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002460 has_vector @@ -4222,7 +4220,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target RO:0002461 partner_in @@ -4235,7 +4233,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002462 subject_participant_in @@ -4248,7 +4246,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002463 target_participant_in @@ -4261,7 +4259,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002469 provides_nutrients_for @@ -4274,7 +4272,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is subject of eating interaction with RO:0002470 @@ -4288,7 +4286,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + eaten by is target of eating interaction with RO:0002471 @@ -4307,7 +4305,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - Chris Mungall + RO:0002473 @@ -4326,7 +4324,7 @@ For example, A and B may be gene products and binding of B by A positively regul ABal nucleus child nucleus of ABa nucleus (in C elegans) c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d - Chris Mungall + This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. RO:0002476 child_nucleus_of @@ -4340,7 +4338,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a hermaphroditic organism - Chris Mungall + RO:0002477 child_nucleus_of_in_hermaphrodite child nucleus of in hermaphrodite @@ -4353,7 +4351,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a male organism - Chris Mungall + RO:0002478 child_nucleus_of_in_male child nucleus of in male @@ -4367,7 +4365,7 @@ For example, A and B may be gene products and binding of B by A positively regul p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall + RO:0002479 has_part_that_occurs_in @@ -4382,7 +4380,7 @@ For example, A and B may be gene products and binding of B by A positively regul An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y Axiomatization to GO to be added later - Chris Mungall + RO:0002480 ubiquitinates ubiquitinates @@ -4396,7 +4394,7 @@ For example, A and B may be gene products and binding of B by A positively regul See notes for inverse relation - Chris Mungall + RO:0002485 receives_input_from receives input from @@ -4409,7 +4407,7 @@ For example, A and B may be gene products and binding of B by A positively regul This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - Chris Mungall + RO:0002486 sends_output_to sends output to @@ -4423,7 +4421,7 @@ For example, A and B may be gene products and binding of B by A positively regul x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - Chris Mungall + RO:0002494 transformation_of transformation of @@ -4437,7 +4435,7 @@ For example, A and B may be gene products and binding of B by A positively regul x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - Chris Mungall + RO:0002495 immediate_transformation_of @@ -4467,7 +4465,7 @@ For example, A and B may be gene products and binding of B by A positively regul p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002501 @@ -4483,7 +4481,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c - Chris Mungall + has intermediate product RO:0002505 @@ -4500,7 +4498,7 @@ For example, A and B may be gene products and binding of B by A positively regul The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002506 @@ -4522,11 +4520,11 @@ For example, A and B may be gene products and binding of B by A positively regul A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future - Chris Mungall + determined by (system to material entity) - Chris Mungall - Pier Buttigieg + + RO:0002507 determined_by @@ -4540,7 +4538,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of determined by - Chris Mungall + determines (material entity to system) RO:0002508 @@ -4559,7 +4557,7 @@ For example, A and B may be gene products and binding of B by A positively regul s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. - Chris Mungall + RO:0002509 determined_by_part_of @@ -4574,7 +4572,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between two entities that have the property of being sequences or having sequences. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. @@ -4594,7 +4592,7 @@ For example, A and B may be gene products and binding of B by A positively regul Two consecutive DNA residues are sequentially adjacent Two exons on a processed transcript that were previously connected by an intron are adjacent x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002515 @@ -4612,7 +4610,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as a start sequence the start codon for that transcript x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence - Chris Mungall + started by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4629,7 +4627,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has start sequence - Chris Mungall + starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4649,7 +4647,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence - Chris Mungall + ended by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4666,7 +4664,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has end sequence - Chris Mungall + ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4684,7 +4682,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. In the SO paper, this was defined as an instance-type relation - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002520 @@ -4701,7 +4699,7 @@ For example, A and B may be gene products and binding of B by A positively regul Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering - Chris Mungall + RO:0002521 is_sequentially_aligned_with @@ -4718,7 +4716,7 @@ For example, A and B may be gene products and binding of B by A positively regul The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y - Chris Mungall + RO:0002522 bounds_sequence_of @@ -4733,7 +4731,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of bounds sequence of - Chris Mungall + RO:0002523 @@ -4751,8 +4749,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x has subsequence y iff all of the sequence parts of x are sequence parts of y - Chris Mungall + x has subsequence y iff all of the sequence parts of y are sequence parts of x + contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4771,7 +4769,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has subsequence - Chris Mungall + contained by RO:0002525 @@ -4788,8 +4786,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. - Chris Mungall + x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. + RO:0002526 overlaps_sequence_of @@ -4803,8 +4801,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. - Chris Mungall + x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + disconnected from RO:0002527 @@ -4820,7 +4818,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of downstream of sequence of - Chris Mungall + RO:0002528 is_upstream_of_sequence_of @@ -4836,7 +4834,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. - Chris Mungall + RO:0002529 is_downstream_of_sequence_of @@ -4852,7 +4850,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y - Chris Mungall + RO:0002530 @@ -4869,7 +4867,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript inverse of immediately downstream of - Chris Mungall + RO:0002531 is_immediately_upstream_of_sequence_of @@ -4889,7 +4887,7 @@ For example, A and B may be gene products and binding of B by A positively regul Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - Chris Mungall + has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). RO:0002551 @@ -4911,7 +4909,7 @@ For example, A and B may be gene products and binding of B by A positively regul p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. - Chris Mungall + RO:0002552 results_in_ending_of results in ending of @@ -4926,7 +4924,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - Chris Mungall + http://eol.org/schema/terms/hyperparasitoidOf https://en.wikipedia.org/wiki/Hyperparasite RO:0002553 @@ -4944,7 +4942,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of hyperparasite of - Chris Mungall + RO:0002554 has epiparasite has hyperparasite @@ -4961,7 +4959,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + http://en.wikipedia.org/wiki/Allelopathy RO:0002555 @@ -4978,7 +4976,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002556 pathogen_of @@ -4991,7 +4989,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002557 has_pathogen @@ -5005,7 +5003,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + causally influenced by (entity-centric) RO:0002559 @@ -5020,7 +5018,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - Chris Mungall + RO:0002565 @@ -5039,8 +5037,8 @@ For example, A and B may be gene products and binding of B by A positively regul The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - Chris Mungall - Vasundra Touré + + causally influences (entity-centric) RO:0002566 @@ -5057,7 +5055,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between elements of a musculoskeletal system or its analogs. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. RO:0002567 biomechanically_related_to @@ -5071,7 +5069,7 @@ For example, A and B may be gene products and binding of B by A positively regul m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - Chris Mungall + Wikipedia:Antagonist_(muscle) RO:0002568 has_muscle_antagonist @@ -5087,7 +5085,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of branching part of - Chris Mungall + RO:0002569 @@ -5104,7 +5102,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - Chris Mungall + UBERON:cjm This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. RO:0002570 @@ -5121,7 +5119,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - Chris Mungall + GOC:cjm RO:0002571 @@ -5137,7 +5135,7 @@ For example, A and B may be gene products and binding of B by A positively regul s is luminal space of x iff s is lumen_of x and s is an immaterial entity - Chris Mungall + RO:0002572 luminal_space_of @@ -5152,7 +5150,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002574 participates_in_a_biotic-biotic_interaction_with @@ -5169,7 +5167,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has skeleton - Chris Mungall + RO:0002576 skeleton_of @@ -5184,7 +5182,7 @@ For example, A and B may be gene products and binding of B by A positively regul p directly regulates q iff p is immediately causally upstream of q and p regulates q. - Chris Mungall + directly regulates (processual) @@ -5205,7 +5203,7 @@ For example, A and B may be gene products and binding of B by A positively regul gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - Chris Mungall + RO:0002584 has_part_structure_that_is_capable_of has part structure that is capable of @@ -5320,7 +5318,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall + RO:0002595 causal_relation_between_material_entity_and_a_process @@ -5723,7 +5721,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. - Vasundra Touré + RO:0003002 represses_expression_of represses expression of @@ -5738,7 +5736,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. - Vasundra Touré + RO:0003003 increases_expression_of increases expression of @@ -5883,7 +5881,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:38:20Z RO:0004000 condition_has_genetic_basis_in @@ -5897,7 +5895,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:20Z RO:0004001 has_material_basis_in_gain_of_function_germline_mutation_in @@ -5913,7 +5911,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:37Z RO:0004002 has_material_basis_in_loss_of_function_germline_mutation_in @@ -5927,7 +5925,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:54Z RO:0004003 has_material_basis_in_germline_mutation_in @@ -5942,7 +5940,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:07Z RO:0004004 has_material_basis_in_somatic_mutation_in @@ -5957,7 +5955,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:26Z RO:0004005 has_major_susceptibility_factor @@ -5971,7 +5969,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:57Z RO:0004006 has_partial_material_basis_in_germline_mutation_in @@ -5985,7 +5983,7 @@ Environmental exposures include those imposed by natural environments, experimen p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - cjm + 2018-12-13T11:26:17Z RO:0004007 @@ -6001,7 +5999,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - cjm + 2018-12-13T11:26:32Z RO:0004008 @@ -6012,8 +6010,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6027,7 +6025,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - cjm + 2018-12-13T11:26:56Z RO:0004009 @@ -6038,8 +6036,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6053,7 +6051,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:53:08Z RO:0004010 is_genetic_basis_for_condition @@ -6067,7 +6065,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:55:51Z RO:0004011 is_causal_gain_of_function_germline_mutation_of_in @@ -6082,7 +6080,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:06Z RO:0004012 is_causal_loss_of_function_germline_mutation_of_in @@ -6098,7 +6096,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:40Z RO:0004013 is_causal_germline_mutation_in @@ -6114,7 +6112,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:57:07Z RO:0004014 is_causal_somatic_mutation_in @@ -6129,7 +6127,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. - cjm + 2017-11-05T02:57:43Z RO:0004015 is_causal_susceptibility_factor_for @@ -6145,7 +6143,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. - cjm + 2017-11-05T02:58:43Z RO:0004016 is_causal_germline_mutation_partially_giving_rise_to @@ -6160,7 +6158,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:01Z RO:0004017 realizable_has_basis_in @@ -6173,7 +6171,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:29Z RO:0004018 is_basis_for_realizable @@ -6188,7 +6186,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:26:47Z RO:0004019 disease_has_basis_in @@ -6204,7 +6202,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) - cjm + 2017-11-05T03:29:32Z RO:0004020 disease_has_basis_in_dysfunction_of @@ -6220,7 +6218,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. disease has basis in disruption of (disease to process) - cjm + 2017-11-05T03:37:52Z RO:0004021 disease_has_basis_in_disruption_of @@ -6244,7 +6242,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. - cjm + 2017-11-05T03:46:07Z RO:0004022 disease_has_basis_in_feature @@ -6260,7 +6258,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. - cjm + 2017-11-05T03:50:54Z RO:0004023 causal_relationship_with_disease_as_subject @@ -6277,7 +6275,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and a process where the disease process disrupts the execution of the process. disease causes disruption of (disease to process) - cjm + 2017-11-05T03:51:09Z RO:0004024 disease_causes_disruption_of @@ -6293,7 +6291,7 @@ Environmental exposures include those imposed by natural environments, experimen disease causes dysfunction of (disease to anatomical entity) - cjm + 2017-11-05T03:58:20Z RO:0004025 disease_causes_dysfunction_of @@ -6319,7 +6317,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. - cjm + 2017-11-05T04:06:02Z RO:0004026 disease_has_location @@ -6343,7 +6341,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity - cjm + 2017-12-26T19:37:31Z RO:0004027 disease_has_inflammation_site @@ -6359,7 +6357,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - cjm + 2017-12-26T19:45:49Z RO:0004028 realized_in_response_to_stimulus @@ -6382,7 +6380,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. - cjm + 2017-12-26T19:50:53Z RO:0004029 disease_has_feature @@ -6397,7 +6395,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. - cjm + 2017-12-26T19:58:44Z RO:0004030 disease_arises_from_alteration_in_structure @@ -6411,7 +6409,7 @@ Environmental exposures include those imposed by natural environments, experimen Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - cjm + 2018-01-25T23:20:13Z RO:0004031 enables_subfunction @@ -6425,7 +6423,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:30Z RO:0004032 @@ -6441,7 +6439,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:51Z RO:0004033 @@ -6458,7 +6456,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - cjm + 2018-01-26T23:53:14Z RO:0004034 @@ -6476,7 +6474,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - cjm + 2018-01-26T23:53:22Z RO:0004035 @@ -6492,7 +6490,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:05Z RO:0004046 causally_upstream_of_or_within,_negative_effect @@ -6506,7 +6504,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:19Z RO:0004047 causally_upstream_of_or_within,_positive_effect @@ -6633,10 +6631,10 @@ Environmental exposures include those imposed by natural environments, experimen An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - Austin Meier - Chris Mungall - David Osumi-Sutherland - Marie Angelique Laporte + + + + RO:0009501 triggered by process realized_in_response_to @@ -6659,7 +6657,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - Vasundra Touré + RO:0011002 regulates_activity_of regulates activity of @@ -6674,7 +6672,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. - Vasundra Touré + RO:0011003 regulates_quantity_of regulates quantity of @@ -6689,7 +6687,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. - Vasundra Touré + RO:0011004 indirectly_regulates_activity_of indirectly regulates activity of @@ -6706,7 +6704,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011007 decreases_by_repression_quantity_of decreases by repression quantity of @@ -6723,7 +6721,7 @@ For example, protein A (transcription factor) indirectly decreases by repression The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011008 increases_by_expression_quantity_of increases by expression quantity of @@ -6738,7 +6736,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly positively regulates the quantity of B. - Vasundra Touré + RO:0011009 directly_positively_regulates_quantity_of directly positively regulates quantity of @@ -6753,7 +6751,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly negatively regulates the quantity of B. - Vasundra Touré + RO:0011010 directly_negatively_regulates_quantity_of directly negatively regulates quantity of @@ -6768,7 +6766,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. - Vasundra Touré + indirectly activates RO:0011013 indirectly_positively_regulates_activity_of @@ -6785,7 +6783,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. - Vasundra Touré + RO:0011014 destabilizes_quantity_of destabilizes quantity of @@ -6801,7 +6799,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. - Vasundra Touré + RO:0011015 stabilizes_quantity_of stabilizes quantity of @@ -6814,7 +6812,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. - Vasundra Touré + indirectly inhibits RO:0011016 indirectly_negatively_regulates_activity_of @@ -6828,7 +6826,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. - Vasundra Touré + RO:0011021 directly_regulates_quantity_of directly regulates quantity of @@ -6841,7 +6839,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011022 indirectly_regulates_quantity_of indirectly regulates quantity of @@ -6854,7 +6852,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011023 indirectly_negatively_regulates_quantity_of indirectly negatively regulates quantity of @@ -6867,7 +6865,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011024 indirectly_positively_regulates_quantity_of indirectly positively regulates quantity of @@ -6880,8 +6878,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is regulated by the small molecule continuant + pg 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -6895,8 +6893,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is activated by the small molecule continuant + pg 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -6910,8 +6908,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant + pg 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -6924,8 +6922,8 @@ For example, protein A (transcription factor) indirectly increases by expression - p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + p acts on population of c iff c' is a collection, has members of type c, and p has participant c + pg 2020-06-08T17:21:33Z RO:0012003 @@ -6941,8 +6939,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process + pg 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -6956,8 +6954,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process + pg 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of @@ -6971,8 +6969,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process + pg 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of @@ -6985,8 +6983,8 @@ For example, protein A (transcription factor) indirectly increases by expression - The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. + pg 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -6999,7 +6997,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + pg 2021-02-26T07:28:29Z RO:0012008 @@ -7016,7 +7014,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + pg 2022-09-26T06:01:01Z RO:0012009 @@ -7032,7 +7030,7 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + pg 2022-09-26T06:06:20Z RO:0012010 @@ -7048,7 +7046,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + pg 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7063,7 +7061,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + pg 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7229,7 +7227,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relation between a group and another group it is part of but does not fully constitute. X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. - Shawn Tan + This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. RO:0015003 subcluster_of @@ -7301,7 +7299,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - http://orcid.org/0000-0002-7463-6306 + 2021-11-05T17:30:44Z RO:0016002 has_disease @@ -7457,7 +7455,7 @@ For example, protein A (transcription factor) indirectly increases by expression This relation groups relations between diseases and any other kind of entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. - cjm + 2018-09-26T00:00:32Z RO:0040035 disease_relationship @@ -7471,7 +7469,7 @@ For example, protein A (transcription factor) indirectly increases by expression p has anatomical participant c iff p has participant c, and c is an anatomical entity - cjm + 2018-09-26T01:08:58Z RO:0040036 results_in_changes_to_anatomical_or_cellular_structure diff --git a/src/ontology/subsets/ro-sequence.obo b/src/ontology/subsets/ro-sequence.obo index 33d92cb8..3df12e6c 100644 --- a/src/ontology/subsets/ro-sequence.obo +++ b/src/ontology/subsets/ro-sequence.obo @@ -13,7 +13,7 @@ id: acquires_nutrients_from name: acquires nutrients from subset: ro-eco xref: RO:0002457 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for @@ -58,7 +58,7 @@ property_value: RO:0004050 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:22Z [Typedef] @@ -71,7 +71,7 @@ property_value: RO:0004049 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:14Z [Typedef] @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z [Typedef] @@ -103,7 +103,7 @@ xref: RO:0004032 property_value: RO:0004049 RO:0002264 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z [Typedef] @@ -120,7 +120,7 @@ property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cy property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 domain: BFO:0000004 range: BFO:0000004 @@ -131,7 +131,7 @@ id: allelopath_of name: allelopath of subset: ro-eco xref: RO:0002555 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string @@ -153,7 +153,7 @@ def: "x anabranch_of y if x is a distributary of y (i.e. it channels a from a la subset: ro-eco xref: RO:0002378 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "anastomoses with" xsd:string is_a: distributary_of ! distributary of disjoint_from: proper_distributary_of ! proper distributary of @@ -165,7 +165,7 @@ name: attached to def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] subset: ro-eco xref: RO:0002371 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: attached_to_part_of ! attached to part of @@ -189,9 +189,8 @@ def: "Relation between a neuron and some structure its axon forms (chemical) syn xref: RO:0002102 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in @@ -202,7 +201,7 @@ id: biomechanically_related_to name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] xref: RO:0002567 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: CARO:0000003 range: CARO:0000003 @@ -214,7 +213,7 @@ name: biotically interacts with def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] subset: ro-eco xref: RO:0002437 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string @@ -231,7 +230,7 @@ def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\ comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco xref: RO:0002007 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 is_a: part_of @@ -242,7 +241,7 @@ def: "x bounds the sequence of y iff the upstream-most part of x is upstream of xref: RO:0002522 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to inverse_of: is_bound_by_sequence_of ! is bound by sequence of @@ -254,7 +253,7 @@ def: "x is a branching part of y if and only if x is part of y and x is connecte subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso FMA:85994 xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with @@ -269,7 +268,7 @@ subset: ro-eco xref: RO:0002215 property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 @@ -302,7 +301,7 @@ id: capable_of_part_of name: capable of part of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ is_a: causal_agent_in_process ! causal agent in process @@ -350,7 +349,7 @@ id: causal_relation_between_entities name: causal relation between entities xref: RO:0002506 property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000002 @@ -363,7 +362,7 @@ name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] xref: RO:0002595 property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 range: BFO:0000015 @@ -374,7 +373,7 @@ id: causal_relation_between_processes name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 @@ -389,7 +388,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: OGMS:0000031 is_a: causally_related_to ! causally related to is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:50:54Z [Typedef] @@ -398,7 +397,7 @@ name: causally downstream of def: "inverse of upstream of" [] xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within is_a: preceded_by inverse_of: causally_upstream_of ! causally upstream of @@ -409,7 +408,7 @@ name: causally downstream of or within def: "inverse of causally upstream of or within" [] subset: RO:0002259 xref: RO:0002427 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -418,7 +417,7 @@ is_a: causal_relation_between_processes ! causal relation between processes id: causally_influenced_by name: causally influenced by xref: RO:0002559 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: causal_relation_between_entities ! causal relation between entities @@ -429,8 +428,8 @@ id: causally_influences name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] xref: RO:0002566 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 @@ -443,7 +442,7 @@ name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] @@ -453,7 +452,7 @@ def: "p is causally upstream of q iff p is causally related to q, the end of p p subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes @@ -465,7 +464,7 @@ def: "p is causally upstream of, negative effect q iff p is casually upstream of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -478,7 +477,7 @@ comment: holds between x and y if and only if x is causally upstream of y and th subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -490,7 +489,7 @@ def: "p is 'causally upstream or within' q iff p is causally related to q, and t synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -502,7 +501,7 @@ name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -511,7 +510,7 @@ name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -537,7 +536,7 @@ name: child nucleus of def: "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" [] xref: RO:0002476 property_value: IAO:0000112 "ABal nucleus child nucleus of ABa nucleus (in C elegans)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." xsd:string domain: GO:0005634 range: GO:0005634 @@ -548,7 +547,7 @@ id: child_nucleus_of_in_hermaphrodite name: child nucleus of in hermaphrodite def: "A child nucleus relationship in which the cells are part of a hermaphroditic organism" [] xref: RO:0002477 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -556,7 +555,7 @@ id: child_nucleus_of_in_male name: child nucleus of in male def: "A child nucleus relationship in which the cells are part of a male organism" [] xref: RO:0002478 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -576,7 +575,7 @@ comment: Example: if we define region of chromosome as any subdivision of a chro subset: ro-eco xref: RO:0002008 property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -585,9 +584,8 @@ name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 -property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -599,7 +597,7 @@ name: commensually interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] subset: ro-eco xref: RO:0002441 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -610,7 +608,7 @@ def: "x composed_primarily_of y if and only if more than half of the mass of x i subset: ro-eco xref: RO:0002473 property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 @@ -639,7 +637,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: BFO:0000017 is_a: causally_related_to ! causally related to inverse_of: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:38:20Z [Typedef] @@ -648,7 +646,7 @@ name: conduit for def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] subset: ro-eco xref: RO:0002570 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 UBERON:cjm xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 @@ -661,7 +659,7 @@ name: confers advantage in subset: ro-eco xref: RO:0002322 property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "adapted for" xsd:string range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -727,7 +725,7 @@ name: continuous with def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 @@ -746,7 +744,7 @@ property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a het property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -771,7 +769,7 @@ id: contributes_to_morphology_of name: contributes to morphology of def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] xref: RO:0002433 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -796,7 +794,7 @@ id: decreases_by_repression_quantity_of name: decreases by repression quantity of def: "The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011007 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_negatively_regulates_quantity_of ! indirectly negatively regulates quantity of @@ -808,8 +806,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in wh xref: RO:0002121 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in @@ -821,7 +819,7 @@ name: destabilizes quantity of def: "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." [] xref: RO:0011014 property_value: IAO:0000112 "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_quantity_of ! directly negatively regulates quantity of @@ -832,11 +830,11 @@ name: determined by def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] subset: ro-eco xref: RO:0002507 -property_value: http://purl.org/dc/terms/creator "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/creator "Pier Buttigieg" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-4366-3088 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "A coral reef environment is determined by a particular coral reef" xsd:string property_value: IAO:0000116 "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602 property_value: IAO:0000589 "determined by (system to material entity)" xsd:string domain: RO:0002577 @@ -852,7 +850,7 @@ name: determined by part of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] subset: ro-eco xref: RO:0002509 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 range: BFO:0000040 is_a: causal_relation_between_entities ! causal relation between entities @@ -865,7 +863,7 @@ def: "inverse of determined by" [] subset: ro-eco subset: RO:0002259 xref: RO:0002508 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "determines (material entity to system)" xsd:string is_a: causally_influences ! causally influences @@ -876,7 +874,7 @@ def: "inverse of has developmental contribution from" [] subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to @@ -886,9 +884,9 @@ name: developmentally induced by def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] xref: RO:0002256 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string property_value: IAO:0000119 GO:0001759 xsd:string @@ -905,7 +903,7 @@ name: developmentally induces def: "Inverse of developmentally induced by" [] xref: RO:0002257 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_induce ! has potential to developmentally induce @@ -917,7 +915,7 @@ comment: This relation groups together various other developmental relations. It xref: RO:0002258 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string domain: BFO:0000002 range: BFO:0000002 @@ -929,7 +927,7 @@ id: developmentally_related_to name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] xref: RO:0002324 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] @@ -939,7 +937,7 @@ def: "x developmentally replaces y if and only if there is some developmental pr xref: RO:0002285 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "replaces" xsd:string is_a: developmentally_preceded_by ! developmentally preceded by @@ -949,7 +947,7 @@ name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] xref: RO:0002286 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -959,10 +957,10 @@ def: "x develops from y if and only if either (a) x directly develops from y or comment: This is the transitive form of the develops from relation xref: RO:0002202 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 domain: BFO:0000004 range: BFO:0000004 is_transitive: true @@ -975,7 +973,7 @@ name: develops from part of def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] xref: RO:0002225 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: develops_from ! develops from [Typedef] @@ -984,7 +982,7 @@ name: develops in def: "x develops_in y if x is located in y whilst x is developing" [] xref: RO:0002226 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string domain: CARO:0000000 @@ -997,9 +995,9 @@ def: "inverse of develops from" [] subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 is_transitive: true is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into @@ -1010,11 +1008,11 @@ id: directly_develops_from name: directly develops from def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] xref: RO:0002207 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "has developmental precursor" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000119 "FBbt" xsd:string property_value: RO:0002575 RO:0002202 is_a: develops_from ! develops from @@ -1060,8 +1058,8 @@ name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] xref: RO:0002449 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1072,7 +1070,7 @@ id: directly_negatively_regulates_quantity_of name: directly negatively regulates quantity of def: "The entity A has an activity that directly negatively regulates the quantity of B." [] xref: RO:0011010 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1107,8 +1105,8 @@ name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] xref: RO:0002450 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1119,7 +1117,7 @@ id: directly_positively_regulates_quantity_of name: directly positively regulates quantity of def: "The entity A has an activity that directly positively regulates the quantity of B." [] xref: RO:0011009 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1142,7 +1140,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002578 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string property_value: RO:0002575 RO:0002211 @@ -1155,8 +1153,8 @@ name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] xref: RO:0002448 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: molecularly_interacts_with ! molecularly interacts with @@ -1167,7 +1165,7 @@ id: directly_regulates_quantity_of name: directly regulates quantity of def: "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B." [] xref: RO:0011021 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -1177,7 +1175,7 @@ def: "A relationship between a disease and an anatomical structure where the mat xref: RO:0004030 range: CARO:0000003 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z [Typedef] @@ -1189,7 +1187,7 @@ property_value: IAO:0000589 "disease causes disruption of (disease to process)" domain: OGMS:0000031 range: BFO:0000015 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:51:09Z [Typedef] @@ -1200,7 +1198,7 @@ property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomica domain: OGMS:0000031 range: CARO:0000006 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z [Typedef] @@ -1210,7 +1208,7 @@ xref: RO:0004019 domain: OGMS:0000031 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject is_a: realizable_has_basis_in ! realizable has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:26:47Z [Typedef] @@ -1221,7 +1219,7 @@ xref: RO:0004021 property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:37:52Z [Typedef] @@ -1232,7 +1230,7 @@ xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string range: CARO:0000006 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z [Typedef] @@ -1243,7 +1241,7 @@ xref: RO:0004022 domain: OGMS:0000031 is_a: disease_has_basis_in ! disease has basis in is_a: has_phenotype ! has phenotype -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:46:07Z [Typedef] @@ -1253,7 +1251,7 @@ def: "A relationship between a disease and some feature of that disease, where t xref: RO:0004029 domain: OGMS:0000031 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:50:53Z [Typedef] @@ -1272,7 +1270,7 @@ xref: RO:0004027 domain: OGMS:0000031 range: BFO:0000004 is_a: disease_has_location ! disease has location -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:37:31Z [Typedef] @@ -1285,7 +1283,7 @@ property_value: IAO:0000232 "This relation is intentionally very general, and co domain: OGMS:0000031 range: BFO:0000004 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T04:06:02Z [Typedef] @@ -1294,7 +1292,7 @@ name: disease relationship def: "This relation groups relations between diseases and any other kind of entity." [] xref: RO:0040035 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z [Typedef] @@ -1306,7 +1304,7 @@ subset: ro-eco xref: RO:0002377 property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string @@ -1316,10 +1314,10 @@ is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: does_not_overlap_sequence_of name: does not overlap sequence of -def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] xref: RO:0002527 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "disconnected from" xsd:string is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -1338,7 +1336,7 @@ id: eats name: eats subset: ro-eco xref: RO:0002470 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -1359,7 +1357,7 @@ def: "A relationship that is mediated in some way by the environment or environm subset: ro-eco xref: RO:0002321 property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string [Typedef] @@ -1377,7 +1375,7 @@ name: electrically_synapsed_to def: "A relation that holds between two neurons that are electrically coupled via gap junctions." [] xref: RO:0002003 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: connected_to ! connected to [Typedef] @@ -1386,7 +1384,7 @@ name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: has_participant @@ -1397,7 +1395,7 @@ def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string property_value: IAO:0000118 "has" xsd:string @@ -1413,7 +1411,7 @@ name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] xref: RO:0004031 is_a: functionally_related_to ! functionally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z [Typedef] @@ -1430,14 +1428,14 @@ inverse_of: has_endoparasite ! has endoparasite id: ends subset: ro-eco xref: RO:0002229 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: ends_with subset: ro-eco xref: RO:0002230 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -1462,7 +1460,7 @@ name: exports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002345 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -1479,7 +1477,7 @@ def: "relationship between a neuron and a neuron projection bundle (e.g.- tract xref: RO:0002101 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 @@ -1492,7 +1490,7 @@ inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron proje id: formed_as_result_of name: formed as result of xref: RO:0002354 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of [Typedef] @@ -1500,7 +1498,7 @@ id: functionally_related_to name: functionally related to def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] xref: RO:0002328 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string [Typedef] @@ -1509,7 +1507,7 @@ name: genetically interacts with xref: RO:0002435 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with @@ -1517,7 +1515,7 @@ is_a: interacts_with ! interacts with [Typedef] id: has_2D_boundary xref: RO:0002002 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1557,7 +1555,7 @@ def: "inverse of branching part of" [] subset: ro-eco subset: RO:0002259 xref: RO:0002569 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: has_part is_a: in_branching_relationship_with ! in branching relationship with @@ -1593,7 +1591,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 "Bill Duncan (https://orcid.org/0000-0001-9625-1899)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant @@ -1622,7 +1620,7 @@ id: has_dendrite_location name: has dendrite location xref: RO:0002360 property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -1632,7 +1630,7 @@ def: "x has developmental contribution from y iff x has some part z such that z xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by @@ -1644,7 +1642,7 @@ name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to @@ -1656,7 +1654,7 @@ def: "p has direct input c iff c is a participant in p, c is present at the star xref: RO:0002400 property_value: IAO:0000112 "'protein catabolic process' SubClassOf has_direct_input some protein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly consumes" xsd:string property_value: IAO:0000232 "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" xsd:string is_a: has_input ! has input @@ -1666,7 +1664,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1711,7 +1709,7 @@ def: "x 'has end location' y if and only if there exists some process z such tha subset: ro-eco xref: RO:0002232 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -1724,7 +1722,7 @@ def: "x has end sequence y if the end of x is identical to the end of y, and x h xref: RO:0002518 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -1776,11 +1774,11 @@ id: has_exposure_stimulus name: has exposure stimulus def: "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002309 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 is_a: related_via_exposure_to ! related via exposure to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:35:04Z [Typedef] @@ -1806,7 +1804,7 @@ def: "The relation between a neuron projection bundle and a neuron projection th xref: RO:0002132 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 @@ -1828,7 +1826,7 @@ subset: ro-eco xref: RO:0002303 property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Pier Buttigieg" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string domain: CARO:0001010 range: ENVO:01000254 @@ -1851,7 +1849,7 @@ name: has host def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] subset: ro-eco xref: RO:0002454 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -1865,7 +1863,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 is_a: has_participant @@ -1886,7 +1884,7 @@ def: "p has intermediate c if and only if p has parts p1, p2 and p1 has output c subset: ro-eco xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string is_a: has_participant @@ -1924,7 +1922,7 @@ name: has major susceptibility factor xref: RO:0004005 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_susceptibility_factor_for ! is causal susceptibility factor for -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:26Z [Typedef] @@ -1935,7 +1933,7 @@ property_value: seeAlso Orphanet:410295 property_value: seeAlso Orphanet:410296 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_gain_of_function_germline_mutation_of_in ! is causal gain of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:20Z [Typedef] @@ -1945,7 +1943,7 @@ xref: RO:0004003 property_value: seeAlso Orphanet:317343 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_in ! is causal germline mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:54Z [Typedef] @@ -1954,7 +1952,7 @@ name: has material basis in loss of function germline mutation in xref: RO:0004002 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_loss_of_function_germline_mutation_of_in ! is causal loss of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:37Z [Typedef] @@ -1964,7 +1962,7 @@ xref: RO:0004004 property_value: seeAlso Orphanet:317344 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z [Typedef] @@ -1980,7 +1978,7 @@ id: has_muscle_antagonist name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string is_a: biomechanically_related_to ! biomechanically related to @@ -1989,7 +1987,7 @@ id: has_muscle_insertion name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} @@ -2001,7 +1999,7 @@ id: has_muscle_origin name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} @@ -2039,7 +2037,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string is_a: has_participant inverse_of: output_of ! output of @@ -2066,7 +2064,7 @@ name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] xref: RO:0002584 property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causal_relation_between_material_entity_and_a_process ! causal relation between material entity and a process is_a: functionally_related_to ! functionally related to @@ -2076,7 +2074,7 @@ name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco xref: RO:0002479 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 range: BFO:0000004 @@ -2086,7 +2084,7 @@ name: has partial material basis in germline mutation in xref: RO:0004006 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_partially_giving_rise_to ! is causal germline mutation partially giving rise to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:57Z [Typedef] @@ -2098,7 +2096,7 @@ id: has_pathogen name: has pathogen subset: ro-eco xref: RO:0002557 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2108,7 +2106,7 @@ def: "A relationship that holds between a biological entity and a phenotype. Her subset: ro-eco xref: RO:0002200 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: UPHENO:0001001 is_a: has_phenotype_or_disease ! has phenotype or disease inverse_of: phenotype_of ! phenotype of @@ -2129,9 +2127,9 @@ def: "Holds between a cell c and a protein complex or protein p if and only if t xref: RO:0002104 property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Alexander Diehl" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 @@ -2157,8 +2155,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in whi xref: RO:0002110 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "synapsed in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2172,7 +2170,7 @@ name: has potential to develop into def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] xref: RO:0002387 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2181,7 +2179,7 @@ name: has potential to developmentally contribute to def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] xref: RO:0002385 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2190,7 +2188,7 @@ name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] xref: RO:0002386 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2199,7 +2197,7 @@ name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] xref: RO:0002388 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_potential_to_develop_into ! has potential to develop into [Typedef] @@ -2223,7 +2221,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -2233,7 +2231,7 @@ def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c o subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -2244,7 +2242,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -2276,7 +2274,7 @@ name: has skeleton def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] xref: RO:0002551 property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 @@ -2321,7 +2319,7 @@ name: has soma location def: "Relation between a neuron and an anatomical structure that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 range: CARO:0000003 @@ -2335,7 +2333,7 @@ def: "x 'has starts location' y if and only if there exists some process z such subset: ro-eco xref: RO:0002231 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -2348,7 +2346,7 @@ def: "x has start sequence y if the start of x is identical to the start of y, a xref: RO:0002516 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2358,10 +2356,10 @@ inverse_of: is_start_sequence_of ! is start sequence of [Typedef] id: has_subsequence name: has subsequence -def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2375,7 +2373,7 @@ id: has_symptom name: has symptom def: "A relation that holds between a disease or an organism and a phenotype" [] xref: RO:0002452 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: OGMS:0000031 is_a: has_phenotype ! has phenotype @@ -2405,7 +2403,7 @@ def: "A general relation between a neuron and some structure in which it either xref: RO:0002130 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has synapse in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2417,7 +2415,7 @@ id: has_synaptic_terminal_of name: has synaptic terminal of xref: RO:0002006 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: overlaps ! overlaps inverse_of: has_synaptic_terminal_in ! has synaptic terminal in @@ -2429,7 +2427,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002339 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2440,7 +2438,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002338 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2448,7 +2446,7 @@ id: has_vector name: has vector subset: ro-eco xref: RO:0002460 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with [Typedef] @@ -2463,7 +2461,7 @@ id: host_of name: host of subset: ro-eco xref: RO:0002453 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2476,7 +2474,7 @@ synonym: "epiparasite of" RELATED [] synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string is_a: has_host ! has host @@ -2492,7 +2490,7 @@ synonym: "has epiparasite" RELATED [] synonym: "has hyperparasite" RELATED [] synonym: "hyperparasitoidized by" RELATED [] xref: RO:0002554 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2500,7 +2498,7 @@ id: immediate_transformation_of name: immediate transformation of def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] xref: RO:0002495 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002494 is_a: directly_develops_from ! directly develops from is_a: transformation_of ! transformation of @@ -2510,7 +2508,7 @@ id: immediately_causally_downstream_of name: immediately causally downstream of xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of is_a: immediately_preceded_by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of @@ -2520,7 +2518,7 @@ id: immediately_causally_upstream_of name: immediately causally upstream of def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: immediately_precedes @@ -2533,7 +2531,7 @@ xref: RO:0002087 id: immediately_precedes subset: ro-eco xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0002575 BFO:0000063 [Typedef] @@ -2542,7 +2540,7 @@ name: imports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002340 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -2551,7 +2549,7 @@ name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] xref: RO:0002375 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 @@ -2577,7 +2575,7 @@ id: increases_by_expression_quantity_of name: increases by expression quantity of def: "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011008 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_positively_regulates_quantity_of ! indirectly positively regulates quantity of @@ -2587,7 +2585,7 @@ id: increases_expression_of name: increases expression of def: "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." [] xref: RO:0003003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -2606,7 +2604,7 @@ id: indirectly_negatively_regulates name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true @@ -2618,7 +2616,7 @@ id: indirectly_negatively_regulates_activity_of name: indirectly negatively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B." [] xref: RO:0011016 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly inhibits" xsd:string is_a: indirectly_regulates_activity_of ! indirectly regulates activity of @@ -2627,7 +2625,7 @@ id: indirectly_negatively_regulates_quantity_of name: indirectly negatively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B." [] xref: RO:0011023 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2635,7 +2633,7 @@ id: indirectly_positively_regulates name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 is_transitive: true @@ -2647,7 +2645,7 @@ id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." [] xref: RO:0011013 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -2658,7 +2656,7 @@ id: indirectly_positively_regulates_quantity_of name: indirectly positively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B." [] xref: RO:0011024 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2676,7 +2674,7 @@ id: indirectly_regulates_activity_of name: indirectly regulates activity of def: "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." [] xref: RO:0011004 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: regulates_activity_of ! regulates activity of @@ -2686,7 +2684,7 @@ id: indirectly_regulates_quantity_of name: indirectly regulates quantity of def: "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B." [] xref: RO:0011022 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -2696,7 +2694,7 @@ def: "inverse of has input" [] subset: ro-eco subset: RO:0002259 xref: RO:0002352 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -2710,7 +2708,7 @@ xref: RO:0002434 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI domain: BFO:0000040 @@ -2723,7 +2721,7 @@ name: interacts with via parasite-host interaction def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] subset: ro-eco xref: RO:0002443 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2751,7 +2749,7 @@ id: involved_in name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] xref: RO:0002331 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in @@ -2763,7 +2761,7 @@ id: involved_in_negative_regulation_of name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] xref: RO:0002430 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2773,7 +2771,7 @@ name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in_process ! causal agent in process @@ -2784,7 +2782,7 @@ id: involved_in_positive_regulation_of name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] xref: RO:0002429 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2793,7 +2791,7 @@ id: involved_in_regulation_of name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] xref: RO:0002428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of @@ -2804,7 +2802,7 @@ def: "c executes activity in d if and only if c enables p and p occurs_in d. As synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -2853,7 +2851,7 @@ id: is_basis_for_realizable name: is basis for realizable xref: RO:0004018 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:29Z [Typedef] @@ -2863,7 +2861,7 @@ def: "inverse of bounds sequence of" [] subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to @@ -2874,7 +2872,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004011 property_value: seeAlso Orphanet:410296 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:55:51Z [Typedef] @@ -2885,7 +2883,7 @@ xref: RO:0004013 property_value: seeAlso Orphanet:317343 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:40Z [Typedef] @@ -2896,7 +2894,7 @@ xref: RO:0004016 property_value: seeAlso Orphanet:317346 is_a: contributes_to_condition ! contributes to condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:58:43Z [Typedef] @@ -2906,7 +2904,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004012 property_value: seeAlso Orphanet:410295 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:06Z [Typedef] @@ -2917,7 +2915,7 @@ xref: RO:0004014 property_value: seeAlso Orphanet:317344 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:07Z [Typedef] @@ -2927,7 +2925,7 @@ def: "Relates a gene to condition, such that a mutation in this gene predisposes xref: RO:0004015 property_value: seeAlso Orphanet:317345 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:43Z [Typedef] @@ -2937,7 +2935,7 @@ def: "x is a consecutive sequence of y iff x has subsequence y, and all the part xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: has_subsequence ! has subsequence @@ -2947,7 +2945,7 @@ name: is downstream of sequence of def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] xref: RO:0002529 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of @@ -2957,7 +2955,7 @@ id: is_eaten_by name: is eaten by subset: ro-eco xref: RO:0002471 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -2969,7 +2967,7 @@ def: "inverse of has end sequence" [] subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2982,7 +2980,7 @@ xref: RO:0004010 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string range: BFO:0000017 is_a: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:53:08Z [Typedef] @@ -2992,7 +2990,7 @@ def: "x is immediately downstream of the sequence of y iff either (1) x and y ha xref: RO:0002530 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002529 is_a: is_downstream_of_sequence_of ! is downstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3004,7 +3002,7 @@ def: "inverse of immediately downstream of" [] xref: RO:0002531 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: is_upstream_of_sequence_of ! is upstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3031,7 +3029,7 @@ def: "x is sequentially aligned with if a significant portion bases of x and y c xref: RO:0002521 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -3071,7 +3069,7 @@ def: "inverse of has start sequence" [] subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3084,7 +3082,7 @@ def: "inverse of has subsequence" [] subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of @@ -3107,7 +3105,7 @@ name: is treated by substance def: "Inverse of 'is substance that treats'" [] subset: RO:0002259 xref: RO:0002302 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 is_a: causally_related_to ! causally related to inverse_of: is_substance_that_treats ! is substance that treats @@ -3117,7 +3115,7 @@ name: is upstream of sequence of def: "inverse of downstream of sequence of" [] xref: RO:0002528 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -3127,7 +3125,7 @@ name: is vector for subset: ro-eco xref: RO:0002459 property_value: IAO:0000112 "Anopheles is a vector for Plasmodium" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: has_vector ! has vector @@ -3179,7 +3177,7 @@ name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco xref: RO:0002571 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:cjm xsd:string range: BFO:0000040 is_a: part_of @@ -3190,7 +3188,7 @@ name: luminal space of def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] subset: ro-eco xref: RO:0002572 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000141 is_a: lumen_of ! lumen of @@ -3202,7 +3200,7 @@ subset: ro-eco xref: RO:0002381 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with is_a: part_of @@ -3212,7 +3210,7 @@ id: mereotopologically_related_to name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] xref: RO:0002323 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string property_value: RO:0001900 RO:0001901 @@ -3230,7 +3228,7 @@ name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 @@ -3243,7 +3241,7 @@ name: mutualistically interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] subset: ro-eco xref: RO:0002442 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -3270,7 +3268,7 @@ name: negatively regulated by def: "inverse of negatively regulates" [] subset: RO:0002259 xref: RO:0002335 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3281,7 +3279,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 @@ -3330,7 +3328,7 @@ def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -3351,10 +3349,10 @@ expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://p [Typedef] id: overlaps_sequence_of name: overlaps sequence of -def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] xref: RO:0002526 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: overlaps ! overlaps is_a: sequentially_related_to ! sequentially related to @@ -3366,7 +3364,7 @@ subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string is_a: has_host ! has host @@ -3379,7 +3377,7 @@ name: parasitized by subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string @@ -3418,7 +3416,7 @@ name: part of developmental precursor of xref: RO:0002287 property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by [Typedef] @@ -3426,7 +3424,7 @@ id: part_of_structure_that_is_capable_of name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] xref: RO:0002329 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean is_a: functionally_related_to ! functionally related to @@ -3455,7 +3453,7 @@ subset: ro-eco synonym: "semibiotically interacts with" RELATED [] xref: RO:0002446 property_value: IAO:0000112 "Porifiera attaches to substrate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: biotically_interacts_with ! biotically interacts with @@ -3464,7 +3462,7 @@ id: participates_in_a_biotic-biotic_interaction_with name: participates in a biotic-biotic interaction with subset: ro-eco xref: RO:0002574 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 domain: CARO:0001010 range: CARO:0001010 @@ -3474,7 +3472,7 @@ is_a: biotically_interacts_with ! biotically interacts with id: partner_in name: partner in xref: RO:0002461 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string is_a: participates_in @@ -3483,7 +3481,7 @@ id: pathogen_of name: pathogen of subset: ro-eco xref: RO:0002556 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_host ! has host inverse_of: has_pathogen ! has pathogen @@ -3495,7 +3493,7 @@ subset: ro-eco subset: RO:0002259 xref: RO:0002201 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_functional: true [Typedef] @@ -3503,7 +3501,7 @@ id: phosphorylates name: phosphorylates xref: RO:0002447 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: molecularly_interacts_with ! molecularly interacts with @@ -3512,7 +3510,7 @@ id: pollinated_by name: pollinated by subset: ro-eco xref: RO:0002456 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string @@ -3525,7 +3523,7 @@ subset: ro-eco xref: RO:0002455 property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with @@ -3537,7 +3535,7 @@ name: positively regulated by def: "inverse of positively regulates" [] subset: RO:0002259 xref: RO:0002336 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3548,7 +3546,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002211 @@ -3583,7 +3581,7 @@ def: "inverse of preys on" [] subset: ro-eco subset: RO:0002259 xref: RO:0002458 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string @@ -3598,9 +3596,9 @@ subset: ro-eco xref: RO:0002439 property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Jorrit Poelen" xsd:string -property_value: IAO:0000117 "Katja Shulz" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7134-3324 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string @@ -3623,7 +3621,7 @@ def: "x proper_distributary_of y iff x distributary_of y and x does not flow bac subset: ro-eco xref: RO:0002382 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: distributary_of ! distributary of [Typedef] @@ -3633,7 +3631,7 @@ def: "x proper_tributary_of y iff x tributary_of y and x does not originate from subset: ro-eco xref: RO:0002383 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: tributary_of ! tributary of [Typedef] @@ -3642,7 +3640,7 @@ name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string @@ -3654,7 +3652,7 @@ id: provides_nutrients_for name: provides nutrients for subset: ro-eco xref: RO:0002469 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3663,7 +3661,7 @@ name: realizable has basis in xref: RO:0004017 is_a: causally_related_to ! causally related to inverse_of: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:01Z [Typedef] @@ -3672,10 +3670,10 @@ name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] synonym: "triggered by process" EXACT [RO:cjm] xref: RO:0009501 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "David Osumi-Sutherland" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string @@ -3692,7 +3690,7 @@ xref: RO:0004028 domain: BFO:0000017 range: BFO:0000040 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:45:49Z [Typedef] @@ -3700,7 +3698,7 @@ id: receives_input_from name: receives input from xref: RO:0002485 property_value: IAO:0000116 "See notes for inverse relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to inverse_of: sends_output_to ! sends output to @@ -3740,7 +3738,7 @@ name: regulated by def: "inverse of regulates" [] subset: RO:0002259 xref: RO:0002334 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 range: BFO:0000015 @@ -3755,9 +3753,9 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Hill" xsd:string -property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 +property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string @@ -3774,7 +3772,7 @@ id: regulates_activity_of name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] xref: RO:0011002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3794,7 +3792,7 @@ id: regulates_in_other_organism name: regulates in other organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] xref: RO:0002010 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 range: BFO:0000015 is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -3805,7 +3803,7 @@ name: regulates levels of def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] xref: RO:0002332 property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 @@ -3817,7 +3815,7 @@ id: regulates_quantity_of name: regulates quantity of def: "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." [] xref: RO:0011003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3836,7 +3834,7 @@ id: related_via_localization_to name: related via localization to def: "A relationship that holds via some process of localization" [] xref: RO:0002337 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 range: BFO:0000002 @@ -3857,7 +3855,7 @@ id: represses_expression_of name: represses expression of def: "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." [] xref: RO:0003002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3871,7 +3869,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -3916,7 +3914,7 @@ name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] @@ -3936,7 +3934,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002348 property_value: IAO:0000112 "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3948,7 +3946,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002349 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3962,7 +3960,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3972,7 +3970,7 @@ id: results_in_developmental_induction_of name: results in developmental induction of def: "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." [] xref: RO:0002357 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3982,7 +3980,7 @@ def: "p results in the developmental progression of s iff p is a developmental p xref: RO:0002295 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 range: CARO:0000000 @@ -3994,7 +3992,7 @@ name: results in developmental regression of xref: RO:0002301 property_value: IAO:0000112 "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4004,7 +4002,7 @@ name: results in disappearance of xref: RO:0002300 property_value: IAO:0000112 "foramen ovale closure SubClassOf results in disappearance of foramen ovale" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4020,7 +4018,7 @@ id: results_in_ending_of name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4034,7 +4032,7 @@ xref: RO:0002297 property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4056,7 +4054,7 @@ id: results_in_growth_of name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4071,7 +4069,7 @@ xref: RO:0002299 property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4087,7 +4085,7 @@ xref: RO:0002298 property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4100,7 +4098,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002565 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4126,7 +4124,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002356 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4135,7 +4133,7 @@ id: results_in_structural_organization_of name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4151,7 +4149,7 @@ name: results in transport across def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002342 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: occurs_across ! occurs across is_a: results_in_transport_to_from_or_in ! results in transport to from or in @@ -4160,7 +4158,7 @@ id: results_in_transport_along name: results in transport along def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] xref: RO:0002341 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4168,7 +4166,7 @@ id: results_in_transport_to_from_or_in name: results in transport to from or in xref: RO:0002344 property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4183,7 +4181,7 @@ id: sends_output_to name: sends output to xref: RO:0002486 property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to [Typedef] @@ -4225,7 +4223,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcript" xsd:string property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -4235,7 +4233,7 @@ name: sequentially related to def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string @@ -4248,7 +4246,7 @@ name: skeleton of def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 is_a: part_of @@ -4259,7 +4257,7 @@ name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] xref: RO:0002379 property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: overlaps ! overlaps @@ -4271,7 +4269,7 @@ subset: ro-eco xref: RO:0002163 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 @@ -4285,7 +4283,7 @@ name: stabilizes quantity of def: "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." [] xref: RO:0011015 property_value: IAO:0000112 "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_quantity_of ! directly positively regulates quantity of @@ -4294,14 +4292,14 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates id: starts subset: ro-eco xref: RO:0002223 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: starts_with subset: ro-eco xref: RO:0002224 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -4317,7 +4315,7 @@ name: subcluster of def: "A relation between a group and another group it is part of but does not fully constitute." [] xref: RO:0015003 property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." xsd:string -property_value: IAO:0000117 "Shawn Tan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true is_a: part_of @@ -4326,7 +4324,7 @@ is_a: part_of id: subject_participant_in name: subject participant in xref: RO:0002462 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4345,7 +4343,7 @@ name: surrounded by def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] xref: RO:0002219 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to inverse_of: surrounds ! surrounds @@ -4357,7 +4355,7 @@ def: "inverse of surrounded by" [] subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to @@ -4367,7 +4365,7 @@ name: symbiotically interacts with def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] subset: ro-eco xref: RO:0002440 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true @@ -4380,8 +4378,8 @@ def: "Relation between an anatomical structure (including cells) and a neuron th xref: RO:0002103 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: receives_input_from ! receives input from inverse_of: synapsed_to ! synapsed to @@ -4406,8 +4404,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002108 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" [] @@ -4420,8 +4418,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002109 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4434,8 +4432,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002112 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4448,8 +4446,8 @@ comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part som xref: RO:0002120 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: sends_output_to ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -4473,8 +4471,8 @@ def: "A relation between a motor neuron and a muscle that it synapses to via a t comment: Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) xref: RO:0002107 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_II_bouton ! synapsed_by_via_type_II_bouton @@ -4488,8 +4486,8 @@ comment: Expands to: has_part some ('type Ib terminal button' that has_part some xref: RO:0002105 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Ib_bouton ! synapsed_by_via_type_Ib_bouton @@ -4503,8 +4501,8 @@ comment: Expands to: has_part some ('type Is terminal button' that has_part some xref: RO:0002106 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Is_bouton ! synapsed_by_via_type_Is_bouton @@ -4514,7 +4512,7 @@ expand_expression_to: "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that id: target_participant_in name: target participant in xref: RO:0002463 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4523,7 +4521,7 @@ id: temporally_related_to subset: ro-eco xref: RO:0002222 property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string [Typedef] @@ -4531,7 +4529,7 @@ id: transformation_of name: transformation of def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] xref: RO:0002494 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: develops_from ! develops from @@ -4541,7 +4539,7 @@ name: transitively provides input for def: "transitive form of directly_provides_input_for" [] xref: RO:0002414 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." xsd:string property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string domain: BFO:0000015 @@ -4556,7 +4554,7 @@ def: "A relationship that holds between a disease and organism" [] xref: RO:0002451 property_value: IAO:0000112 "all dengue disease transmitted by some mosquito" xsd:string property_value: IAO:0000116 "Add domain and range constraints" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -4576,7 +4574,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002313 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "regulates localization of" xsd:string is_a: related_via_localization_to ! related via localization to is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4590,7 +4588,7 @@ xref: RO:0002376 property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string @@ -4608,7 +4606,7 @@ name: trophically interacts with def: "An interaction relationship in which the partners are related via a feeding relationship." [] subset: ro-eco xref: RO:0002438 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4618,7 +4616,7 @@ name: ubiquitinates def: "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" [] xref: RO:0002480 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with [Typedef] diff --git a/src/ontology/subsets/ro-sequence.owl b/src/ontology/subsets/ro-sequence.owl index e0f35ac5..bfa36ffb 100644 --- a/src/ontology/subsets/ro-sequence.owl +++ b/src/ontology/subsets/ro-sequence.owl @@ -409,7 +409,7 @@ - David Osumi-Sutherland + RO:0002002 has_2D_boundary @@ -421,7 +421,7 @@ A relation that holds between two neurons that are electrically coupled via gap junctions. - David Osumi-Sutherland + RO:0002003 electrically_synapsed_to @@ -435,7 +435,7 @@ - David Osumi-Sutherland + RO:0002006 has_synaptic_terminal_of @@ -469,7 +469,7 @@ has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland + RO:0002007 bounding_layer_of @@ -505,9 +505,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. + A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. Note from NCEAS meeting: consider changing primary label - David Osumi-Sutherland + RO:0002008 coincident_with @@ -524,7 +524,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - David Osumi-Sutherland + RO:0002010 regulates_in_other_organism regulates in other organism @@ -553,7 +553,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + dos 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -568,7 +568,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + dos 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -584,7 +584,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + dos 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -599,7 +599,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -613,7 +613,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -630,7 +630,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + dos 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -644,7 +644,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + dos 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -658,7 +658,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + dos 2017-07-20T17:11:08Z RO:0002020 transports @@ -672,7 +672,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + dos 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -686,7 +686,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -697,7 +697,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + GOC:dos @@ -708,7 +708,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + dos 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -718,7 +718,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + GOC:dos @@ -729,7 +729,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + dos 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -739,7 +739,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + GOC:dos @@ -750,7 +750,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + dos 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -761,7 +761,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + GOC:dos @@ -780,7 +780,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + dos 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -797,7 +797,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + GOC:dos @@ -814,7 +814,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + RO:0002090 @@ -831,7 +831,7 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure that its soma is part of. - David Osumi-Sutherland + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -852,9 +852,9 @@ Examples include: the relationship between two channels collected simultaneously relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - David Osumi-Sutherland + fasciculates with - (forall (?x ?y) + (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) @@ -890,9 +890,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure its axon forms (chemical) synapses in. - Chris Mungall - David Osumi-Sutherland - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -924,8 +923,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -945,9 +944,9 @@ Examples include: the relationship between two channels collected simultaneously Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - Alexander Diehl - Chris Mungall - Lindsay Cowell + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) @@ -965,8 +964,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -985,8 +984,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -1005,8 +1004,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) RO:0002107 @@ -1023,8 +1022,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1043,8 +1042,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1064,8 +1063,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - Chris Mungall - David Osumi-Sutherland + + synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( @@ -1085,8 +1084,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1168,8 +1167,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -1196,8 +1195,8 @@ N1 SubclassOf ( Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -1218,7 +1217,7 @@ N1 SubclassOf ( A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - David Osumi-Sutherland + has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) @@ -1267,9 +1266,9 @@ N1 SubclassOf ( The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - David Osumi-Sutherland + has fasciculating component - (forall (?x ?y) + (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) @@ -1309,8 +1308,8 @@ N1 SubclassOf ( - X continuous_with Y if and only if X and Y share a fiat boundary. - David Osumi-Sutherland + X continuous_with Y if and only if X and Y share a fiat boundary. + connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) @@ -1329,8 +1328,8 @@ N1 SubclassOf ( x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom - proper overlaps - (forall (?x ?y) + proper overlaps + (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and @@ -1353,7 +1352,7 @@ N1 SubclassOf ( A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - Chris Mungall + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) @@ -1361,7 +1360,7 @@ N1 SubclassOf ( RO:0002163 spatially_disjoint_from - spatially disjoint from + spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern @@ -1498,7 +1497,7 @@ N1 SubclassOf ( A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - Chris Mungall + RO:0002200 has_phenotype @@ -1513,7 +1512,7 @@ N1 SubclassOf ( inverse of has phenotype - Chris Mungall + RO:0002201 @@ -1533,10 +1532,10 @@ N1 SubclassOf ( x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - Terry Meehan + + + + RO:0002202 develops_from This is the transitive form of the develops from relation @@ -1554,9 +1553,9 @@ N1 SubclassOf ( inverse of develops from - Chris Mungall - David Osumi-Sutherland - Terry Meehan + + + RO:0002203 develops_into @@ -1588,12 +1587,12 @@ N1 SubclassOf ( Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - Chris Mungall - David Osumi-Sutherland - has developmental precursor + + FBbt RO:0002207 + has developmental precursor directly_develops_from TODO - add child relations from DOS directly develops from @@ -1651,9 +1650,9 @@ N1 SubclassOf ( p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - Chris Mungall - David Hill - Tanya Berardini + + + GO Regulation precludes parthood; the regulatory process may not be within the regulated process. @@ -1676,7 +1675,7 @@ N1 SubclassOf ( p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - Chris Mungall + negatively regulates (process to process) @@ -1698,7 +1697,7 @@ N1 SubclassOf ( p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - Chris Mungall + positively regulates (process to process) @@ -1721,7 +1720,7 @@ N1 SubclassOf ( mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - Chris Mungall + has function realized in @@ -1740,7 +1739,7 @@ N1 SubclassOf ( c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - Chris Mungall + has function in RO:0002216 capable_of_part_of @@ -1757,7 +1756,7 @@ N1 SubclassOf ( x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - Chris Mungall + RO:0002219 surrounded_by @@ -1779,7 +1778,7 @@ N1 SubclassOf ( x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - Chris Mungall + RO:0002220 @@ -1803,7 +1802,7 @@ N1 SubclassOf ( inverse of surrounded by - Chris Mungall + RO:0002221 @@ -1816,7 +1815,7 @@ N1 SubclassOf ( - Chris Mungall + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 @@ -1830,7 +1829,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002223 starts @@ -1842,7 +1841,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002224 starts_with @@ -1856,7 +1855,7 @@ N1 SubclassOf ( x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - Chris Mungall + RO:0002225 develops_from_part_of develops from part of @@ -1871,7 +1870,7 @@ N1 SubclassOf ( x develops_in y if x is located in y whilst x is developing - Chris Mungall + EHDAA2 Jonathan Bard, EHDAA2 RO:0002226 @@ -1909,7 +1908,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002229 ends @@ -1921,7 +1920,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002230 ends_with @@ -1937,7 +1936,7 @@ N1 SubclassOf ( x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - Chris Mungall + starts with process that occurs in RO:0002231 @@ -1955,7 +1954,7 @@ N1 SubclassOf ( x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - Chris Mungall + ends with process that occurs in RO:0002232 @@ -1973,7 +1972,7 @@ N1 SubclassOf ( p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + consumes RO:0002233 @@ -1993,7 +1992,7 @@ N1 SubclassOf ( p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - Chris Mungall + produces RO:0002234 @@ -2047,7 +2046,7 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - Bill Duncan (https://orcid.org/0000-0001-9625-1899) + This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. @@ -2196,7 +2195,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y - Chris Mungall + RO:0002254 has_developmental_contribution_from has developmental contribution from @@ -2211,7 +2210,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho inverse of has developmental contribution from - Chris Mungall + RO:0002255 developmentally_contributes_to @@ -2229,9 +2228,9 @@ If you need an axiom that says 'has_participant min 2 object', you sho t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - Chris Mungall - David Osumi-Sutherland - Melissa Haendel + + + induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) @@ -2251,7 +2250,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally induced by - Chris Mungall + RO:0002257 developmentally_induces developmentally induces @@ -2269,7 +2268,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - Chris Mungall + In general you should not use this relation to make assertions - use one of the more specific relations below this one RO:0002258 developmentally_preceded_by @@ -2317,7 +2316,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - Chris Mungall + replaces RO:0002285 developmentally_replaces @@ -2332,7 +2331,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally preceded by - Chris Mungall + RO:0002286 developmentally_succeeded_by developmentally succeeded by @@ -2346,7 +2345,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - Chris Mungall + RO:0002287 part_of_developmental_precursor_of part of developmental precursor of @@ -2363,7 +2362,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - Chris Mungall + RO:0002295 results_in_developmental_progression_of results in developmental progression of @@ -2380,7 +2379,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - Chris Mungall + http://www.geneontology.org/GO.doc.development.shtml RO:0002296 @@ -2401,7 +2400,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002297 @@ -2422,7 +2421,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002298 @@ -2443,7 +2442,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002299 @@ -2461,7 +2460,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho foramen ovale closure SubClassOf results in disappearance of foramen ovale - Chris Mungall + May be merged into parent relation RO:0002300 results_in_disappearance_of @@ -2476,7 +2475,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) - Chris Mungall + May be merged into parent relation RO:0002301 results_in_developmental_regression_of @@ -2491,7 +2490,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of 'is substance that treats' - cjm + RO:0002302 is_treated_by_substance @@ -2511,7 +2510,7 @@ where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. - Pier Buttigieg + adapted for living in RO:0002303 @@ -2529,7 +2528,7 @@ where p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - cjm + RO:0002304 @@ -2547,7 +2546,7 @@ where p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - cjm + RO:0002305 @@ -2562,10 +2561,10 @@ where A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. - Austin Meier - Chris Mungall - Marie Angelique Laporte - cjm + + + + 2017-06-05T17:35:04Z RO:0002309 has_exposure_stimulus @@ -2580,7 +2579,7 @@ where Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. - Chris Mungall + regulates localization of RO:0002313 @@ -2600,7 +2599,7 @@ where an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002315 @@ -2617,7 +2616,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions RO:0002321 @@ -2633,7 +2632,7 @@ where An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. - Chris Mungall + adapted for RO:0002322 @@ -2647,7 +2646,7 @@ where A mereological relationship or a topological relationship - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships RO:0002323 @@ -2661,7 +2660,7 @@ where A relationship that holds between entities participating in some developmental process (GO:0032502) - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development RO:0002324 developmentally_related_to @@ -2678,9 +2677,8 @@ where Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. - Chris Mungall + In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - Gene Ontology Consortium RO:0002325 colocalizes_with @@ -2708,7 +2706,7 @@ then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. - Chris Mungall + In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 @@ -2725,7 +2723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - Chris Mungall + catalyzes executes has @@ -2744,7 +2742,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 functionally_related_to @@ -2758,7 +2756,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati this relation holds between c and p when c is part of some c', and c' is capable of p. - Chris Mungall + false RO:0002329 part_of_structure_that_is_capable_of @@ -2773,7 +2771,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati c involved_in p if and only if c enables some process p', and p' is part of p - Chris Mungall + actively involved in enables part of RO:0002331 @@ -2792,7 +2790,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - Chris Mungall + regulates levels of (process to entity) RO:0002332 @@ -2808,7 +2806,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables - Chris Mungall + RO:0002333 enabled_by @@ -2825,7 +2823,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of regulates - Chris Mungall + regulated by (processual) RO:0002334 @@ -2840,7 +2838,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of negatively regulates - Chris Mungall + RO:0002335 negatively_regulated_by @@ -2854,7 +2852,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of positively regulates - Chris Mungall + RO:0002336 positively_regulated_by @@ -2869,7 +2867,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds via some process of localization - Chris Mungall + Do not use this relation directly. It is a grouping relation. RO:0002337 related_via_localization_to @@ -2883,7 +2881,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - Chris Mungall + RO:0002338 @@ -2899,7 +2897,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - Chris Mungall + RO:0002339 @@ -2915,7 +2913,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. - Chris Mungall + RO:0002340 imports @@ -2929,7 +2927,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - Chris Mungall + RO:0002341 results_in_transport_along results in transport along @@ -2943,7 +2941,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - Chris Mungall + RO:0002342 results_in_transport_across @@ -2958,7 +2956,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'pollen tube growth' results_in growth_of some 'pollen tube' - Chris Mungall + RO:0002343 results_in_growth_of results in growth of @@ -2971,7 +2969,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - Chris Mungall + RO:0002344 results_in_transport_to_from_or_in results in transport to from or in @@ -2983,8 +2981,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. - Chris Mungall + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. + RO:0002345 exports @@ -3000,7 +2998,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - Chris Mungall + RO:0002348 @@ -3017,7 +3015,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - Chris Mungall + RO:0002349 @@ -3034,7 +3032,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has input - Chris Mungall + RO:0002352 @@ -3050,7 +3048,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has output - Chris Mungall + RO:0002353 @@ -3064,7 +3062,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002354 formed_as_result_of formed as result of @@ -3078,7 +3076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. - Chris Mungall + RO:0002355 results_in_structural_organization_of results in structural organization of @@ -3092,7 +3090,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - Chris Mungall + RO:0002356 @@ -3108,7 +3106,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. - Chris Mungall + RO:0002357 results_in_developmental_induction_of results in developmental induction of @@ -3120,7 +3118,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + http://neurolex.org/wiki/Property:DendriteLocation RO:0002360 has_dendrite_location @@ -3136,7 +3134,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - Chris Mungall + attached to (anatomical structure to anatomical structure) RO:0002371 @@ -3153,7 +3151,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002372 has_muscle_origin @@ -3176,7 +3174,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002373 has_muscle_insertion @@ -3200,7 +3198,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) @@ -3222,7 +3220,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - Chris Mungall + drains into drains to tributary channel of @@ -3247,7 +3245,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Deschutes River distributary_of Little Lava Lake x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - Chris Mungall + branch of distributary channel of http://en.wikipedia.org/wiki/Distributary @@ -3273,7 +3271,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. - Chris Mungall + anastomoses with RO:0002378 @@ -3289,7 +3287,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - Chris Mungall + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios RO:0002379 spatially_coextensive_with @@ -3312,7 +3310,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - Chris Mungall + RO:0002380 branching_part_of @@ -3331,7 +3329,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. - Chris Mungall + RO:0002381 main_stem_of @@ -3347,7 +3345,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_distributary_of y iff x distributary_of y and x does not flow back into y - Chris Mungall + RO:0002382 proper_distributary_of @@ -3362,7 +3360,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_tributary_of y iff x tributary_of y and x does not originate from y - Chris Mungall + RO:0002383 proper_tributary_of @@ -3379,7 +3377,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - Chris Mungall + RO:0002384 has_developmental_potential_involving has developmental potential involving @@ -3393,7 +3391,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - Chris Mungall + RO:0002385 has_potential_to_developmentally_contribute_to has potential to developmentally contribute to @@ -3407,7 +3405,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - Chris Mungall + RO:0002386 has_potential_to_developmentally_induce has potential to developmentally induce @@ -3421,7 +3419,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has the potential to develop into y iff x develops into y or if x is capable of developing into y - Chris Mungall + RO:0002387 has_potential_to_develop_into has potential to develop into @@ -3435,7 +3433,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - Chris Mungall + RO:0002388 has_potential_to_directly_develop_into has potential to directly develop into @@ -3450,7 +3448,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' RO:0002400 @@ -3468,7 +3466,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of upstream of - Chris Mungall + RO:0002404 causally_downstream_of causally downstream of @@ -3483,7 +3481,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002405 immediately_causally_downstream_of immediately causally downstream of @@ -3498,7 +3496,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - Chris Mungall + indirectly activates RO:0002407 @@ -3515,7 +3513,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - Chris Mungall + indirectly inhibits RO:0002409 @@ -3544,7 +3542,7 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002410 causally_related_to @@ -3566,7 +3564,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - Chris Mungall + RO:0002411 @@ -3582,7 +3580,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - Chris Mungall + RO:0002412 immediately_causally_upstream_of @@ -3598,7 +3596,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit - Chris Mungall + directly provides input for directly provides input for (process to process) @@ -3618,7 +3616,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different transitive form of directly_provides_input_for - Chris Mungall + This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. transitively provides input for (process to process) RO:0002414 @@ -3636,7 +3634,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall + influences (processual) RO:0002418 affects @@ -3652,7 +3650,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - Chris Mungall + RO:0002427 @@ -3668,7 +3666,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - Chris Mungall + RO:0002428 involved_in_regulation_of involved in regulation of @@ -3681,7 +3679,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - Chris Mungall + RO:0002429 involved_in_positive_regulation_of @@ -3695,7 +3693,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - Chris Mungall + RO:0002430 involved_in_negative_regulation_of @@ -3712,7 +3710,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - Chris Mungall + involved in or reguates RO:0002431 involved_in_or_involved_in_regulation_of @@ -3728,7 +3726,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall + executes activity in RO:0002432 enables activity in @@ -3740,8 +3738,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + GOC:cjm + GOC:dos @@ -3751,7 +3749,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - Chris Mungall + RO:0002433 contributes_to_morphology_of contributes to morphology of @@ -3768,7 +3766,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. - Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. RO:0002434 in pairwise interaction with @@ -3787,7 +3785,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) - Chris Mungall + RO:0002435 genetically_interacts_with genetically interacts with @@ -3803,7 +3801,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - Chris Mungall + binds molecularly binds with RO:0002436 @@ -3824,7 +3822,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - Chris Mungall + interacts with on organism level RO:0002437 @@ -3841,7 +3839,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the partners are related via a feeding relationship. - Chris Mungall + RO:0002438 trophically_interacts_with @@ -3859,9 +3857,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] Baleen whale preys on krill An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - Chris Mungall - Jorrit Poelen - Katja Shulz + + + is subject of predation interaction with preys upon RO:0002439 @@ -3880,7 +3878,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A biotic interaction in which the two organisms live together in more or less intimate association. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism RO:0002440 @@ -3896,7 +3894,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002441 @@ -3911,7 +3909,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002442 @@ -3926,7 +3924,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 This relation groups a pair of inverse relations, parasite of and parasitized by RO:0002443 @@ -3944,7 +3942,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human - Chris Mungall + parasitizes RO:0002444 direct parasite of @@ -3961,7 +3959,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + has parasite parasitised by RO:0002445 @@ -3980,7 +3978,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - Chris Mungall + RO:0002446 semibiotically interacts with @@ -3996,7 +3994,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. RO:0002447 phosphorylates @@ -4015,8 +4013,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - Chris Mungall - Vasundra Touré + + RO:0002448 molecularly controls directly_regulates_activity_of @@ -4033,8 +4031,8 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly inhibits RO:0002449 molecularly decreases activity of @@ -4052,8 +4050,8 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly activates RO:0002450 molecularly increases activity of @@ -4070,7 +4068,7 @@ For example, A and B may be gene products and binding of B by A positively regul all dengue disease transmitted by some mosquito A relationship that holds between a disease and organism Add domain and range constraints - Chris Mungall + RO:0002451 transmitted_by transmitted by @@ -4084,7 +4082,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between a disease or an organism and a phenotype - Chris Mungall + RO:0002452 has_symptom has symptom @@ -4096,7 +4094,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) RO:0002453 @@ -4111,7 +4109,7 @@ For example, A and B may be gene products and binding of B by A positively regul X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y - Chris Mungall + RO:0002454 has_host @@ -4128,7 +4126,7 @@ For example, A and B may be gene products and binding of B by A positively regul Bees pollinate Flowers This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - Chris Mungall + is subject of pollination interaction with RO:0002455 @@ -4143,7 +4141,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + has polinator is target of pollination interaction with RO:0002456 @@ -4160,7 +4158,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4175,7 +4173,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of preys on - Chris Mungall + has predator is target of predation interaction with RO:0002458 @@ -4195,7 +4193,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anopheles is a vector for Plasmodium - Chris Mungall + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism RO:0002459 @@ -4209,7 +4207,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002460 has_vector @@ -4222,7 +4220,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target RO:0002461 partner_in @@ -4235,7 +4233,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002462 subject_participant_in @@ -4248,7 +4246,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002463 target_participant_in @@ -4261,7 +4259,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002469 provides_nutrients_for @@ -4274,7 +4272,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is subject of eating interaction with RO:0002470 @@ -4288,7 +4286,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + eaten by is target of eating interaction with RO:0002471 @@ -4307,7 +4305,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - Chris Mungall + RO:0002473 @@ -4326,7 +4324,7 @@ For example, A and B may be gene products and binding of B by A positively regul ABal nucleus child nucleus of ABa nucleus (in C elegans) c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d - Chris Mungall + This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. RO:0002476 child_nucleus_of @@ -4340,7 +4338,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a hermaphroditic organism - Chris Mungall + RO:0002477 child_nucleus_of_in_hermaphrodite child nucleus of in hermaphrodite @@ -4353,7 +4351,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a male organism - Chris Mungall + RO:0002478 child_nucleus_of_in_male child nucleus of in male @@ -4367,7 +4365,7 @@ For example, A and B may be gene products and binding of B by A positively regul p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall + RO:0002479 has_part_that_occurs_in @@ -4382,7 +4380,7 @@ For example, A and B may be gene products and binding of B by A positively regul An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y Axiomatization to GO to be added later - Chris Mungall + RO:0002480 ubiquitinates ubiquitinates @@ -4396,7 +4394,7 @@ For example, A and B may be gene products and binding of B by A positively regul See notes for inverse relation - Chris Mungall + RO:0002485 receives_input_from receives input from @@ -4409,7 +4407,7 @@ For example, A and B may be gene products and binding of B by A positively regul This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - Chris Mungall + RO:0002486 sends_output_to sends output to @@ -4423,7 +4421,7 @@ For example, A and B may be gene products and binding of B by A positively regul x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - Chris Mungall + RO:0002494 transformation_of transformation of @@ -4437,7 +4435,7 @@ For example, A and B may be gene products and binding of B by A positively regul x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - Chris Mungall + RO:0002495 immediate_transformation_of @@ -4467,7 +4465,7 @@ For example, A and B may be gene products and binding of B by A positively regul p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002501 @@ -4483,7 +4481,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c - Chris Mungall + has intermediate product RO:0002505 @@ -4500,7 +4498,7 @@ For example, A and B may be gene products and binding of B by A positively regul The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002506 @@ -4522,11 +4520,11 @@ For example, A and B may be gene products and binding of B by A positively regul A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future - Chris Mungall + determined by (system to material entity) - Chris Mungall - Pier Buttigieg + + RO:0002507 determined_by @@ -4540,7 +4538,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of determined by - Chris Mungall + determines (material entity to system) RO:0002508 @@ -4559,7 +4557,7 @@ For example, A and B may be gene products and binding of B by A positively regul s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. - Chris Mungall + RO:0002509 determined_by_part_of @@ -4574,7 +4572,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between two entities that have the property of being sequences or having sequences. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. @@ -4594,7 +4592,7 @@ For example, A and B may be gene products and binding of B by A positively regul Two consecutive DNA residues are sequentially adjacent Two exons on a processed transcript that were previously connected by an intron are adjacent x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002515 @@ -4612,7 +4610,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as a start sequence the start codon for that transcript x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence - Chris Mungall + started by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4629,7 +4627,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has start sequence - Chris Mungall + starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4649,7 +4647,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence - Chris Mungall + ended by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4666,7 +4664,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has end sequence - Chris Mungall + ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4684,7 +4682,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. In the SO paper, this was defined as an instance-type relation - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002520 @@ -4701,7 +4699,7 @@ For example, A and B may be gene products and binding of B by A positively regul Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering - Chris Mungall + RO:0002521 is_sequentially_aligned_with @@ -4718,7 +4716,7 @@ For example, A and B may be gene products and binding of B by A positively regul The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y - Chris Mungall + RO:0002522 bounds_sequence_of @@ -4733,7 +4731,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of bounds sequence of - Chris Mungall + RO:0002523 @@ -4751,8 +4749,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x has subsequence y iff all of the sequence parts of x are sequence parts of y - Chris Mungall + x has subsequence y iff all of the sequence parts of y are sequence parts of x + contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4771,7 +4769,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has subsequence - Chris Mungall + contained by RO:0002525 @@ -4788,8 +4786,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. - Chris Mungall + x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. + RO:0002526 overlaps_sequence_of @@ -4803,8 +4801,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. - Chris Mungall + x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + disconnected from RO:0002527 @@ -4820,7 +4818,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of downstream of sequence of - Chris Mungall + RO:0002528 is_upstream_of_sequence_of @@ -4836,7 +4834,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. - Chris Mungall + RO:0002529 is_downstream_of_sequence_of @@ -4852,7 +4850,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y - Chris Mungall + RO:0002530 @@ -4869,7 +4867,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript inverse of immediately downstream of - Chris Mungall + RO:0002531 is_immediately_upstream_of_sequence_of @@ -4889,7 +4887,7 @@ For example, A and B may be gene products and binding of B by A positively regul Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - Chris Mungall + has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). RO:0002551 @@ -4911,7 +4909,7 @@ For example, A and B may be gene products and binding of B by A positively regul p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. - Chris Mungall + RO:0002552 results_in_ending_of results in ending of @@ -4926,7 +4924,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - Chris Mungall + http://eol.org/schema/terms/hyperparasitoidOf https://en.wikipedia.org/wiki/Hyperparasite RO:0002553 @@ -4944,7 +4942,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of hyperparasite of - Chris Mungall + RO:0002554 has epiparasite has hyperparasite @@ -4961,7 +4959,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + http://en.wikipedia.org/wiki/Allelopathy RO:0002555 @@ -4978,7 +4976,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002556 pathogen_of @@ -4991,7 +4989,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002557 has_pathogen @@ -5005,7 +5003,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + causally influenced by (entity-centric) RO:0002559 @@ -5020,7 +5018,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - Chris Mungall + RO:0002565 @@ -5039,8 +5037,8 @@ For example, A and B may be gene products and binding of B by A positively regul The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - Chris Mungall - Vasundra Touré + + causally influences (entity-centric) RO:0002566 @@ -5057,7 +5055,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between elements of a musculoskeletal system or its analogs. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. RO:0002567 biomechanically_related_to @@ -5071,7 +5069,7 @@ For example, A and B may be gene products and binding of B by A positively regul m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - Chris Mungall + Wikipedia:Antagonist_(muscle) RO:0002568 has_muscle_antagonist @@ -5087,7 +5085,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of branching part of - Chris Mungall + RO:0002569 @@ -5104,7 +5102,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - Chris Mungall + UBERON:cjm This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. RO:0002570 @@ -5121,7 +5119,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - Chris Mungall + GOC:cjm RO:0002571 @@ -5137,7 +5135,7 @@ For example, A and B may be gene products and binding of B by A positively regul s is luminal space of x iff s is lumen_of x and s is an immaterial entity - Chris Mungall + RO:0002572 luminal_space_of @@ -5152,7 +5150,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002574 participates_in_a_biotic-biotic_interaction_with @@ -5169,7 +5167,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has skeleton - Chris Mungall + RO:0002576 skeleton_of @@ -5184,7 +5182,7 @@ For example, A and B may be gene products and binding of B by A positively regul p directly regulates q iff p is immediately causally upstream of q and p regulates q. - Chris Mungall + directly regulates (processual) @@ -5205,7 +5203,7 @@ For example, A and B may be gene products and binding of B by A positively regul gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - Chris Mungall + RO:0002584 has_part_structure_that_is_capable_of has part structure that is capable of @@ -5320,7 +5318,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall + RO:0002595 causal_relation_between_material_entity_and_a_process @@ -5723,7 +5721,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. - Vasundra Touré + RO:0003002 represses_expression_of represses expression of @@ -5738,7 +5736,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. - Vasundra Touré + RO:0003003 increases_expression_of increases expression of @@ -5883,7 +5881,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:38:20Z RO:0004000 condition_has_genetic_basis_in @@ -5897,7 +5895,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:20Z RO:0004001 has_material_basis_in_gain_of_function_germline_mutation_in @@ -5913,7 +5911,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:37Z RO:0004002 has_material_basis_in_loss_of_function_germline_mutation_in @@ -5927,7 +5925,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:54Z RO:0004003 has_material_basis_in_germline_mutation_in @@ -5942,7 +5940,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:07Z RO:0004004 has_material_basis_in_somatic_mutation_in @@ -5957,7 +5955,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:26Z RO:0004005 has_major_susceptibility_factor @@ -5971,7 +5969,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:57Z RO:0004006 has_partial_material_basis_in_germline_mutation_in @@ -5985,7 +5983,7 @@ Environmental exposures include those imposed by natural environments, experimen p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - cjm + 2018-12-13T11:26:17Z RO:0004007 @@ -6001,7 +5999,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - cjm + 2018-12-13T11:26:32Z RO:0004008 @@ -6012,8 +6010,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6027,7 +6025,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - cjm + 2018-12-13T11:26:56Z RO:0004009 @@ -6038,8 +6036,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6053,7 +6051,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:53:08Z RO:0004010 is_genetic_basis_for_condition @@ -6067,7 +6065,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:55:51Z RO:0004011 is_causal_gain_of_function_germline_mutation_of_in @@ -6082,7 +6080,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:06Z RO:0004012 is_causal_loss_of_function_germline_mutation_of_in @@ -6098,7 +6096,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:40Z RO:0004013 is_causal_germline_mutation_in @@ -6114,7 +6112,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:57:07Z RO:0004014 is_causal_somatic_mutation_in @@ -6129,7 +6127,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. - cjm + 2017-11-05T02:57:43Z RO:0004015 is_causal_susceptibility_factor_for @@ -6145,7 +6143,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. - cjm + 2017-11-05T02:58:43Z RO:0004016 is_causal_germline_mutation_partially_giving_rise_to @@ -6160,7 +6158,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:01Z RO:0004017 realizable_has_basis_in @@ -6173,7 +6171,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:29Z RO:0004018 is_basis_for_realizable @@ -6188,7 +6186,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:26:47Z RO:0004019 disease_has_basis_in @@ -6204,7 +6202,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) - cjm + 2017-11-05T03:29:32Z RO:0004020 disease_has_basis_in_dysfunction_of @@ -6220,7 +6218,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. disease has basis in disruption of (disease to process) - cjm + 2017-11-05T03:37:52Z RO:0004021 disease_has_basis_in_disruption_of @@ -6244,7 +6242,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. - cjm + 2017-11-05T03:46:07Z RO:0004022 disease_has_basis_in_feature @@ -6260,7 +6258,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. - cjm + 2017-11-05T03:50:54Z RO:0004023 causal_relationship_with_disease_as_subject @@ -6277,7 +6275,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and a process where the disease process disrupts the execution of the process. disease causes disruption of (disease to process) - cjm + 2017-11-05T03:51:09Z RO:0004024 disease_causes_disruption_of @@ -6293,7 +6291,7 @@ Environmental exposures include those imposed by natural environments, experimen disease causes dysfunction of (disease to anatomical entity) - cjm + 2017-11-05T03:58:20Z RO:0004025 disease_causes_dysfunction_of @@ -6319,7 +6317,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. - cjm + 2017-11-05T04:06:02Z RO:0004026 disease_has_location @@ -6343,7 +6341,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity - cjm + 2017-12-26T19:37:31Z RO:0004027 disease_has_inflammation_site @@ -6359,7 +6357,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - cjm + 2017-12-26T19:45:49Z RO:0004028 realized_in_response_to_stimulus @@ -6382,7 +6380,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. - cjm + 2017-12-26T19:50:53Z RO:0004029 disease_has_feature @@ -6397,7 +6395,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. - cjm + 2017-12-26T19:58:44Z RO:0004030 disease_arises_from_alteration_in_structure @@ -6411,7 +6409,7 @@ Environmental exposures include those imposed by natural environments, experimen Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - cjm + 2018-01-25T23:20:13Z RO:0004031 enables_subfunction @@ -6425,7 +6423,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:30Z RO:0004032 @@ -6441,7 +6439,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:51Z RO:0004033 @@ -6458,7 +6456,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - cjm + 2018-01-26T23:53:14Z RO:0004034 @@ -6476,7 +6474,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - cjm + 2018-01-26T23:53:22Z RO:0004035 @@ -6492,7 +6490,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:05Z RO:0004046 causally_upstream_of_or_within,_negative_effect @@ -6506,7 +6504,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:19Z RO:0004047 causally_upstream_of_or_within,_positive_effect @@ -6633,10 +6631,10 @@ Environmental exposures include those imposed by natural environments, experimen An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - Austin Meier - Chris Mungall - David Osumi-Sutherland - Marie Angelique Laporte + + + + RO:0009501 triggered by process realized_in_response_to @@ -6659,7 +6657,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - Vasundra Touré + RO:0011002 regulates_activity_of regulates activity of @@ -6674,7 +6672,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. - Vasundra Touré + RO:0011003 regulates_quantity_of regulates quantity of @@ -6689,7 +6687,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. - Vasundra Touré + RO:0011004 indirectly_regulates_activity_of indirectly regulates activity of @@ -6706,7 +6704,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011007 decreases_by_repression_quantity_of decreases by repression quantity of @@ -6723,7 +6721,7 @@ For example, protein A (transcription factor) indirectly decreases by repression The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011008 increases_by_expression_quantity_of increases by expression quantity of @@ -6738,7 +6736,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly positively regulates the quantity of B. - Vasundra Touré + RO:0011009 directly_positively_regulates_quantity_of directly positively regulates quantity of @@ -6753,7 +6751,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly negatively regulates the quantity of B. - Vasundra Touré + RO:0011010 directly_negatively_regulates_quantity_of directly negatively regulates quantity of @@ -6768,7 +6766,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. - Vasundra Touré + indirectly activates RO:0011013 indirectly_positively_regulates_activity_of @@ -6785,7 +6783,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. - Vasundra Touré + RO:0011014 destabilizes_quantity_of destabilizes quantity of @@ -6801,7 +6799,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. - Vasundra Touré + RO:0011015 stabilizes_quantity_of stabilizes quantity of @@ -6814,7 +6812,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. - Vasundra Touré + indirectly inhibits RO:0011016 indirectly_negatively_regulates_activity_of @@ -6828,7 +6826,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. - Vasundra Touré + RO:0011021 directly_regulates_quantity_of directly regulates quantity of @@ -6841,7 +6839,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011022 indirectly_regulates_quantity_of indirectly regulates quantity of @@ -6854,7 +6852,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011023 indirectly_negatively_regulates_quantity_of indirectly negatively regulates quantity of @@ -6867,7 +6865,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011024 indirectly_positively_regulates_quantity_of indirectly positively regulates quantity of @@ -6880,8 +6878,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is regulated by the small molecule continuant + pg 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -6895,8 +6893,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is activated by the small molecule continuant + pg 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -6910,8 +6908,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant + pg 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -6924,8 +6922,8 @@ For example, protein A (transcription factor) indirectly increases by expression - p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + p acts on population of c iff c' is a collection, has members of type c, and p has participant c + pg 2020-06-08T17:21:33Z RO:0012003 @@ -6941,8 +6939,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process + pg 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -6956,8 +6954,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process + pg 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of @@ -6971,8 +6969,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process + pg 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of @@ -6985,8 +6983,8 @@ For example, protein A (transcription factor) indirectly increases by expression - The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. + pg 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -6999,7 +6997,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + pg 2021-02-26T07:28:29Z RO:0012008 @@ -7016,7 +7014,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + pg 2022-09-26T06:01:01Z RO:0012009 @@ -7032,7 +7030,7 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + pg 2022-09-26T06:06:20Z RO:0012010 @@ -7048,7 +7046,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + pg 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7063,7 +7061,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + pg 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7229,7 +7227,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relation between a group and another group it is part of but does not fully constitute. X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. - Shawn Tan + This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. RO:0015003 subcluster_of @@ -7301,7 +7299,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - http://orcid.org/0000-0002-7463-6306 + 2021-11-05T17:30:44Z RO:0016002 has_disease @@ -7457,7 +7455,7 @@ For example, protein A (transcription factor) indirectly increases by expression This relation groups relations between diseases and any other kind of entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. - cjm + 2018-09-26T00:00:32Z RO:0040035 disease_relationship @@ -7471,7 +7469,7 @@ For example, protein A (transcription factor) indirectly increases by expression p has anatomical participant c iff p has participant c, and c is an anatomical entity - cjm + 2018-09-26T01:08:58Z RO:0040036 results_in_changes_to_anatomical_or_cellular_structure diff --git a/src/ontology/subsets/ro-time-interval.obo b/src/ontology/subsets/ro-time-interval.obo index 32edb9a6..7aeb28f2 100644 --- a/src/ontology/subsets/ro-time-interval.obo +++ b/src/ontology/subsets/ro-time-interval.obo @@ -13,7 +13,7 @@ id: acquires_nutrients_from name: acquires nutrients from subset: ro-eco xref: RO:0002457 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for @@ -58,7 +58,7 @@ property_value: RO:0004050 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:22Z [Typedef] @@ -71,7 +71,7 @@ property_value: RO:0004049 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:14Z [Typedef] @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z [Typedef] @@ -103,7 +103,7 @@ xref: RO:0004032 property_value: RO:0004049 RO:0002264 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z [Typedef] @@ -120,7 +120,7 @@ property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cy property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 domain: BFO:0000004 range: BFO:0000004 @@ -131,7 +131,7 @@ id: allelopath_of name: allelopath of subset: ro-eco xref: RO:0002555 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string @@ -153,7 +153,7 @@ def: "x anabranch_of y if x is a distributary of y (i.e. it channels a from a la subset: ro-eco xref: RO:0002378 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "anastomoses with" xsd:string is_a: distributary_of ! distributary of disjoint_from: proper_distributary_of ! proper distributary of @@ -165,7 +165,7 @@ name: attached to def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] subset: ro-eco xref: RO:0002371 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: attached_to_part_of ! attached to part of @@ -189,9 +189,8 @@ def: "Relation between a neuron and some structure its axon forms (chemical) syn xref: RO:0002102 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in @@ -202,7 +201,7 @@ id: biomechanically_related_to name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] xref: RO:0002567 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: CARO:0000003 range: CARO:0000003 @@ -214,7 +213,7 @@ name: biotically interacts with def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] subset: ro-eco xref: RO:0002437 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string @@ -231,7 +230,7 @@ def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\ comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco xref: RO:0002007 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 is_a: part_of @@ -242,7 +241,7 @@ def: "x bounds the sequence of y iff the upstream-most part of x is upstream of xref: RO:0002522 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to inverse_of: is_bound_by_sequence_of ! is bound by sequence of @@ -254,7 +253,7 @@ def: "x is a branching part of y if and only if x is part of y and x is connecte subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso FMA:85994 xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with @@ -269,7 +268,7 @@ subset: ro-eco xref: RO:0002215 property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 @@ -302,7 +301,7 @@ id: capable_of_part_of name: capable of part of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ is_a: causal_agent_in_process ! causal agent in process @@ -350,7 +349,7 @@ id: causal_relation_between_entities name: causal relation between entities xref: RO:0002506 property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000002 @@ -363,7 +362,7 @@ name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] xref: RO:0002595 property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 range: BFO:0000015 @@ -374,7 +373,7 @@ id: causal_relation_between_processes name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 @@ -389,7 +388,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: OGMS:0000031 is_a: causally_related_to ! causally related to is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:50:54Z [Typedef] @@ -398,7 +397,7 @@ name: causally downstream of def: "inverse of upstream of" [] xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within is_a: preceded_by inverse_of: causally_upstream_of ! causally upstream of @@ -409,7 +408,7 @@ name: causally downstream of or within def: "inverse of causally upstream of or within" [] subset: RO:0002259 xref: RO:0002427 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -418,7 +417,7 @@ is_a: causal_relation_between_processes ! causal relation between processes id: causally_influenced_by name: causally influenced by xref: RO:0002559 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: causal_relation_between_entities ! causal relation between entities @@ -429,8 +428,8 @@ id: causally_influences name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] xref: RO:0002566 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 @@ -443,7 +442,7 @@ name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] @@ -453,7 +452,7 @@ def: "p is causally upstream of q iff p is causally related to q, the end of p p subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes @@ -465,7 +464,7 @@ def: "p is causally upstream of, negative effect q iff p is casually upstream of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -478,7 +477,7 @@ comment: holds between x and y if and only if x is causally upstream of y and th subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -490,7 +489,7 @@ def: "p is 'causally upstream or within' q iff p is causally related to q, and t synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -502,7 +501,7 @@ name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -511,7 +510,7 @@ name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -537,7 +536,7 @@ name: child nucleus of def: "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" [] xref: RO:0002476 property_value: IAO:0000112 "ABal nucleus child nucleus of ABa nucleus (in C elegans)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." xsd:string domain: GO:0005634 range: GO:0005634 @@ -548,7 +547,7 @@ id: child_nucleus_of_in_hermaphrodite name: child nucleus of in hermaphrodite def: "A child nucleus relationship in which the cells are part of a hermaphroditic organism" [] xref: RO:0002477 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -556,7 +555,7 @@ id: child_nucleus_of_in_male name: child nucleus of in male def: "A child nucleus relationship in which the cells are part of a male organism" [] xref: RO:0002478 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -576,7 +575,7 @@ comment: Example: if we define region of chromosome as any subdivision of a chro subset: ro-eco xref: RO:0002008 property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -585,9 +584,8 @@ name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 -property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -599,7 +597,7 @@ name: commensually interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] subset: ro-eco xref: RO:0002441 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -610,7 +608,7 @@ def: "x composed_primarily_of y if and only if more than half of the mass of x i subset: ro-eco xref: RO:0002473 property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 @@ -639,7 +637,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: BFO:0000017 is_a: causally_related_to ! causally related to inverse_of: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:38:20Z [Typedef] @@ -648,7 +646,7 @@ name: conduit for def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] subset: ro-eco xref: RO:0002570 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 UBERON:cjm xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 @@ -661,7 +659,7 @@ name: confers advantage in subset: ro-eco xref: RO:0002322 property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "adapted for" xsd:string range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -727,7 +725,7 @@ name: continuous with def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 @@ -746,7 +744,7 @@ property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a het property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -771,7 +769,7 @@ id: contributes_to_morphology_of name: contributes to morphology of def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] xref: RO:0002433 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -796,7 +794,7 @@ id: decreases_by_repression_quantity_of name: decreases by repression quantity of def: "The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011007 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_negatively_regulates_quantity_of ! indirectly negatively regulates quantity of @@ -808,8 +806,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in wh xref: RO:0002121 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in @@ -821,7 +819,7 @@ name: destabilizes quantity of def: "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." [] xref: RO:0011014 property_value: IAO:0000112 "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_quantity_of ! directly negatively regulates quantity of @@ -832,11 +830,11 @@ name: determined by def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] subset: ro-eco xref: RO:0002507 -property_value: http://purl.org/dc/terms/creator "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/creator "Pier Buttigieg" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-4366-3088 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "A coral reef environment is determined by a particular coral reef" xsd:string property_value: IAO:0000116 "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602 property_value: IAO:0000589 "determined by (system to material entity)" xsd:string domain: RO:0002577 @@ -852,7 +850,7 @@ name: determined by part of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] subset: ro-eco xref: RO:0002509 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 range: BFO:0000040 is_a: causal_relation_between_entities ! causal relation between entities @@ -865,7 +863,7 @@ def: "inverse of determined by" [] subset: ro-eco subset: RO:0002259 xref: RO:0002508 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "determines (material entity to system)" xsd:string is_a: causally_influences ! causally influences @@ -876,7 +874,7 @@ def: "inverse of has developmental contribution from" [] subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to @@ -886,9 +884,9 @@ name: developmentally induced by def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] xref: RO:0002256 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string property_value: IAO:0000119 GO:0001759 xsd:string @@ -905,7 +903,7 @@ name: developmentally induces def: "Inverse of developmentally induced by" [] xref: RO:0002257 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_induce ! has potential to developmentally induce @@ -917,7 +915,7 @@ comment: This relation groups together various other developmental relations. It xref: RO:0002258 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string domain: BFO:0000002 range: BFO:0000002 @@ -929,7 +927,7 @@ id: developmentally_related_to name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] xref: RO:0002324 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] @@ -939,7 +937,7 @@ def: "x developmentally replaces y if and only if there is some developmental pr xref: RO:0002285 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "replaces" xsd:string is_a: developmentally_preceded_by ! developmentally preceded by @@ -949,7 +947,7 @@ name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] xref: RO:0002286 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -959,10 +957,10 @@ def: "x develops from y if and only if either (a) x directly develops from y or comment: This is the transitive form of the develops from relation xref: RO:0002202 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 domain: BFO:0000004 range: BFO:0000004 is_transitive: true @@ -975,7 +973,7 @@ name: develops from part of def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] xref: RO:0002225 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: develops_from ! develops from [Typedef] @@ -984,7 +982,7 @@ name: develops in def: "x develops_in y if x is located in y whilst x is developing" [] xref: RO:0002226 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string domain: CARO:0000000 @@ -997,9 +995,9 @@ def: "inverse of develops from" [] subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 is_transitive: true is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into @@ -1010,11 +1008,11 @@ id: directly_develops_from name: directly develops from def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] xref: RO:0002207 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "has developmental precursor" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000119 "FBbt" xsd:string property_value: RO:0002575 RO:0002202 is_a: develops_from ! develops from @@ -1060,8 +1058,8 @@ name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] xref: RO:0002449 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1072,7 +1070,7 @@ id: directly_negatively_regulates_quantity_of name: directly negatively regulates quantity of def: "The entity A has an activity that directly negatively regulates the quantity of B." [] xref: RO:0011010 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1107,8 +1105,8 @@ name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] xref: RO:0002450 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1119,7 +1117,7 @@ id: directly_positively_regulates_quantity_of name: directly positively regulates quantity of def: "The entity A has an activity that directly positively regulates the quantity of B." [] xref: RO:0011009 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1142,7 +1140,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002578 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string property_value: RO:0002575 RO:0002211 @@ -1155,8 +1153,8 @@ name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] xref: RO:0002448 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: molecularly_interacts_with ! molecularly interacts with @@ -1167,7 +1165,7 @@ id: directly_regulates_quantity_of name: directly regulates quantity of def: "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B." [] xref: RO:0011021 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -1177,7 +1175,7 @@ def: "A relationship between a disease and an anatomical structure where the mat xref: RO:0004030 range: CARO:0000003 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z [Typedef] @@ -1189,7 +1187,7 @@ property_value: IAO:0000589 "disease causes disruption of (disease to process)" domain: OGMS:0000031 range: BFO:0000015 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:51:09Z [Typedef] @@ -1200,7 +1198,7 @@ property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomica domain: OGMS:0000031 range: CARO:0000006 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z [Typedef] @@ -1210,7 +1208,7 @@ xref: RO:0004019 domain: OGMS:0000031 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject is_a: realizable_has_basis_in ! realizable has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:26:47Z [Typedef] @@ -1221,7 +1219,7 @@ xref: RO:0004021 property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:37:52Z [Typedef] @@ -1232,7 +1230,7 @@ xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string range: CARO:0000006 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z [Typedef] @@ -1243,7 +1241,7 @@ xref: RO:0004022 domain: OGMS:0000031 is_a: disease_has_basis_in ! disease has basis in is_a: has_phenotype ! has phenotype -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:46:07Z [Typedef] @@ -1253,7 +1251,7 @@ def: "A relationship between a disease and some feature of that disease, where t xref: RO:0004029 domain: OGMS:0000031 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:50:53Z [Typedef] @@ -1272,7 +1270,7 @@ xref: RO:0004027 domain: OGMS:0000031 range: BFO:0000004 is_a: disease_has_location ! disease has location -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:37:31Z [Typedef] @@ -1285,7 +1283,7 @@ property_value: IAO:0000232 "This relation is intentionally very general, and co domain: OGMS:0000031 range: BFO:0000004 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T04:06:02Z [Typedef] @@ -1294,7 +1292,7 @@ name: disease relationship def: "This relation groups relations between diseases and any other kind of entity." [] xref: RO:0040035 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z [Typedef] @@ -1306,7 +1304,7 @@ subset: ro-eco xref: RO:0002377 property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string @@ -1316,10 +1314,10 @@ is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: does_not_overlap_sequence_of name: does not overlap sequence of -def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] xref: RO:0002527 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "disconnected from" xsd:string is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -1338,7 +1336,7 @@ id: eats name: eats subset: ro-eco xref: RO:0002470 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -1359,7 +1357,7 @@ def: "A relationship that is mediated in some way by the environment or environm subset: ro-eco xref: RO:0002321 property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string [Typedef] @@ -1377,7 +1375,7 @@ name: electrically_synapsed_to def: "A relation that holds between two neurons that are electrically coupled via gap junctions." [] xref: RO:0002003 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: connected_to ! connected to [Typedef] @@ -1386,7 +1384,7 @@ name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: has_participant @@ -1397,7 +1395,7 @@ def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string property_value: IAO:0000118 "has" xsd:string @@ -1413,7 +1411,7 @@ name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] xref: RO:0004031 is_a: functionally_related_to ! functionally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z [Typedef] @@ -1430,14 +1428,14 @@ inverse_of: has_endoparasite ! has endoparasite id: ends subset: ro-eco xref: RO:0002229 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: ends_with subset: ro-eco xref: RO:0002230 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -1462,7 +1460,7 @@ name: exports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002345 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -1479,7 +1477,7 @@ def: "relationship between a neuron and a neuron projection bundle (e.g.- tract xref: RO:0002101 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 @@ -1492,7 +1490,7 @@ inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron proje id: formed_as_result_of name: formed as result of xref: RO:0002354 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of [Typedef] @@ -1500,7 +1498,7 @@ id: functionally_related_to name: functionally related to def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] xref: RO:0002328 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string [Typedef] @@ -1509,7 +1507,7 @@ name: genetically interacts with xref: RO:0002435 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with @@ -1517,7 +1515,7 @@ is_a: interacts_with ! interacts with [Typedef] id: has_2D_boundary xref: RO:0002002 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1557,7 +1555,7 @@ def: "inverse of branching part of" [] subset: ro-eco subset: RO:0002259 xref: RO:0002569 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: has_part is_a: in_branching_relationship_with ! in branching relationship with @@ -1593,7 +1591,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 "Bill Duncan (https://orcid.org/0000-0001-9625-1899)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant @@ -1622,7 +1620,7 @@ id: has_dendrite_location name: has dendrite location xref: RO:0002360 property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -1632,7 +1630,7 @@ def: "x has developmental contribution from y iff x has some part z such that z xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by @@ -1644,7 +1642,7 @@ name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to @@ -1656,7 +1654,7 @@ def: "p has direct input c iff c is a participant in p, c is present at the star xref: RO:0002400 property_value: IAO:0000112 "'protein catabolic process' SubClassOf has_direct_input some protein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly consumes" xsd:string property_value: IAO:0000232 "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" xsd:string is_a: has_input ! has input @@ -1666,7 +1664,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1711,7 +1709,7 @@ def: "x 'has end location' y if and only if there exists some process z such tha subset: ro-eco xref: RO:0002232 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -1724,7 +1722,7 @@ def: "x has end sequence y if the end of x is identical to the end of y, and x h xref: RO:0002518 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -1776,11 +1774,11 @@ id: has_exposure_stimulus name: has exposure stimulus def: "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002309 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 is_a: related_via_exposure_to ! related via exposure to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:35:04Z [Typedef] @@ -1806,7 +1804,7 @@ def: "The relation between a neuron projection bundle and a neuron projection th xref: RO:0002132 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 @@ -1828,7 +1826,7 @@ subset: ro-eco xref: RO:0002303 property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Pier Buttigieg" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string domain: CARO:0001010 range: ENVO:01000254 @@ -1851,7 +1849,7 @@ name: has host def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] subset: ro-eco xref: RO:0002454 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -1865,7 +1863,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 is_a: has_participant @@ -1886,7 +1884,7 @@ def: "p has intermediate c if and only if p has parts p1, p2 and p1 has output c subset: ro-eco xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string is_a: has_participant @@ -1924,7 +1922,7 @@ name: has major susceptibility factor xref: RO:0004005 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_susceptibility_factor_for ! is causal susceptibility factor for -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:26Z [Typedef] @@ -1935,7 +1933,7 @@ property_value: seeAlso Orphanet:410295 property_value: seeAlso Orphanet:410296 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_gain_of_function_germline_mutation_of_in ! is causal gain of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:20Z [Typedef] @@ -1945,7 +1943,7 @@ xref: RO:0004003 property_value: seeAlso Orphanet:317343 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_in ! is causal germline mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:54Z [Typedef] @@ -1954,7 +1952,7 @@ name: has material basis in loss of function germline mutation in xref: RO:0004002 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_loss_of_function_germline_mutation_of_in ! is causal loss of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:37Z [Typedef] @@ -1964,7 +1962,7 @@ xref: RO:0004004 property_value: seeAlso Orphanet:317344 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z [Typedef] @@ -1980,7 +1978,7 @@ id: has_muscle_antagonist name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string is_a: biomechanically_related_to ! biomechanically related to @@ -1989,7 +1987,7 @@ id: has_muscle_insertion name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} @@ -2001,7 +1999,7 @@ id: has_muscle_origin name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} @@ -2039,7 +2037,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string is_a: has_participant inverse_of: output_of ! output of @@ -2066,7 +2064,7 @@ name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] xref: RO:0002584 property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causal_relation_between_material_entity_and_a_process ! causal relation between material entity and a process is_a: functionally_related_to ! functionally related to @@ -2076,7 +2074,7 @@ name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco xref: RO:0002479 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 range: BFO:0000004 @@ -2086,7 +2084,7 @@ name: has partial material basis in germline mutation in xref: RO:0004006 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_partially_giving_rise_to ! is causal germline mutation partially giving rise to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:57Z [Typedef] @@ -2098,7 +2096,7 @@ id: has_pathogen name: has pathogen subset: ro-eco xref: RO:0002557 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2108,7 +2106,7 @@ def: "A relationship that holds between a biological entity and a phenotype. Her subset: ro-eco xref: RO:0002200 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: UPHENO:0001001 is_a: has_phenotype_or_disease ! has phenotype or disease inverse_of: phenotype_of ! phenotype of @@ -2129,9 +2127,9 @@ def: "Holds between a cell c and a protein complex or protein p if and only if t xref: RO:0002104 property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Alexander Diehl" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 @@ -2157,8 +2155,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in whi xref: RO:0002110 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "synapsed in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2172,7 +2170,7 @@ name: has potential to develop into def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] xref: RO:0002387 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2181,7 +2179,7 @@ name: has potential to developmentally contribute to def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] xref: RO:0002385 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2190,7 +2188,7 @@ name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] xref: RO:0002386 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2199,7 +2197,7 @@ name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] xref: RO:0002388 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_potential_to_develop_into ! has potential to develop into [Typedef] @@ -2223,7 +2221,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -2233,7 +2231,7 @@ def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c o subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -2244,7 +2242,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -2276,7 +2274,7 @@ name: has skeleton def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] xref: RO:0002551 property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 @@ -2321,7 +2319,7 @@ name: has soma location def: "Relation between a neuron and an anatomical structure that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 range: CARO:0000003 @@ -2335,7 +2333,7 @@ def: "x 'has starts location' y if and only if there exists some process z such subset: ro-eco xref: RO:0002231 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -2348,7 +2346,7 @@ def: "x has start sequence y if the start of x is identical to the start of y, a xref: RO:0002516 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2358,10 +2356,10 @@ inverse_of: is_start_sequence_of ! is start sequence of [Typedef] id: has_subsequence name: has subsequence -def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2375,7 +2373,7 @@ id: has_symptom name: has symptom def: "A relation that holds between a disease or an organism and a phenotype" [] xref: RO:0002452 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: OGMS:0000031 is_a: has_phenotype ! has phenotype @@ -2405,7 +2403,7 @@ def: "A general relation between a neuron and some structure in which it either xref: RO:0002130 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has synapse in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2417,7 +2415,7 @@ id: has_synaptic_terminal_of name: has synaptic terminal of xref: RO:0002006 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: overlaps ! overlaps inverse_of: has_synaptic_terminal_in ! has synaptic terminal in @@ -2429,7 +2427,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002339 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2440,7 +2438,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002338 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2448,7 +2446,7 @@ id: has_vector name: has vector subset: ro-eco xref: RO:0002460 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with [Typedef] @@ -2463,7 +2461,7 @@ id: host_of name: host of subset: ro-eco xref: RO:0002453 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2476,7 +2474,7 @@ synonym: "epiparasite of" RELATED [] synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string is_a: has_host ! has host @@ -2492,7 +2490,7 @@ synonym: "has epiparasite" RELATED [] synonym: "has hyperparasite" RELATED [] synonym: "hyperparasitoidized by" RELATED [] xref: RO:0002554 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2500,7 +2498,7 @@ id: immediate_transformation_of name: immediate transformation of def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] xref: RO:0002495 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002494 is_a: directly_develops_from ! directly develops from is_a: transformation_of ! transformation of @@ -2510,7 +2508,7 @@ id: immediately_causally_downstream_of name: immediately causally downstream of xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of is_a: immediately_preceded_by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of @@ -2520,7 +2518,7 @@ id: immediately_causally_upstream_of name: immediately causally upstream of def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: immediately_precedes @@ -2533,7 +2531,7 @@ xref: RO:0002087 id: immediately_precedes subset: ro-eco xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0002575 BFO:0000063 [Typedef] @@ -2542,7 +2540,7 @@ name: imports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002340 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -2551,7 +2549,7 @@ name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] xref: RO:0002375 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 @@ -2577,7 +2575,7 @@ id: increases_by_expression_quantity_of name: increases by expression quantity of def: "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011008 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_positively_regulates_quantity_of ! indirectly positively regulates quantity of @@ -2587,7 +2585,7 @@ id: increases_expression_of name: increases expression of def: "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." [] xref: RO:0003003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -2606,7 +2604,7 @@ id: indirectly_negatively_regulates name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true @@ -2618,7 +2616,7 @@ id: indirectly_negatively_regulates_activity_of name: indirectly negatively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B." [] xref: RO:0011016 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly inhibits" xsd:string is_a: indirectly_regulates_activity_of ! indirectly regulates activity of @@ -2627,7 +2625,7 @@ id: indirectly_negatively_regulates_quantity_of name: indirectly negatively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B." [] xref: RO:0011023 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2635,7 +2633,7 @@ id: indirectly_positively_regulates name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 is_transitive: true @@ -2647,7 +2645,7 @@ id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." [] xref: RO:0011013 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -2658,7 +2656,7 @@ id: indirectly_positively_regulates_quantity_of name: indirectly positively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B." [] xref: RO:0011024 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2676,7 +2674,7 @@ id: indirectly_regulates_activity_of name: indirectly regulates activity of def: "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." [] xref: RO:0011004 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: regulates_activity_of ! regulates activity of @@ -2686,7 +2684,7 @@ id: indirectly_regulates_quantity_of name: indirectly regulates quantity of def: "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B." [] xref: RO:0011022 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -2696,7 +2694,7 @@ def: "inverse of has input" [] subset: ro-eco subset: RO:0002259 xref: RO:0002352 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -2710,7 +2708,7 @@ xref: RO:0002434 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI domain: BFO:0000040 @@ -2723,7 +2721,7 @@ name: interacts with via parasite-host interaction def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] subset: ro-eco xref: RO:0002443 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2751,7 +2749,7 @@ id: involved_in name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] xref: RO:0002331 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in @@ -2763,7 +2761,7 @@ id: involved_in_negative_regulation_of name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] xref: RO:0002430 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2773,7 +2771,7 @@ name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in_process ! causal agent in process @@ -2784,7 +2782,7 @@ id: involved_in_positive_regulation_of name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] xref: RO:0002429 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2793,7 +2791,7 @@ id: involved_in_regulation_of name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] xref: RO:0002428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of @@ -2804,7 +2802,7 @@ def: "c executes activity in d if and only if c enables p and p occurs_in d. As synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -2853,7 +2851,7 @@ id: is_basis_for_realizable name: is basis for realizable xref: RO:0004018 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:29Z [Typedef] @@ -2863,7 +2861,7 @@ def: "inverse of bounds sequence of" [] subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to @@ -2874,7 +2872,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004011 property_value: seeAlso Orphanet:410296 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:55:51Z [Typedef] @@ -2885,7 +2883,7 @@ xref: RO:0004013 property_value: seeAlso Orphanet:317343 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:40Z [Typedef] @@ -2896,7 +2894,7 @@ xref: RO:0004016 property_value: seeAlso Orphanet:317346 is_a: contributes_to_condition ! contributes to condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:58:43Z [Typedef] @@ -2906,7 +2904,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004012 property_value: seeAlso Orphanet:410295 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:06Z [Typedef] @@ -2917,7 +2915,7 @@ xref: RO:0004014 property_value: seeAlso Orphanet:317344 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:07Z [Typedef] @@ -2927,7 +2925,7 @@ def: "Relates a gene to condition, such that a mutation in this gene predisposes xref: RO:0004015 property_value: seeAlso Orphanet:317345 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:43Z [Typedef] @@ -2937,7 +2935,7 @@ def: "x is a consecutive sequence of y iff x has subsequence y, and all the part xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: has_subsequence ! has subsequence @@ -2947,7 +2945,7 @@ name: is downstream of sequence of def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] xref: RO:0002529 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of @@ -2957,7 +2955,7 @@ id: is_eaten_by name: is eaten by subset: ro-eco xref: RO:0002471 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -2969,7 +2967,7 @@ def: "inverse of has end sequence" [] subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2982,7 +2980,7 @@ xref: RO:0004010 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string range: BFO:0000017 is_a: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:53:08Z [Typedef] @@ -2992,7 +2990,7 @@ def: "x is immediately downstream of the sequence of y iff either (1) x and y ha xref: RO:0002530 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002529 is_a: is_downstream_of_sequence_of ! is downstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3004,7 +3002,7 @@ def: "inverse of immediately downstream of" [] xref: RO:0002531 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: is_upstream_of_sequence_of ! is upstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3031,7 +3029,7 @@ def: "x is sequentially aligned with if a significant portion bases of x and y c xref: RO:0002521 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -3071,7 +3069,7 @@ def: "inverse of has start sequence" [] subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3084,7 +3082,7 @@ def: "inverse of has subsequence" [] subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of @@ -3107,7 +3105,7 @@ name: is treated by substance def: "Inverse of 'is substance that treats'" [] subset: RO:0002259 xref: RO:0002302 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 is_a: causally_related_to ! causally related to inverse_of: is_substance_that_treats ! is substance that treats @@ -3117,7 +3115,7 @@ name: is upstream of sequence of def: "inverse of downstream of sequence of" [] xref: RO:0002528 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -3127,7 +3125,7 @@ name: is vector for subset: ro-eco xref: RO:0002459 property_value: IAO:0000112 "Anopheles is a vector for Plasmodium" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: has_vector ! has vector @@ -3179,7 +3177,7 @@ name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco xref: RO:0002571 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:cjm xsd:string range: BFO:0000040 is_a: part_of @@ -3190,7 +3188,7 @@ name: luminal space of def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] subset: ro-eco xref: RO:0002572 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000141 is_a: lumen_of ! lumen of @@ -3202,7 +3200,7 @@ subset: ro-eco xref: RO:0002381 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with is_a: part_of @@ -3212,7 +3210,7 @@ id: mereotopologically_related_to name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] xref: RO:0002323 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string property_value: RO:0001900 RO:0001901 @@ -3230,7 +3228,7 @@ name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 @@ -3243,7 +3241,7 @@ name: mutualistically interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] subset: ro-eco xref: RO:0002442 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -3270,7 +3268,7 @@ name: negatively regulated by def: "inverse of negatively regulates" [] subset: RO:0002259 xref: RO:0002335 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3281,7 +3279,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 @@ -3330,7 +3328,7 @@ def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -3351,10 +3349,10 @@ expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://p [Typedef] id: overlaps_sequence_of name: overlaps sequence of -def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] xref: RO:0002526 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: overlaps ! overlaps is_a: sequentially_related_to ! sequentially related to @@ -3366,7 +3364,7 @@ subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string is_a: has_host ! has host @@ -3379,7 +3377,7 @@ name: parasitized by subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string @@ -3418,7 +3416,7 @@ name: part of developmental precursor of xref: RO:0002287 property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by [Typedef] @@ -3426,7 +3424,7 @@ id: part_of_structure_that_is_capable_of name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] xref: RO:0002329 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean is_a: functionally_related_to ! functionally related to @@ -3455,7 +3453,7 @@ subset: ro-eco synonym: "semibiotically interacts with" RELATED [] xref: RO:0002446 property_value: IAO:0000112 "Porifiera attaches to substrate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: biotically_interacts_with ! biotically interacts with @@ -3464,7 +3462,7 @@ id: participates_in_a_biotic-biotic_interaction_with name: participates in a biotic-biotic interaction with subset: ro-eco xref: RO:0002574 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 domain: CARO:0001010 range: CARO:0001010 @@ -3474,7 +3472,7 @@ is_a: biotically_interacts_with ! biotically interacts with id: partner_in name: partner in xref: RO:0002461 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string is_a: participates_in @@ -3483,7 +3481,7 @@ id: pathogen_of name: pathogen of subset: ro-eco xref: RO:0002556 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_host ! has host inverse_of: has_pathogen ! has pathogen @@ -3495,7 +3493,7 @@ subset: ro-eco subset: RO:0002259 xref: RO:0002201 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_functional: true [Typedef] @@ -3503,7 +3501,7 @@ id: phosphorylates name: phosphorylates xref: RO:0002447 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: molecularly_interacts_with ! molecularly interacts with @@ -3512,7 +3510,7 @@ id: pollinated_by name: pollinated by subset: ro-eco xref: RO:0002456 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string @@ -3525,7 +3523,7 @@ subset: ro-eco xref: RO:0002455 property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with @@ -3537,7 +3535,7 @@ name: positively regulated by def: "inverse of positively regulates" [] subset: RO:0002259 xref: RO:0002336 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3548,7 +3546,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002211 @@ -3583,7 +3581,7 @@ def: "inverse of preys on" [] subset: ro-eco subset: RO:0002259 xref: RO:0002458 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string @@ -3598,9 +3596,9 @@ subset: ro-eco xref: RO:0002439 property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Jorrit Poelen" xsd:string -property_value: IAO:0000117 "Katja Shulz" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7134-3324 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string @@ -3623,7 +3621,7 @@ def: "x proper_distributary_of y iff x distributary_of y and x does not flow bac subset: ro-eco xref: RO:0002382 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: distributary_of ! distributary of [Typedef] @@ -3633,7 +3631,7 @@ def: "x proper_tributary_of y iff x tributary_of y and x does not originate from subset: ro-eco xref: RO:0002383 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: tributary_of ! tributary of [Typedef] @@ -3642,7 +3640,7 @@ name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string @@ -3654,7 +3652,7 @@ id: provides_nutrients_for name: provides nutrients for subset: ro-eco xref: RO:0002469 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3663,7 +3661,7 @@ name: realizable has basis in xref: RO:0004017 is_a: causally_related_to ! causally related to inverse_of: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:01Z [Typedef] @@ -3672,10 +3670,10 @@ name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] synonym: "triggered by process" EXACT [RO:cjm] xref: RO:0009501 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "David Osumi-Sutherland" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string @@ -3692,7 +3690,7 @@ xref: RO:0004028 domain: BFO:0000017 range: BFO:0000040 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:45:49Z [Typedef] @@ -3700,7 +3698,7 @@ id: receives_input_from name: receives input from xref: RO:0002485 property_value: IAO:0000116 "See notes for inverse relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to inverse_of: sends_output_to ! sends output to @@ -3740,7 +3738,7 @@ name: regulated by def: "inverse of regulates" [] subset: RO:0002259 xref: RO:0002334 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 range: BFO:0000015 @@ -3755,9 +3753,9 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Hill" xsd:string -property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 +property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string @@ -3774,7 +3772,7 @@ id: regulates_activity_of name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] xref: RO:0011002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3794,7 +3792,7 @@ id: regulates_in_other_organism name: regulates in other organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] xref: RO:0002010 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 range: BFO:0000015 is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -3805,7 +3803,7 @@ name: regulates levels of def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] xref: RO:0002332 property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 @@ -3817,7 +3815,7 @@ id: regulates_quantity_of name: regulates quantity of def: "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." [] xref: RO:0011003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3836,7 +3834,7 @@ id: related_via_localization_to name: related via localization to def: "A relationship that holds via some process of localization" [] xref: RO:0002337 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 range: BFO:0000002 @@ -3857,7 +3855,7 @@ id: represses_expression_of name: represses expression of def: "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." [] xref: RO:0003002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3871,7 +3869,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -3916,7 +3914,7 @@ name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] @@ -3936,7 +3934,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002348 property_value: IAO:0000112 "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3948,7 +3946,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002349 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3962,7 +3960,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3972,7 +3970,7 @@ id: results_in_developmental_induction_of name: results in developmental induction of def: "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." [] xref: RO:0002357 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3982,7 +3980,7 @@ def: "p results in the developmental progression of s iff p is a developmental p xref: RO:0002295 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 range: CARO:0000000 @@ -3994,7 +3992,7 @@ name: results in developmental regression of xref: RO:0002301 property_value: IAO:0000112 "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4004,7 +4002,7 @@ name: results in disappearance of xref: RO:0002300 property_value: IAO:0000112 "foramen ovale closure SubClassOf results in disappearance of foramen ovale" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4020,7 +4018,7 @@ id: results_in_ending_of name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4034,7 +4032,7 @@ xref: RO:0002297 property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4056,7 +4054,7 @@ id: results_in_growth_of name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4071,7 +4069,7 @@ xref: RO:0002299 property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4087,7 +4085,7 @@ xref: RO:0002298 property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4100,7 +4098,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002565 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4126,7 +4124,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002356 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4135,7 +4133,7 @@ id: results_in_structural_organization_of name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4151,7 +4149,7 @@ name: results in transport across def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002342 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: occurs_across ! occurs across is_a: results_in_transport_to_from_or_in ! results in transport to from or in @@ -4160,7 +4158,7 @@ id: results_in_transport_along name: results in transport along def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] xref: RO:0002341 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4168,7 +4166,7 @@ id: results_in_transport_to_from_or_in name: results in transport to from or in xref: RO:0002344 property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4183,7 +4181,7 @@ id: sends_output_to name: sends output to xref: RO:0002486 property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to [Typedef] @@ -4225,7 +4223,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcript" xsd:string property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -4235,7 +4233,7 @@ name: sequentially related to def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string @@ -4248,7 +4246,7 @@ name: skeleton of def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 is_a: part_of @@ -4259,7 +4257,7 @@ name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] xref: RO:0002379 property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: overlaps ! overlaps @@ -4271,7 +4269,7 @@ subset: ro-eco xref: RO:0002163 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 @@ -4285,7 +4283,7 @@ name: stabilizes quantity of def: "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." [] xref: RO:0011015 property_value: IAO:0000112 "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_quantity_of ! directly positively regulates quantity of @@ -4294,14 +4292,14 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates id: starts subset: ro-eco xref: RO:0002223 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: starts_with subset: ro-eco xref: RO:0002224 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -4317,7 +4315,7 @@ name: subcluster of def: "A relation between a group and another group it is part of but does not fully constitute." [] xref: RO:0015003 property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." xsd:string -property_value: IAO:0000117 "Shawn Tan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true is_a: part_of @@ -4326,7 +4324,7 @@ is_a: part_of id: subject_participant_in name: subject participant in xref: RO:0002462 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4345,7 +4343,7 @@ name: surrounded by def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] xref: RO:0002219 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to inverse_of: surrounds ! surrounds @@ -4357,7 +4355,7 @@ def: "inverse of surrounded by" [] subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to @@ -4367,7 +4365,7 @@ name: symbiotically interacts with def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] subset: ro-eco xref: RO:0002440 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true @@ -4380,8 +4378,8 @@ def: "Relation between an anatomical structure (including cells) and a neuron th xref: RO:0002103 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: receives_input_from ! receives input from inverse_of: synapsed_to ! synapsed to @@ -4406,8 +4404,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002108 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" [] @@ -4420,8 +4418,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002109 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4434,8 +4432,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002112 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4448,8 +4446,8 @@ comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part som xref: RO:0002120 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: sends_output_to ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -4473,8 +4471,8 @@ def: "A relation between a motor neuron and a muscle that it synapses to via a t comment: Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) xref: RO:0002107 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_II_bouton ! synapsed_by_via_type_II_bouton @@ -4488,8 +4486,8 @@ comment: Expands to: has_part some ('type Ib terminal button' that has_part some xref: RO:0002105 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Ib_bouton ! synapsed_by_via_type_Ib_bouton @@ -4503,8 +4501,8 @@ comment: Expands to: has_part some ('type Is terminal button' that has_part some xref: RO:0002106 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Is_bouton ! synapsed_by_via_type_Is_bouton @@ -4514,7 +4512,7 @@ expand_expression_to: "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that id: target_participant_in name: target participant in xref: RO:0002463 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4523,7 +4521,7 @@ id: temporally_related_to subset: ro-eco xref: RO:0002222 property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string [Typedef] @@ -4531,7 +4529,7 @@ id: transformation_of name: transformation of def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] xref: RO:0002494 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: develops_from ! develops from @@ -4541,7 +4539,7 @@ name: transitively provides input for def: "transitive form of directly_provides_input_for" [] xref: RO:0002414 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." xsd:string property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string domain: BFO:0000015 @@ -4556,7 +4554,7 @@ def: "A relationship that holds between a disease and organism" [] xref: RO:0002451 property_value: IAO:0000112 "all dengue disease transmitted by some mosquito" xsd:string property_value: IAO:0000116 "Add domain and range constraints" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -4576,7 +4574,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002313 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "regulates localization of" xsd:string is_a: related_via_localization_to ! related via localization to is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4590,7 +4588,7 @@ xref: RO:0002376 property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string @@ -4608,7 +4606,7 @@ name: trophically interacts with def: "An interaction relationship in which the partners are related via a feeding relationship." [] subset: ro-eco xref: RO:0002438 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4618,7 +4616,7 @@ name: ubiquitinates def: "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" [] xref: RO:0002480 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with [Typedef] diff --git a/src/ontology/subsets/ro-time-interval.owl b/src/ontology/subsets/ro-time-interval.owl index 06c5dfb4..85959a1e 100644 --- a/src/ontology/subsets/ro-time-interval.owl +++ b/src/ontology/subsets/ro-time-interval.owl @@ -409,7 +409,7 @@ - David Osumi-Sutherland + RO:0002002 has_2D_boundary @@ -421,7 +421,7 @@ A relation that holds between two neurons that are electrically coupled via gap junctions. - David Osumi-Sutherland + RO:0002003 electrically_synapsed_to @@ -435,7 +435,7 @@ - David Osumi-Sutherland + RO:0002006 has_synaptic_terminal_of @@ -469,7 +469,7 @@ has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland + RO:0002007 bounding_layer_of @@ -505,9 +505,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. + A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. Note from NCEAS meeting: consider changing primary label - David Osumi-Sutherland + RO:0002008 coincident_with @@ -524,7 +524,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - David Osumi-Sutherland + RO:0002010 regulates_in_other_organism regulates in other organism @@ -553,7 +553,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + dos 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -568,7 +568,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + dos 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -584,7 +584,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + dos 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -599,7 +599,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -613,7 +613,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -630,7 +630,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + dos 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -644,7 +644,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + dos 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -658,7 +658,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + dos 2017-07-20T17:11:08Z RO:0002020 transports @@ -672,7 +672,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + dos 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -686,7 +686,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -697,7 +697,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + GOC:dos @@ -708,7 +708,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + dos 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -718,7 +718,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + GOC:dos @@ -729,7 +729,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + dos 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -739,7 +739,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + GOC:dos @@ -750,7 +750,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + dos 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -761,7 +761,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + GOC:dos @@ -780,7 +780,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + dos 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -797,7 +797,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + GOC:dos @@ -814,7 +814,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + RO:0002090 @@ -831,7 +831,7 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure that its soma is part of. - David Osumi-Sutherland + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -852,9 +852,9 @@ Examples include: the relationship between two channels collected simultaneously relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - David Osumi-Sutherland + fasciculates with - (forall (?x ?y) + (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) @@ -890,9 +890,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure its axon forms (chemical) synapses in. - Chris Mungall - David Osumi-Sutherland - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -924,8 +923,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -945,9 +944,9 @@ Examples include: the relationship between two channels collected simultaneously Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - Alexander Diehl - Chris Mungall - Lindsay Cowell + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) @@ -965,8 +964,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -985,8 +984,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -1005,8 +1004,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) RO:0002107 @@ -1023,8 +1022,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1043,8 +1042,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1064,8 +1063,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - Chris Mungall - David Osumi-Sutherland + + synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( @@ -1085,8 +1084,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1168,8 +1167,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -1196,8 +1195,8 @@ N1 SubclassOf ( Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -1218,7 +1217,7 @@ N1 SubclassOf ( A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - David Osumi-Sutherland + has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) @@ -1267,9 +1266,9 @@ N1 SubclassOf ( The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - David Osumi-Sutherland + has fasciculating component - (forall (?x ?y) + (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) @@ -1309,8 +1308,8 @@ N1 SubclassOf ( - X continuous_with Y if and only if X and Y share a fiat boundary. - David Osumi-Sutherland + X continuous_with Y if and only if X and Y share a fiat boundary. + connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) @@ -1329,8 +1328,8 @@ N1 SubclassOf ( x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom - proper overlaps - (forall (?x ?y) + proper overlaps + (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and @@ -1353,7 +1352,7 @@ N1 SubclassOf ( A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - Chris Mungall + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) @@ -1361,7 +1360,7 @@ N1 SubclassOf ( RO:0002163 spatially_disjoint_from - spatially disjoint from + spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern @@ -1498,7 +1497,7 @@ N1 SubclassOf ( A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - Chris Mungall + RO:0002200 has_phenotype @@ -1513,7 +1512,7 @@ N1 SubclassOf ( inverse of has phenotype - Chris Mungall + RO:0002201 @@ -1533,10 +1532,10 @@ N1 SubclassOf ( x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - Terry Meehan + + + + RO:0002202 develops_from This is the transitive form of the develops from relation @@ -1554,9 +1553,9 @@ N1 SubclassOf ( inverse of develops from - Chris Mungall - David Osumi-Sutherland - Terry Meehan + + + RO:0002203 develops_into @@ -1588,12 +1587,12 @@ N1 SubclassOf ( Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - Chris Mungall - David Osumi-Sutherland - has developmental precursor + + FBbt RO:0002207 + has developmental precursor directly_develops_from TODO - add child relations from DOS directly develops from @@ -1651,9 +1650,9 @@ N1 SubclassOf ( p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - Chris Mungall - David Hill - Tanya Berardini + + + GO Regulation precludes parthood; the regulatory process may not be within the regulated process. @@ -1676,7 +1675,7 @@ N1 SubclassOf ( p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - Chris Mungall + negatively regulates (process to process) @@ -1698,7 +1697,7 @@ N1 SubclassOf ( p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - Chris Mungall + positively regulates (process to process) @@ -1721,7 +1720,7 @@ N1 SubclassOf ( mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - Chris Mungall + has function realized in @@ -1740,7 +1739,7 @@ N1 SubclassOf ( c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - Chris Mungall + has function in RO:0002216 capable_of_part_of @@ -1757,7 +1756,7 @@ N1 SubclassOf ( x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - Chris Mungall + RO:0002219 surrounded_by @@ -1779,7 +1778,7 @@ N1 SubclassOf ( x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - Chris Mungall + RO:0002220 @@ -1803,7 +1802,7 @@ N1 SubclassOf ( inverse of surrounded by - Chris Mungall + RO:0002221 @@ -1816,7 +1815,7 @@ N1 SubclassOf ( - Chris Mungall + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 @@ -1830,7 +1829,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002223 starts @@ -1842,7 +1841,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002224 starts_with @@ -1856,7 +1855,7 @@ N1 SubclassOf ( x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - Chris Mungall + RO:0002225 develops_from_part_of develops from part of @@ -1871,7 +1870,7 @@ N1 SubclassOf ( x develops_in y if x is located in y whilst x is developing - Chris Mungall + EHDAA2 Jonathan Bard, EHDAA2 RO:0002226 @@ -1909,7 +1908,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002229 ends @@ -1921,7 +1920,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002230 ends_with @@ -1937,7 +1936,7 @@ N1 SubclassOf ( x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - Chris Mungall + starts with process that occurs in RO:0002231 @@ -1955,7 +1954,7 @@ N1 SubclassOf ( x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - Chris Mungall + ends with process that occurs in RO:0002232 @@ -1973,7 +1972,7 @@ N1 SubclassOf ( p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + consumes RO:0002233 @@ -1993,7 +1992,7 @@ N1 SubclassOf ( p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - Chris Mungall + produces RO:0002234 @@ -2047,7 +2046,7 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - Bill Duncan (https://orcid.org/0000-0001-9625-1899) + This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. @@ -2196,7 +2195,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y - Chris Mungall + RO:0002254 has_developmental_contribution_from has developmental contribution from @@ -2211,7 +2210,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho inverse of has developmental contribution from - Chris Mungall + RO:0002255 developmentally_contributes_to @@ -2229,9 +2228,9 @@ If you need an axiom that says 'has_participant min 2 object', you sho t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - Chris Mungall - David Osumi-Sutherland - Melissa Haendel + + + induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) @@ -2251,7 +2250,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally induced by - Chris Mungall + RO:0002257 developmentally_induces developmentally induces @@ -2269,7 +2268,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - Chris Mungall + In general you should not use this relation to make assertions - use one of the more specific relations below this one RO:0002258 developmentally_preceded_by @@ -2317,7 +2316,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - Chris Mungall + replaces RO:0002285 developmentally_replaces @@ -2332,7 +2331,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally preceded by - Chris Mungall + RO:0002286 developmentally_succeeded_by developmentally succeeded by @@ -2346,7 +2345,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - Chris Mungall + RO:0002287 part_of_developmental_precursor_of part of developmental precursor of @@ -2363,7 +2362,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - Chris Mungall + RO:0002295 results_in_developmental_progression_of results in developmental progression of @@ -2380,7 +2379,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - Chris Mungall + http://www.geneontology.org/GO.doc.development.shtml RO:0002296 @@ -2401,7 +2400,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002297 @@ -2422,7 +2421,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002298 @@ -2443,7 +2442,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002299 @@ -2461,7 +2460,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho foramen ovale closure SubClassOf results in disappearance of foramen ovale - Chris Mungall + May be merged into parent relation RO:0002300 results_in_disappearance_of @@ -2476,7 +2475,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) - Chris Mungall + May be merged into parent relation RO:0002301 results_in_developmental_regression_of @@ -2491,7 +2490,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of 'is substance that treats' - cjm + RO:0002302 is_treated_by_substance @@ -2511,7 +2510,7 @@ where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. - Pier Buttigieg + adapted for living in RO:0002303 @@ -2529,7 +2528,7 @@ where p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - cjm + RO:0002304 @@ -2547,7 +2546,7 @@ where p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - cjm + RO:0002305 @@ -2562,10 +2561,10 @@ where A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. - Austin Meier - Chris Mungall - Marie Angelique Laporte - cjm + + + + 2017-06-05T17:35:04Z RO:0002309 has_exposure_stimulus @@ -2580,7 +2579,7 @@ where Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. - Chris Mungall + regulates localization of RO:0002313 @@ -2600,7 +2599,7 @@ where an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002315 @@ -2617,7 +2616,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions RO:0002321 @@ -2633,7 +2632,7 @@ where An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. - Chris Mungall + adapted for RO:0002322 @@ -2647,7 +2646,7 @@ where A mereological relationship or a topological relationship - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships RO:0002323 @@ -2661,7 +2660,7 @@ where A relationship that holds between entities participating in some developmental process (GO:0032502) - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development RO:0002324 developmentally_related_to @@ -2678,9 +2677,8 @@ where Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. - Chris Mungall + In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - Gene Ontology Consortium RO:0002325 colocalizes_with @@ -2708,7 +2706,7 @@ then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. - Chris Mungall + In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 @@ -2725,7 +2723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - Chris Mungall + catalyzes executes has @@ -2744,7 +2742,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 functionally_related_to @@ -2758,7 +2756,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati this relation holds between c and p when c is part of some c', and c' is capable of p. - Chris Mungall + false RO:0002329 part_of_structure_that_is_capable_of @@ -2773,7 +2771,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati c involved_in p if and only if c enables some process p', and p' is part of p - Chris Mungall + actively involved in enables part of RO:0002331 @@ -2792,7 +2790,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - Chris Mungall + regulates levels of (process to entity) RO:0002332 @@ -2808,7 +2806,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables - Chris Mungall + RO:0002333 enabled_by @@ -2825,7 +2823,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of regulates - Chris Mungall + regulated by (processual) RO:0002334 @@ -2840,7 +2838,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of negatively regulates - Chris Mungall + RO:0002335 negatively_regulated_by @@ -2854,7 +2852,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of positively regulates - Chris Mungall + RO:0002336 positively_regulated_by @@ -2869,7 +2867,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds via some process of localization - Chris Mungall + Do not use this relation directly. It is a grouping relation. RO:0002337 related_via_localization_to @@ -2883,7 +2881,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - Chris Mungall + RO:0002338 @@ -2899,7 +2897,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - Chris Mungall + RO:0002339 @@ -2915,7 +2913,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. - Chris Mungall + RO:0002340 imports @@ -2929,7 +2927,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - Chris Mungall + RO:0002341 results_in_transport_along results in transport along @@ -2943,7 +2941,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - Chris Mungall + RO:0002342 results_in_transport_across @@ -2958,7 +2956,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'pollen tube growth' results_in growth_of some 'pollen tube' - Chris Mungall + RO:0002343 results_in_growth_of results in growth of @@ -2971,7 +2969,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - Chris Mungall + RO:0002344 results_in_transport_to_from_or_in results in transport to from or in @@ -2983,8 +2981,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. - Chris Mungall + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. + RO:0002345 exports @@ -3000,7 +2998,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - Chris Mungall + RO:0002348 @@ -3017,7 +3015,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - Chris Mungall + RO:0002349 @@ -3034,7 +3032,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has input - Chris Mungall + RO:0002352 @@ -3050,7 +3048,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has output - Chris Mungall + RO:0002353 @@ -3064,7 +3062,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002354 formed_as_result_of formed as result of @@ -3078,7 +3076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. - Chris Mungall + RO:0002355 results_in_structural_organization_of results in structural organization of @@ -3092,7 +3090,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - Chris Mungall + RO:0002356 @@ -3108,7 +3106,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. - Chris Mungall + RO:0002357 results_in_developmental_induction_of results in developmental induction of @@ -3120,7 +3118,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + http://neurolex.org/wiki/Property:DendriteLocation RO:0002360 has_dendrite_location @@ -3136,7 +3134,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - Chris Mungall + attached to (anatomical structure to anatomical structure) RO:0002371 @@ -3153,7 +3151,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002372 has_muscle_origin @@ -3176,7 +3174,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002373 has_muscle_insertion @@ -3200,7 +3198,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) @@ -3222,7 +3220,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - Chris Mungall + drains into drains to tributary channel of @@ -3247,7 +3245,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Deschutes River distributary_of Little Lava Lake x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - Chris Mungall + branch of distributary channel of http://en.wikipedia.org/wiki/Distributary @@ -3273,7 +3271,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. - Chris Mungall + anastomoses with RO:0002378 @@ -3289,7 +3287,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - Chris Mungall + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios RO:0002379 spatially_coextensive_with @@ -3312,7 +3310,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - Chris Mungall + RO:0002380 branching_part_of @@ -3331,7 +3329,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. - Chris Mungall + RO:0002381 main_stem_of @@ -3347,7 +3345,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_distributary_of y iff x distributary_of y and x does not flow back into y - Chris Mungall + RO:0002382 proper_distributary_of @@ -3362,7 +3360,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_tributary_of y iff x tributary_of y and x does not originate from y - Chris Mungall + RO:0002383 proper_tributary_of @@ -3379,7 +3377,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - Chris Mungall + RO:0002384 has_developmental_potential_involving has developmental potential involving @@ -3393,7 +3391,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - Chris Mungall + RO:0002385 has_potential_to_developmentally_contribute_to has potential to developmentally contribute to @@ -3407,7 +3405,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - Chris Mungall + RO:0002386 has_potential_to_developmentally_induce has potential to developmentally induce @@ -3421,7 +3419,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has the potential to develop into y iff x develops into y or if x is capable of developing into y - Chris Mungall + RO:0002387 has_potential_to_develop_into has potential to develop into @@ -3435,7 +3433,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - Chris Mungall + RO:0002388 has_potential_to_directly_develop_into has potential to directly develop into @@ -3450,7 +3448,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' RO:0002400 @@ -3468,7 +3466,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of upstream of - Chris Mungall + RO:0002404 causally_downstream_of causally downstream of @@ -3483,7 +3481,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002405 immediately_causally_downstream_of immediately causally downstream of @@ -3498,7 +3496,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - Chris Mungall + indirectly activates RO:0002407 @@ -3515,7 +3513,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - Chris Mungall + indirectly inhibits RO:0002409 @@ -3544,7 +3542,7 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002410 causally_related_to @@ -3566,7 +3564,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - Chris Mungall + RO:0002411 @@ -3582,7 +3580,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - Chris Mungall + RO:0002412 immediately_causally_upstream_of @@ -3598,7 +3596,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit - Chris Mungall + directly provides input for directly provides input for (process to process) @@ -3618,7 +3616,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different transitive form of directly_provides_input_for - Chris Mungall + This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. transitively provides input for (process to process) RO:0002414 @@ -3636,7 +3634,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall + influences (processual) RO:0002418 affects @@ -3652,7 +3650,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - Chris Mungall + RO:0002427 @@ -3668,7 +3666,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - Chris Mungall + RO:0002428 involved_in_regulation_of involved in regulation of @@ -3681,7 +3679,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - Chris Mungall + RO:0002429 involved_in_positive_regulation_of @@ -3695,7 +3693,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - Chris Mungall + RO:0002430 involved_in_negative_regulation_of @@ -3712,7 +3710,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - Chris Mungall + involved in or reguates RO:0002431 involved_in_or_involved_in_regulation_of @@ -3728,7 +3726,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall + executes activity in RO:0002432 enables activity in @@ -3740,8 +3738,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + GOC:cjm + GOC:dos @@ -3751,7 +3749,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - Chris Mungall + RO:0002433 contributes_to_morphology_of contributes to morphology of @@ -3768,7 +3766,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. - Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. RO:0002434 in pairwise interaction with @@ -3787,7 +3785,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) - Chris Mungall + RO:0002435 genetically_interacts_with genetically interacts with @@ -3803,7 +3801,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - Chris Mungall + binds molecularly binds with RO:0002436 @@ -3824,7 +3822,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - Chris Mungall + interacts with on organism level RO:0002437 @@ -3841,7 +3839,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the partners are related via a feeding relationship. - Chris Mungall + RO:0002438 trophically_interacts_with @@ -3859,9 +3857,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] Baleen whale preys on krill An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - Chris Mungall - Jorrit Poelen - Katja Shulz + + + is subject of predation interaction with preys upon RO:0002439 @@ -3880,7 +3878,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A biotic interaction in which the two organisms live together in more or less intimate association. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism RO:0002440 @@ -3896,7 +3894,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002441 @@ -3911,7 +3909,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002442 @@ -3926,7 +3924,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 This relation groups a pair of inverse relations, parasite of and parasitized by RO:0002443 @@ -3944,7 +3942,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human - Chris Mungall + parasitizes RO:0002444 direct parasite of @@ -3961,7 +3959,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + has parasite parasitised by RO:0002445 @@ -3980,7 +3978,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - Chris Mungall + RO:0002446 semibiotically interacts with @@ -3996,7 +3994,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. RO:0002447 phosphorylates @@ -4015,8 +4013,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - Chris Mungall - Vasundra Touré + + RO:0002448 molecularly controls directly_regulates_activity_of @@ -4033,8 +4031,8 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly inhibits RO:0002449 molecularly decreases activity of @@ -4052,8 +4050,8 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly activates RO:0002450 molecularly increases activity of @@ -4070,7 +4068,7 @@ For example, A and B may be gene products and binding of B by A positively regul all dengue disease transmitted by some mosquito A relationship that holds between a disease and organism Add domain and range constraints - Chris Mungall + RO:0002451 transmitted_by transmitted by @@ -4084,7 +4082,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between a disease or an organism and a phenotype - Chris Mungall + RO:0002452 has_symptom has symptom @@ -4096,7 +4094,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) RO:0002453 @@ -4111,7 +4109,7 @@ For example, A and B may be gene products and binding of B by A positively regul X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y - Chris Mungall + RO:0002454 has_host @@ -4128,7 +4126,7 @@ For example, A and B may be gene products and binding of B by A positively regul Bees pollinate Flowers This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - Chris Mungall + is subject of pollination interaction with RO:0002455 @@ -4143,7 +4141,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + has polinator is target of pollination interaction with RO:0002456 @@ -4160,7 +4158,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4175,7 +4173,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of preys on - Chris Mungall + has predator is target of predation interaction with RO:0002458 @@ -4195,7 +4193,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anopheles is a vector for Plasmodium - Chris Mungall + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism RO:0002459 @@ -4209,7 +4207,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002460 has_vector @@ -4222,7 +4220,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target RO:0002461 partner_in @@ -4235,7 +4233,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002462 subject_participant_in @@ -4248,7 +4246,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002463 target_participant_in @@ -4261,7 +4259,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002469 provides_nutrients_for @@ -4274,7 +4272,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is subject of eating interaction with RO:0002470 @@ -4288,7 +4286,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + eaten by is target of eating interaction with RO:0002471 @@ -4307,7 +4305,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - Chris Mungall + RO:0002473 @@ -4326,7 +4324,7 @@ For example, A and B may be gene products and binding of B by A positively regul ABal nucleus child nucleus of ABa nucleus (in C elegans) c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d - Chris Mungall + This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. RO:0002476 child_nucleus_of @@ -4340,7 +4338,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a hermaphroditic organism - Chris Mungall + RO:0002477 child_nucleus_of_in_hermaphrodite child nucleus of in hermaphrodite @@ -4353,7 +4351,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a male organism - Chris Mungall + RO:0002478 child_nucleus_of_in_male child nucleus of in male @@ -4367,7 +4365,7 @@ For example, A and B may be gene products and binding of B by A positively regul p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall + RO:0002479 has_part_that_occurs_in @@ -4382,7 +4380,7 @@ For example, A and B may be gene products and binding of B by A positively regul An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y Axiomatization to GO to be added later - Chris Mungall + RO:0002480 ubiquitinates ubiquitinates @@ -4396,7 +4394,7 @@ For example, A and B may be gene products and binding of B by A positively regul See notes for inverse relation - Chris Mungall + RO:0002485 receives_input_from receives input from @@ -4409,7 +4407,7 @@ For example, A and B may be gene products and binding of B by A positively regul This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - Chris Mungall + RO:0002486 sends_output_to sends output to @@ -4423,7 +4421,7 @@ For example, A and B may be gene products and binding of B by A positively regul x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - Chris Mungall + RO:0002494 transformation_of transformation of @@ -4437,7 +4435,7 @@ For example, A and B may be gene products and binding of B by A positively regul x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - Chris Mungall + RO:0002495 immediate_transformation_of @@ -4467,7 +4465,7 @@ For example, A and B may be gene products and binding of B by A positively regul p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002501 @@ -4483,7 +4481,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c - Chris Mungall + has intermediate product RO:0002505 @@ -4500,7 +4498,7 @@ For example, A and B may be gene products and binding of B by A positively regul The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002506 @@ -4522,11 +4520,11 @@ For example, A and B may be gene products and binding of B by A positively regul A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future - Chris Mungall + determined by (system to material entity) - Chris Mungall - Pier Buttigieg + + RO:0002507 determined_by @@ -4540,7 +4538,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of determined by - Chris Mungall + determines (material entity to system) RO:0002508 @@ -4559,7 +4557,7 @@ For example, A and B may be gene products and binding of B by A positively regul s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. - Chris Mungall + RO:0002509 determined_by_part_of @@ -4574,7 +4572,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between two entities that have the property of being sequences or having sequences. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. @@ -4594,7 +4592,7 @@ For example, A and B may be gene products and binding of B by A positively regul Two consecutive DNA residues are sequentially adjacent Two exons on a processed transcript that were previously connected by an intron are adjacent x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002515 @@ -4612,7 +4610,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as a start sequence the start codon for that transcript x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence - Chris Mungall + started by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4629,7 +4627,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has start sequence - Chris Mungall + starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4649,7 +4647,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence - Chris Mungall + ended by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4666,7 +4664,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has end sequence - Chris Mungall + ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4684,7 +4682,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. In the SO paper, this was defined as an instance-type relation - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002520 @@ -4701,7 +4699,7 @@ For example, A and B may be gene products and binding of B by A positively regul Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering - Chris Mungall + RO:0002521 is_sequentially_aligned_with @@ -4718,7 +4716,7 @@ For example, A and B may be gene products and binding of B by A positively regul The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y - Chris Mungall + RO:0002522 bounds_sequence_of @@ -4733,7 +4731,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of bounds sequence of - Chris Mungall + RO:0002523 @@ -4751,8 +4749,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x has subsequence y iff all of the sequence parts of x are sequence parts of y - Chris Mungall + x has subsequence y iff all of the sequence parts of y are sequence parts of x + contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4771,7 +4769,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has subsequence - Chris Mungall + contained by RO:0002525 @@ -4788,8 +4786,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. - Chris Mungall + x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. + RO:0002526 overlaps_sequence_of @@ -4803,8 +4801,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. - Chris Mungall + x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + disconnected from RO:0002527 @@ -4820,7 +4818,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of downstream of sequence of - Chris Mungall + RO:0002528 is_upstream_of_sequence_of @@ -4836,7 +4834,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. - Chris Mungall + RO:0002529 is_downstream_of_sequence_of @@ -4852,7 +4850,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y - Chris Mungall + RO:0002530 @@ -4869,7 +4867,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript inverse of immediately downstream of - Chris Mungall + RO:0002531 is_immediately_upstream_of_sequence_of @@ -4889,7 +4887,7 @@ For example, A and B may be gene products and binding of B by A positively regul Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - Chris Mungall + has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). RO:0002551 @@ -4911,7 +4909,7 @@ For example, A and B may be gene products and binding of B by A positively regul p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. - Chris Mungall + RO:0002552 results_in_ending_of results in ending of @@ -4926,7 +4924,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - Chris Mungall + http://eol.org/schema/terms/hyperparasitoidOf https://en.wikipedia.org/wiki/Hyperparasite RO:0002553 @@ -4944,7 +4942,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of hyperparasite of - Chris Mungall + RO:0002554 has epiparasite has hyperparasite @@ -4961,7 +4959,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + http://en.wikipedia.org/wiki/Allelopathy RO:0002555 @@ -4978,7 +4976,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002556 pathogen_of @@ -4991,7 +4989,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002557 has_pathogen @@ -5005,7 +5003,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + causally influenced by (entity-centric) RO:0002559 @@ -5020,7 +5018,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - Chris Mungall + RO:0002565 @@ -5039,8 +5037,8 @@ For example, A and B may be gene products and binding of B by A positively regul The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - Chris Mungall - Vasundra Touré + + causally influences (entity-centric) RO:0002566 @@ -5057,7 +5055,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between elements of a musculoskeletal system or its analogs. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. RO:0002567 biomechanically_related_to @@ -5071,7 +5069,7 @@ For example, A and B may be gene products and binding of B by A positively regul m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - Chris Mungall + Wikipedia:Antagonist_(muscle) RO:0002568 has_muscle_antagonist @@ -5087,7 +5085,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of branching part of - Chris Mungall + RO:0002569 @@ -5104,7 +5102,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - Chris Mungall + UBERON:cjm This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. RO:0002570 @@ -5121,7 +5119,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - Chris Mungall + GOC:cjm RO:0002571 @@ -5137,7 +5135,7 @@ For example, A and B may be gene products and binding of B by A positively regul s is luminal space of x iff s is lumen_of x and s is an immaterial entity - Chris Mungall + RO:0002572 luminal_space_of @@ -5152,7 +5150,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002574 participates_in_a_biotic-biotic_interaction_with @@ -5169,7 +5167,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has skeleton - Chris Mungall + RO:0002576 skeleton_of @@ -5184,7 +5182,7 @@ For example, A and B may be gene products and binding of B by A positively regul p directly regulates q iff p is immediately causally upstream of q and p regulates q. - Chris Mungall + directly regulates (processual) @@ -5205,7 +5203,7 @@ For example, A and B may be gene products and binding of B by A positively regul gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - Chris Mungall + RO:0002584 has_part_structure_that_is_capable_of has part structure that is capable of @@ -5320,7 +5318,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall + RO:0002595 causal_relation_between_material_entity_and_a_process @@ -5723,7 +5721,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. - Vasundra Touré + RO:0003002 represses_expression_of represses expression of @@ -5738,7 +5736,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. - Vasundra Touré + RO:0003003 increases_expression_of increases expression of @@ -5883,7 +5881,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:38:20Z RO:0004000 condition_has_genetic_basis_in @@ -5897,7 +5895,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:20Z RO:0004001 has_material_basis_in_gain_of_function_germline_mutation_in @@ -5913,7 +5911,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:37Z RO:0004002 has_material_basis_in_loss_of_function_germline_mutation_in @@ -5927,7 +5925,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:54Z RO:0004003 has_material_basis_in_germline_mutation_in @@ -5942,7 +5940,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:07Z RO:0004004 has_material_basis_in_somatic_mutation_in @@ -5957,7 +5955,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:26Z RO:0004005 has_major_susceptibility_factor @@ -5971,7 +5969,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:57Z RO:0004006 has_partial_material_basis_in_germline_mutation_in @@ -5985,7 +5983,7 @@ Environmental exposures include those imposed by natural environments, experimen p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - cjm + 2018-12-13T11:26:17Z RO:0004007 @@ -6001,7 +5999,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - cjm + 2018-12-13T11:26:32Z RO:0004008 @@ -6012,8 +6010,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6027,7 +6025,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - cjm + 2018-12-13T11:26:56Z RO:0004009 @@ -6038,8 +6036,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6053,7 +6051,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:53:08Z RO:0004010 is_genetic_basis_for_condition @@ -6067,7 +6065,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:55:51Z RO:0004011 is_causal_gain_of_function_germline_mutation_of_in @@ -6082,7 +6080,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:06Z RO:0004012 is_causal_loss_of_function_germline_mutation_of_in @@ -6098,7 +6096,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:40Z RO:0004013 is_causal_germline_mutation_in @@ -6114,7 +6112,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:57:07Z RO:0004014 is_causal_somatic_mutation_in @@ -6129,7 +6127,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. - cjm + 2017-11-05T02:57:43Z RO:0004015 is_causal_susceptibility_factor_for @@ -6145,7 +6143,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. - cjm + 2017-11-05T02:58:43Z RO:0004016 is_causal_germline_mutation_partially_giving_rise_to @@ -6160,7 +6158,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:01Z RO:0004017 realizable_has_basis_in @@ -6173,7 +6171,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:29Z RO:0004018 is_basis_for_realizable @@ -6188,7 +6186,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:26:47Z RO:0004019 disease_has_basis_in @@ -6204,7 +6202,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) - cjm + 2017-11-05T03:29:32Z RO:0004020 disease_has_basis_in_dysfunction_of @@ -6220,7 +6218,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. disease has basis in disruption of (disease to process) - cjm + 2017-11-05T03:37:52Z RO:0004021 disease_has_basis_in_disruption_of @@ -6244,7 +6242,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. - cjm + 2017-11-05T03:46:07Z RO:0004022 disease_has_basis_in_feature @@ -6260,7 +6258,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. - cjm + 2017-11-05T03:50:54Z RO:0004023 causal_relationship_with_disease_as_subject @@ -6277,7 +6275,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and a process where the disease process disrupts the execution of the process. disease causes disruption of (disease to process) - cjm + 2017-11-05T03:51:09Z RO:0004024 disease_causes_disruption_of @@ -6293,7 +6291,7 @@ Environmental exposures include those imposed by natural environments, experimen disease causes dysfunction of (disease to anatomical entity) - cjm + 2017-11-05T03:58:20Z RO:0004025 disease_causes_dysfunction_of @@ -6319,7 +6317,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. - cjm + 2017-11-05T04:06:02Z RO:0004026 disease_has_location @@ -6343,7 +6341,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity - cjm + 2017-12-26T19:37:31Z RO:0004027 disease_has_inflammation_site @@ -6359,7 +6357,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - cjm + 2017-12-26T19:45:49Z RO:0004028 realized_in_response_to_stimulus @@ -6382,7 +6380,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. - cjm + 2017-12-26T19:50:53Z RO:0004029 disease_has_feature @@ -6397,7 +6395,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. - cjm + 2017-12-26T19:58:44Z RO:0004030 disease_arises_from_alteration_in_structure @@ -6411,7 +6409,7 @@ Environmental exposures include those imposed by natural environments, experimen Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - cjm + 2018-01-25T23:20:13Z RO:0004031 enables_subfunction @@ -6425,7 +6423,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:30Z RO:0004032 @@ -6441,7 +6439,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:51Z RO:0004033 @@ -6458,7 +6456,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - cjm + 2018-01-26T23:53:14Z RO:0004034 @@ -6476,7 +6474,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - cjm + 2018-01-26T23:53:22Z RO:0004035 @@ -6492,7 +6490,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:05Z RO:0004046 causally_upstream_of_or_within,_negative_effect @@ -6506,7 +6504,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:19Z RO:0004047 causally_upstream_of_or_within,_positive_effect @@ -6633,10 +6631,10 @@ Environmental exposures include those imposed by natural environments, experimen An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - Austin Meier - Chris Mungall - David Osumi-Sutherland - Marie Angelique Laporte + + + + RO:0009501 triggered by process realized_in_response_to @@ -6659,7 +6657,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - Vasundra Touré + RO:0011002 regulates_activity_of regulates activity of @@ -6674,7 +6672,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. - Vasundra Touré + RO:0011003 regulates_quantity_of regulates quantity of @@ -6689,7 +6687,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. - Vasundra Touré + RO:0011004 indirectly_regulates_activity_of indirectly regulates activity of @@ -6706,7 +6704,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011007 decreases_by_repression_quantity_of decreases by repression quantity of @@ -6723,7 +6721,7 @@ For example, protein A (transcription factor) indirectly decreases by repression The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011008 increases_by_expression_quantity_of increases by expression quantity of @@ -6738,7 +6736,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly positively regulates the quantity of B. - Vasundra Touré + RO:0011009 directly_positively_regulates_quantity_of directly positively regulates quantity of @@ -6753,7 +6751,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly negatively regulates the quantity of B. - Vasundra Touré + RO:0011010 directly_negatively_regulates_quantity_of directly negatively regulates quantity of @@ -6768,7 +6766,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. - Vasundra Touré + indirectly activates RO:0011013 indirectly_positively_regulates_activity_of @@ -6785,7 +6783,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. - Vasundra Touré + RO:0011014 destabilizes_quantity_of destabilizes quantity of @@ -6801,7 +6799,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. - Vasundra Touré + RO:0011015 stabilizes_quantity_of stabilizes quantity of @@ -6814,7 +6812,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. - Vasundra Touré + indirectly inhibits RO:0011016 indirectly_negatively_regulates_activity_of @@ -6828,7 +6826,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. - Vasundra Touré + RO:0011021 directly_regulates_quantity_of directly regulates quantity of @@ -6841,7 +6839,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011022 indirectly_regulates_quantity_of indirectly regulates quantity of @@ -6854,7 +6852,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011023 indirectly_negatively_regulates_quantity_of indirectly negatively regulates quantity of @@ -6867,7 +6865,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011024 indirectly_positively_regulates_quantity_of indirectly positively regulates quantity of @@ -6880,8 +6878,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is regulated by the small molecule continuant + pg 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -6895,8 +6893,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is activated by the small molecule continuant + pg 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -6910,8 +6908,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant + pg 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -6924,8 +6922,8 @@ For example, protein A (transcription factor) indirectly increases by expression - p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + p acts on population of c iff c' is a collection, has members of type c, and p has participant c + pg 2020-06-08T17:21:33Z RO:0012003 @@ -6941,8 +6939,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process + pg 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -6956,8 +6954,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process + pg 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of @@ -6971,8 +6969,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process + pg 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of @@ -6985,8 +6983,8 @@ For example, protein A (transcription factor) indirectly increases by expression - The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. + pg 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -6999,7 +6997,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + pg 2021-02-26T07:28:29Z RO:0012008 @@ -7016,7 +7014,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + pg 2022-09-26T06:01:01Z RO:0012009 @@ -7032,7 +7030,7 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + pg 2022-09-26T06:06:20Z RO:0012010 @@ -7048,7 +7046,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + pg 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7063,7 +7061,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + pg 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7229,7 +7227,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relation between a group and another group it is part of but does not fully constitute. X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. - Shawn Tan + This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. RO:0015003 subcluster_of @@ -7301,7 +7299,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - http://orcid.org/0000-0002-7463-6306 + 2021-11-05T17:30:44Z RO:0016002 has_disease @@ -7457,7 +7455,7 @@ For example, protein A (transcription factor) indirectly increases by expression This relation groups relations between diseases and any other kind of entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. - cjm + 2018-09-26T00:00:32Z RO:0040035 disease_relationship @@ -7471,7 +7469,7 @@ For example, protein A (transcription factor) indirectly increases by expression p has anatomical participant c iff p has participant c, and c is an anatomical entity - cjm + 2018-09-26T01:08:58Z RO:0040036 results_in_changes_to_anatomical_or_cellular_structure diff --git a/subsets/ro-causal.obo b/subsets/ro-causal.obo index 35c639dc..9472403f 100644 --- a/subsets/ro-causal.obo +++ b/subsets/ro-causal.obo @@ -13,7 +13,7 @@ id: acquires_nutrients_from name: acquires nutrients from subset: ro-eco xref: RO:0002457 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for @@ -58,7 +58,7 @@ property_value: RO:0004050 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:22Z [Typedef] @@ -71,7 +71,7 @@ property_value: RO:0004049 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:14Z [Typedef] @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z [Typedef] @@ -103,7 +103,7 @@ xref: RO:0004032 property_value: RO:0004049 RO:0002264 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z [Typedef] @@ -120,7 +120,7 @@ property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cy property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 domain: BFO:0000004 range: BFO:0000004 @@ -131,7 +131,7 @@ id: allelopath_of name: allelopath of subset: ro-eco xref: RO:0002555 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string @@ -153,7 +153,7 @@ def: "x anabranch_of y if x is a distributary of y (i.e. it channels a from a la subset: ro-eco xref: RO:0002378 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "anastomoses with" xsd:string is_a: distributary_of ! distributary of disjoint_from: proper_distributary_of ! proper distributary of @@ -165,7 +165,7 @@ name: attached to def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] subset: ro-eco xref: RO:0002371 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: attached_to_part_of ! attached to part of @@ -189,9 +189,8 @@ def: "Relation between a neuron and some structure its axon forms (chemical) syn xref: RO:0002102 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in @@ -202,7 +201,7 @@ id: biomechanically_related_to name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] xref: RO:0002567 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: CARO:0000003 range: CARO:0000003 @@ -214,7 +213,7 @@ name: biotically interacts with def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] subset: ro-eco xref: RO:0002437 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string @@ -231,7 +230,7 @@ def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\ comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco xref: RO:0002007 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 is_a: part_of @@ -242,7 +241,7 @@ def: "x bounds the sequence of y iff the upstream-most part of x is upstream of xref: RO:0002522 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to inverse_of: is_bound_by_sequence_of ! is bound by sequence of @@ -254,7 +253,7 @@ def: "x is a branching part of y if and only if x is part of y and x is connecte subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso FMA:85994 xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with @@ -269,7 +268,7 @@ subset: ro-eco xref: RO:0002215 property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 @@ -302,7 +301,7 @@ id: capable_of_part_of name: capable of part of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ is_a: causal_agent_in_process ! causal agent in process @@ -350,7 +349,7 @@ id: causal_relation_between_entities name: causal relation between entities xref: RO:0002506 property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000002 @@ -363,7 +362,7 @@ name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] xref: RO:0002595 property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 range: BFO:0000015 @@ -374,7 +373,7 @@ id: causal_relation_between_processes name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 @@ -389,7 +388,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: OGMS:0000031 is_a: causally_related_to ! causally related to is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:50:54Z [Typedef] @@ -398,7 +397,7 @@ name: causally downstream of def: "inverse of upstream of" [] xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within is_a: preceded_by inverse_of: causally_upstream_of ! causally upstream of @@ -409,7 +408,7 @@ name: causally downstream of or within def: "inverse of causally upstream of or within" [] subset: RO:0002259 xref: RO:0002427 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -418,7 +417,7 @@ is_a: causal_relation_between_processes ! causal relation between processes id: causally_influenced_by name: causally influenced by xref: RO:0002559 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: causal_relation_between_entities ! causal relation between entities @@ -429,8 +428,8 @@ id: causally_influences name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] xref: RO:0002566 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 @@ -443,7 +442,7 @@ name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] @@ -453,7 +452,7 @@ def: "p is causally upstream of q iff p is causally related to q, the end of p p subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes @@ -465,7 +464,7 @@ def: "p is causally upstream of, negative effect q iff p is casually upstream of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -478,7 +477,7 @@ comment: holds between x and y if and only if x is causally upstream of y and th subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -490,7 +489,7 @@ def: "p is 'causally upstream or within' q iff p is causally related to q, and t synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -502,7 +501,7 @@ name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -511,7 +510,7 @@ name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -537,7 +536,7 @@ name: child nucleus of def: "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" [] xref: RO:0002476 property_value: IAO:0000112 "ABal nucleus child nucleus of ABa nucleus (in C elegans)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." xsd:string domain: GO:0005634 range: GO:0005634 @@ -548,7 +547,7 @@ id: child_nucleus_of_in_hermaphrodite name: child nucleus of in hermaphrodite def: "A child nucleus relationship in which the cells are part of a hermaphroditic organism" [] xref: RO:0002477 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -556,7 +555,7 @@ id: child_nucleus_of_in_male name: child nucleus of in male def: "A child nucleus relationship in which the cells are part of a male organism" [] xref: RO:0002478 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -576,7 +575,7 @@ comment: Example: if we define region of chromosome as any subdivision of a chro subset: ro-eco xref: RO:0002008 property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -585,9 +584,8 @@ name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 -property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -599,7 +597,7 @@ name: commensually interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] subset: ro-eco xref: RO:0002441 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -610,7 +608,7 @@ def: "x composed_primarily_of y if and only if more than half of the mass of x i subset: ro-eco xref: RO:0002473 property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 @@ -639,7 +637,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: BFO:0000017 is_a: causally_related_to ! causally related to inverse_of: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:38:20Z [Typedef] @@ -648,7 +646,7 @@ name: conduit for def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] subset: ro-eco xref: RO:0002570 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 UBERON:cjm xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 @@ -661,7 +659,7 @@ name: confers advantage in subset: ro-eco xref: RO:0002322 property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "adapted for" xsd:string range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -727,7 +725,7 @@ name: continuous with def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 @@ -746,7 +744,7 @@ property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a het property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -771,7 +769,7 @@ id: contributes_to_morphology_of name: contributes to morphology of def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] xref: RO:0002433 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -796,7 +794,7 @@ id: decreases_by_repression_quantity_of name: decreases by repression quantity of def: "The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011007 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_negatively_regulates_quantity_of ! indirectly negatively regulates quantity of @@ -808,8 +806,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in wh xref: RO:0002121 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in @@ -821,7 +819,7 @@ name: destabilizes quantity of def: "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." [] xref: RO:0011014 property_value: IAO:0000112 "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_quantity_of ! directly negatively regulates quantity of @@ -832,11 +830,11 @@ name: determined by def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] subset: ro-eco xref: RO:0002507 -property_value: http://purl.org/dc/terms/creator "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/creator "Pier Buttigieg" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-4366-3088 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "A coral reef environment is determined by a particular coral reef" xsd:string property_value: IAO:0000116 "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602 property_value: IAO:0000589 "determined by (system to material entity)" xsd:string domain: RO:0002577 @@ -852,7 +850,7 @@ name: determined by part of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] subset: ro-eco xref: RO:0002509 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 range: BFO:0000040 is_a: causal_relation_between_entities ! causal relation between entities @@ -865,7 +863,7 @@ def: "inverse of determined by" [] subset: ro-eco subset: RO:0002259 xref: RO:0002508 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "determines (material entity to system)" xsd:string is_a: causally_influences ! causally influences @@ -876,7 +874,7 @@ def: "inverse of has developmental contribution from" [] subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to @@ -886,9 +884,9 @@ name: developmentally induced by def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] xref: RO:0002256 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string property_value: IAO:0000119 GO:0001759 xsd:string @@ -905,7 +903,7 @@ name: developmentally induces def: "Inverse of developmentally induced by" [] xref: RO:0002257 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_induce ! has potential to developmentally induce @@ -917,7 +915,7 @@ comment: This relation groups together various other developmental relations. It xref: RO:0002258 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string domain: BFO:0000002 range: BFO:0000002 @@ -929,7 +927,7 @@ id: developmentally_related_to name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] xref: RO:0002324 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] @@ -939,7 +937,7 @@ def: "x developmentally replaces y if and only if there is some developmental pr xref: RO:0002285 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "replaces" xsd:string is_a: developmentally_preceded_by ! developmentally preceded by @@ -949,7 +947,7 @@ name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] xref: RO:0002286 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -959,10 +957,10 @@ def: "x develops from y if and only if either (a) x directly develops from y or comment: This is the transitive form of the develops from relation xref: RO:0002202 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 domain: BFO:0000004 range: BFO:0000004 is_transitive: true @@ -975,7 +973,7 @@ name: develops from part of def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] xref: RO:0002225 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: develops_from ! develops from [Typedef] @@ -984,7 +982,7 @@ name: develops in def: "x develops_in y if x is located in y whilst x is developing" [] xref: RO:0002226 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string domain: CARO:0000000 @@ -997,9 +995,9 @@ def: "inverse of develops from" [] subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 is_transitive: true is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into @@ -1010,11 +1008,11 @@ id: directly_develops_from name: directly develops from def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] xref: RO:0002207 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "has developmental precursor" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000119 "FBbt" xsd:string property_value: RO:0002575 RO:0002202 is_a: develops_from ! develops from @@ -1060,8 +1058,8 @@ name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] xref: RO:0002449 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1072,7 +1070,7 @@ id: directly_negatively_regulates_quantity_of name: directly negatively regulates quantity of def: "The entity A has an activity that directly negatively regulates the quantity of B." [] xref: RO:0011010 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1107,8 +1105,8 @@ name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] xref: RO:0002450 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1119,7 +1117,7 @@ id: directly_positively_regulates_quantity_of name: directly positively regulates quantity of def: "The entity A has an activity that directly positively regulates the quantity of B." [] xref: RO:0011009 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1142,7 +1140,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002578 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string property_value: RO:0002575 RO:0002211 @@ -1155,8 +1153,8 @@ name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] xref: RO:0002448 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: molecularly_interacts_with ! molecularly interacts with @@ -1167,7 +1165,7 @@ id: directly_regulates_quantity_of name: directly regulates quantity of def: "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B." [] xref: RO:0011021 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -1177,7 +1175,7 @@ def: "A relationship between a disease and an anatomical structure where the mat xref: RO:0004030 range: CARO:0000003 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z [Typedef] @@ -1189,7 +1187,7 @@ property_value: IAO:0000589 "disease causes disruption of (disease to process)" domain: OGMS:0000031 range: BFO:0000015 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:51:09Z [Typedef] @@ -1200,7 +1198,7 @@ property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomica domain: OGMS:0000031 range: CARO:0000006 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z [Typedef] @@ -1210,7 +1208,7 @@ xref: RO:0004019 domain: OGMS:0000031 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject is_a: realizable_has_basis_in ! realizable has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:26:47Z [Typedef] @@ -1221,7 +1219,7 @@ xref: RO:0004021 property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:37:52Z [Typedef] @@ -1232,7 +1230,7 @@ xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string range: CARO:0000006 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z [Typedef] @@ -1243,7 +1241,7 @@ xref: RO:0004022 domain: OGMS:0000031 is_a: disease_has_basis_in ! disease has basis in is_a: has_phenotype ! has phenotype -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:46:07Z [Typedef] @@ -1253,7 +1251,7 @@ def: "A relationship between a disease and some feature of that disease, where t xref: RO:0004029 domain: OGMS:0000031 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:50:53Z [Typedef] @@ -1272,7 +1270,7 @@ xref: RO:0004027 domain: OGMS:0000031 range: BFO:0000004 is_a: disease_has_location ! disease has location -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:37:31Z [Typedef] @@ -1285,7 +1283,7 @@ property_value: IAO:0000232 "This relation is intentionally very general, and co domain: OGMS:0000031 range: BFO:0000004 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T04:06:02Z [Typedef] @@ -1294,7 +1292,7 @@ name: disease relationship def: "This relation groups relations between diseases and any other kind of entity." [] xref: RO:0040035 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z [Typedef] @@ -1306,7 +1304,7 @@ subset: ro-eco xref: RO:0002377 property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string @@ -1316,10 +1314,10 @@ is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: does_not_overlap_sequence_of name: does not overlap sequence of -def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] xref: RO:0002527 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "disconnected from" xsd:string is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -1338,7 +1336,7 @@ id: eats name: eats subset: ro-eco xref: RO:0002470 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -1359,7 +1357,7 @@ def: "A relationship that is mediated in some way by the environment or environm subset: ro-eco xref: RO:0002321 property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string [Typedef] @@ -1377,7 +1375,7 @@ name: electrically_synapsed_to def: "A relation that holds between two neurons that are electrically coupled via gap junctions." [] xref: RO:0002003 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: connected_to ! connected to [Typedef] @@ -1386,7 +1384,7 @@ name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: has_participant @@ -1397,7 +1395,7 @@ def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string property_value: IAO:0000118 "has" xsd:string @@ -1413,7 +1411,7 @@ name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] xref: RO:0004031 is_a: functionally_related_to ! functionally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z [Typedef] @@ -1430,14 +1428,14 @@ inverse_of: has_endoparasite ! has endoparasite id: ends subset: ro-eco xref: RO:0002229 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: ends_with subset: ro-eco xref: RO:0002230 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -1462,7 +1460,7 @@ name: exports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002345 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -1479,7 +1477,7 @@ def: "relationship between a neuron and a neuron projection bundle (e.g.- tract xref: RO:0002101 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 @@ -1492,7 +1490,7 @@ inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron proje id: formed_as_result_of name: formed as result of xref: RO:0002354 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of [Typedef] @@ -1500,7 +1498,7 @@ id: functionally_related_to name: functionally related to def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] xref: RO:0002328 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string [Typedef] @@ -1509,7 +1507,7 @@ name: genetically interacts with xref: RO:0002435 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with @@ -1517,7 +1515,7 @@ is_a: interacts_with ! interacts with [Typedef] id: has_2D_boundary xref: RO:0002002 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1557,7 +1555,7 @@ def: "inverse of branching part of" [] subset: ro-eco subset: RO:0002259 xref: RO:0002569 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: has_part is_a: in_branching_relationship_with ! in branching relationship with @@ -1593,7 +1591,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 "Bill Duncan (https://orcid.org/0000-0001-9625-1899)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant @@ -1622,7 +1620,7 @@ id: has_dendrite_location name: has dendrite location xref: RO:0002360 property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -1632,7 +1630,7 @@ def: "x has developmental contribution from y iff x has some part z such that z xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by @@ -1644,7 +1642,7 @@ name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to @@ -1656,7 +1654,7 @@ def: "p has direct input c iff c is a participant in p, c is present at the star xref: RO:0002400 property_value: IAO:0000112 "'protein catabolic process' SubClassOf has_direct_input some protein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly consumes" xsd:string property_value: IAO:0000232 "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" xsd:string is_a: has_input ! has input @@ -1666,7 +1664,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1711,7 +1709,7 @@ def: "x 'has end location' y if and only if there exists some process z such tha subset: ro-eco xref: RO:0002232 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -1724,7 +1722,7 @@ def: "x has end sequence y if the end of x is identical to the end of y, and x h xref: RO:0002518 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -1776,11 +1774,11 @@ id: has_exposure_stimulus name: has exposure stimulus def: "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002309 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 is_a: related_via_exposure_to ! related via exposure to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:35:04Z [Typedef] @@ -1806,7 +1804,7 @@ def: "The relation between a neuron projection bundle and a neuron projection th xref: RO:0002132 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 @@ -1828,7 +1826,7 @@ subset: ro-eco xref: RO:0002303 property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Pier Buttigieg" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string domain: CARO:0001010 range: ENVO:01000254 @@ -1851,7 +1849,7 @@ name: has host def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] subset: ro-eco xref: RO:0002454 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -1865,7 +1863,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 is_a: has_participant @@ -1886,7 +1884,7 @@ def: "p has intermediate c if and only if p has parts p1, p2 and p1 has output c subset: ro-eco xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string is_a: has_participant @@ -1924,7 +1922,7 @@ name: has major susceptibility factor xref: RO:0004005 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_susceptibility_factor_for ! is causal susceptibility factor for -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:26Z [Typedef] @@ -1935,7 +1933,7 @@ property_value: seeAlso Orphanet:410295 property_value: seeAlso Orphanet:410296 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_gain_of_function_germline_mutation_of_in ! is causal gain of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:20Z [Typedef] @@ -1945,7 +1943,7 @@ xref: RO:0004003 property_value: seeAlso Orphanet:317343 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_in ! is causal germline mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:54Z [Typedef] @@ -1954,7 +1952,7 @@ name: has material basis in loss of function germline mutation in xref: RO:0004002 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_loss_of_function_germline_mutation_of_in ! is causal loss of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:37Z [Typedef] @@ -1964,7 +1962,7 @@ xref: RO:0004004 property_value: seeAlso Orphanet:317344 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z [Typedef] @@ -1980,7 +1978,7 @@ id: has_muscle_antagonist name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string is_a: biomechanically_related_to ! biomechanically related to @@ -1989,7 +1987,7 @@ id: has_muscle_insertion name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} @@ -2001,7 +1999,7 @@ id: has_muscle_origin name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} @@ -2039,7 +2037,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string is_a: has_participant inverse_of: output_of ! output of @@ -2066,7 +2064,7 @@ name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] xref: RO:0002584 property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causal_relation_between_material_entity_and_a_process ! causal relation between material entity and a process is_a: functionally_related_to ! functionally related to @@ -2076,7 +2074,7 @@ name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco xref: RO:0002479 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 range: BFO:0000004 @@ -2086,7 +2084,7 @@ name: has partial material basis in germline mutation in xref: RO:0004006 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_partially_giving_rise_to ! is causal germline mutation partially giving rise to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:57Z [Typedef] @@ -2098,7 +2096,7 @@ id: has_pathogen name: has pathogen subset: ro-eco xref: RO:0002557 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2108,7 +2106,7 @@ def: "A relationship that holds between a biological entity and a phenotype. Her subset: ro-eco xref: RO:0002200 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: UPHENO:0001001 is_a: has_phenotype_or_disease ! has phenotype or disease inverse_of: phenotype_of ! phenotype of @@ -2129,9 +2127,9 @@ def: "Holds between a cell c and a protein complex or protein p if and only if t xref: RO:0002104 property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Alexander Diehl" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 @@ -2157,8 +2155,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in whi xref: RO:0002110 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "synapsed in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2172,7 +2170,7 @@ name: has potential to develop into def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] xref: RO:0002387 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2181,7 +2179,7 @@ name: has potential to developmentally contribute to def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] xref: RO:0002385 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2190,7 +2188,7 @@ name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] xref: RO:0002386 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2199,7 +2197,7 @@ name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] xref: RO:0002388 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_potential_to_develop_into ! has potential to develop into [Typedef] @@ -2223,7 +2221,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -2233,7 +2231,7 @@ def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c o subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -2244,7 +2242,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -2276,7 +2274,7 @@ name: has skeleton def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] xref: RO:0002551 property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 @@ -2321,7 +2319,7 @@ name: has soma location def: "Relation between a neuron and an anatomical structure that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 range: CARO:0000003 @@ -2335,7 +2333,7 @@ def: "x 'has starts location' y if and only if there exists some process z such subset: ro-eco xref: RO:0002231 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -2348,7 +2346,7 @@ def: "x has start sequence y if the start of x is identical to the start of y, a xref: RO:0002516 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2358,10 +2356,10 @@ inverse_of: is_start_sequence_of ! is start sequence of [Typedef] id: has_subsequence name: has subsequence -def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2375,7 +2373,7 @@ id: has_symptom name: has symptom def: "A relation that holds between a disease or an organism and a phenotype" [] xref: RO:0002452 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: OGMS:0000031 is_a: has_phenotype ! has phenotype @@ -2405,7 +2403,7 @@ def: "A general relation between a neuron and some structure in which it either xref: RO:0002130 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has synapse in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2417,7 +2415,7 @@ id: has_synaptic_terminal_of name: has synaptic terminal of xref: RO:0002006 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: overlaps ! overlaps inverse_of: has_synaptic_terminal_in ! has synaptic terminal in @@ -2429,7 +2427,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002339 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2440,7 +2438,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002338 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2448,7 +2446,7 @@ id: has_vector name: has vector subset: ro-eco xref: RO:0002460 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with [Typedef] @@ -2463,7 +2461,7 @@ id: host_of name: host of subset: ro-eco xref: RO:0002453 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2476,7 +2474,7 @@ synonym: "epiparasite of" RELATED [] synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string is_a: has_host ! has host @@ -2492,7 +2490,7 @@ synonym: "has epiparasite" RELATED [] synonym: "has hyperparasite" RELATED [] synonym: "hyperparasitoidized by" RELATED [] xref: RO:0002554 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2500,7 +2498,7 @@ id: immediate_transformation_of name: immediate transformation of def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] xref: RO:0002495 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002494 is_a: directly_develops_from ! directly develops from is_a: transformation_of ! transformation of @@ -2510,7 +2508,7 @@ id: immediately_causally_downstream_of name: immediately causally downstream of xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of is_a: immediately_preceded_by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of @@ -2520,7 +2518,7 @@ id: immediately_causally_upstream_of name: immediately causally upstream of def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: immediately_precedes @@ -2533,7 +2531,7 @@ xref: RO:0002087 id: immediately_precedes subset: ro-eco xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0002575 BFO:0000063 [Typedef] @@ -2542,7 +2540,7 @@ name: imports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002340 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -2551,7 +2549,7 @@ name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] xref: RO:0002375 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 @@ -2577,7 +2575,7 @@ id: increases_by_expression_quantity_of name: increases by expression quantity of def: "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011008 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_positively_regulates_quantity_of ! indirectly positively regulates quantity of @@ -2587,7 +2585,7 @@ id: increases_expression_of name: increases expression of def: "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." [] xref: RO:0003003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -2606,7 +2604,7 @@ id: indirectly_negatively_regulates name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true @@ -2618,7 +2616,7 @@ id: indirectly_negatively_regulates_activity_of name: indirectly negatively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B." [] xref: RO:0011016 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly inhibits" xsd:string is_a: indirectly_regulates_activity_of ! indirectly regulates activity of @@ -2627,7 +2625,7 @@ id: indirectly_negatively_regulates_quantity_of name: indirectly negatively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B." [] xref: RO:0011023 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2635,7 +2633,7 @@ id: indirectly_positively_regulates name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 is_transitive: true @@ -2647,7 +2645,7 @@ id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." [] xref: RO:0011013 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -2658,7 +2656,7 @@ id: indirectly_positively_regulates_quantity_of name: indirectly positively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B." [] xref: RO:0011024 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2676,7 +2674,7 @@ id: indirectly_regulates_activity_of name: indirectly regulates activity of def: "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." [] xref: RO:0011004 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: regulates_activity_of ! regulates activity of @@ -2686,7 +2684,7 @@ id: indirectly_regulates_quantity_of name: indirectly regulates quantity of def: "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B." [] xref: RO:0011022 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -2696,7 +2694,7 @@ def: "inverse of has input" [] subset: ro-eco subset: RO:0002259 xref: RO:0002352 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -2710,7 +2708,7 @@ xref: RO:0002434 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI domain: BFO:0000040 @@ -2723,7 +2721,7 @@ name: interacts with via parasite-host interaction def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] subset: ro-eco xref: RO:0002443 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2751,7 +2749,7 @@ id: involved_in name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] xref: RO:0002331 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in @@ -2763,7 +2761,7 @@ id: involved_in_negative_regulation_of name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] xref: RO:0002430 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2773,7 +2771,7 @@ name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in_process ! causal agent in process @@ -2784,7 +2782,7 @@ id: involved_in_positive_regulation_of name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] xref: RO:0002429 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2793,7 +2791,7 @@ id: involved_in_regulation_of name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] xref: RO:0002428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of @@ -2804,7 +2802,7 @@ def: "c executes activity in d if and only if c enables p and p occurs_in d. As synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -2853,7 +2851,7 @@ id: is_basis_for_realizable name: is basis for realizable xref: RO:0004018 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:29Z [Typedef] @@ -2863,7 +2861,7 @@ def: "inverse of bounds sequence of" [] subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to @@ -2874,7 +2872,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004011 property_value: seeAlso Orphanet:410296 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:55:51Z [Typedef] @@ -2885,7 +2883,7 @@ xref: RO:0004013 property_value: seeAlso Orphanet:317343 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:40Z [Typedef] @@ -2896,7 +2894,7 @@ xref: RO:0004016 property_value: seeAlso Orphanet:317346 is_a: contributes_to_condition ! contributes to condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:58:43Z [Typedef] @@ -2906,7 +2904,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004012 property_value: seeAlso Orphanet:410295 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:06Z [Typedef] @@ -2917,7 +2915,7 @@ xref: RO:0004014 property_value: seeAlso Orphanet:317344 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:07Z [Typedef] @@ -2927,7 +2925,7 @@ def: "Relates a gene to condition, such that a mutation in this gene predisposes xref: RO:0004015 property_value: seeAlso Orphanet:317345 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:43Z [Typedef] @@ -2937,7 +2935,7 @@ def: "x is a consecutive sequence of y iff x has subsequence y, and all the part xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: has_subsequence ! has subsequence @@ -2947,7 +2945,7 @@ name: is downstream of sequence of def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] xref: RO:0002529 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of @@ -2957,7 +2955,7 @@ id: is_eaten_by name: is eaten by subset: ro-eco xref: RO:0002471 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -2969,7 +2967,7 @@ def: "inverse of has end sequence" [] subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2982,7 +2980,7 @@ xref: RO:0004010 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string range: BFO:0000017 is_a: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:53:08Z [Typedef] @@ -2992,7 +2990,7 @@ def: "x is immediately downstream of the sequence of y iff either (1) x and y ha xref: RO:0002530 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002529 is_a: is_downstream_of_sequence_of ! is downstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3004,7 +3002,7 @@ def: "inverse of immediately downstream of" [] xref: RO:0002531 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: is_upstream_of_sequence_of ! is upstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3031,7 +3029,7 @@ def: "x is sequentially aligned with if a significant portion bases of x and y c xref: RO:0002521 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -3071,7 +3069,7 @@ def: "inverse of has start sequence" [] subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3084,7 +3082,7 @@ def: "inverse of has subsequence" [] subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of @@ -3107,7 +3105,7 @@ name: is treated by substance def: "Inverse of 'is substance that treats'" [] subset: RO:0002259 xref: RO:0002302 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 is_a: causally_related_to ! causally related to inverse_of: is_substance_that_treats ! is substance that treats @@ -3117,7 +3115,7 @@ name: is upstream of sequence of def: "inverse of downstream of sequence of" [] xref: RO:0002528 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -3127,7 +3125,7 @@ name: is vector for subset: ro-eco xref: RO:0002459 property_value: IAO:0000112 "Anopheles is a vector for Plasmodium" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: has_vector ! has vector @@ -3179,7 +3177,7 @@ name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco xref: RO:0002571 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:cjm xsd:string range: BFO:0000040 is_a: part_of @@ -3190,7 +3188,7 @@ name: luminal space of def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] subset: ro-eco xref: RO:0002572 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000141 is_a: lumen_of ! lumen of @@ -3202,7 +3200,7 @@ subset: ro-eco xref: RO:0002381 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with is_a: part_of @@ -3212,7 +3210,7 @@ id: mereotopologically_related_to name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] xref: RO:0002323 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string property_value: RO:0001900 RO:0001901 @@ -3230,7 +3228,7 @@ name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 @@ -3243,7 +3241,7 @@ name: mutualistically interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] subset: ro-eco xref: RO:0002442 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -3270,7 +3268,7 @@ name: negatively regulated by def: "inverse of negatively regulates" [] subset: RO:0002259 xref: RO:0002335 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3281,7 +3279,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 @@ -3330,7 +3328,7 @@ def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -3351,10 +3349,10 @@ expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://p [Typedef] id: overlaps_sequence_of name: overlaps sequence of -def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] xref: RO:0002526 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: overlaps ! overlaps is_a: sequentially_related_to ! sequentially related to @@ -3366,7 +3364,7 @@ subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string is_a: has_host ! has host @@ -3379,7 +3377,7 @@ name: parasitized by subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string @@ -3418,7 +3416,7 @@ name: part of developmental precursor of xref: RO:0002287 property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by [Typedef] @@ -3426,7 +3424,7 @@ id: part_of_structure_that_is_capable_of name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] xref: RO:0002329 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean is_a: functionally_related_to ! functionally related to @@ -3455,7 +3453,7 @@ subset: ro-eco synonym: "semibiotically interacts with" RELATED [] xref: RO:0002446 property_value: IAO:0000112 "Porifiera attaches to substrate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: biotically_interacts_with ! biotically interacts with @@ -3464,7 +3462,7 @@ id: participates_in_a_biotic-biotic_interaction_with name: participates in a biotic-biotic interaction with subset: ro-eco xref: RO:0002574 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 domain: CARO:0001010 range: CARO:0001010 @@ -3474,7 +3472,7 @@ is_a: biotically_interacts_with ! biotically interacts with id: partner_in name: partner in xref: RO:0002461 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string is_a: participates_in @@ -3483,7 +3481,7 @@ id: pathogen_of name: pathogen of subset: ro-eco xref: RO:0002556 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_host ! has host inverse_of: has_pathogen ! has pathogen @@ -3495,7 +3493,7 @@ subset: ro-eco subset: RO:0002259 xref: RO:0002201 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_functional: true [Typedef] @@ -3503,7 +3501,7 @@ id: phosphorylates name: phosphorylates xref: RO:0002447 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: molecularly_interacts_with ! molecularly interacts with @@ -3512,7 +3510,7 @@ id: pollinated_by name: pollinated by subset: ro-eco xref: RO:0002456 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string @@ -3525,7 +3523,7 @@ subset: ro-eco xref: RO:0002455 property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with @@ -3537,7 +3535,7 @@ name: positively regulated by def: "inverse of positively regulates" [] subset: RO:0002259 xref: RO:0002336 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3548,7 +3546,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002211 @@ -3583,7 +3581,7 @@ def: "inverse of preys on" [] subset: ro-eco subset: RO:0002259 xref: RO:0002458 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string @@ -3598,9 +3596,9 @@ subset: ro-eco xref: RO:0002439 property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Jorrit Poelen" xsd:string -property_value: IAO:0000117 "Katja Shulz" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7134-3324 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string @@ -3623,7 +3621,7 @@ def: "x proper_distributary_of y iff x distributary_of y and x does not flow bac subset: ro-eco xref: RO:0002382 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: distributary_of ! distributary of [Typedef] @@ -3633,7 +3631,7 @@ def: "x proper_tributary_of y iff x tributary_of y and x does not originate from subset: ro-eco xref: RO:0002383 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: tributary_of ! tributary of [Typedef] @@ -3642,7 +3640,7 @@ name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string @@ -3654,7 +3652,7 @@ id: provides_nutrients_for name: provides nutrients for subset: ro-eco xref: RO:0002469 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3663,7 +3661,7 @@ name: realizable has basis in xref: RO:0004017 is_a: causally_related_to ! causally related to inverse_of: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:01Z [Typedef] @@ -3672,10 +3670,10 @@ name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] synonym: "triggered by process" EXACT [RO:cjm] xref: RO:0009501 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "David Osumi-Sutherland" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string @@ -3692,7 +3690,7 @@ xref: RO:0004028 domain: BFO:0000017 range: BFO:0000040 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:45:49Z [Typedef] @@ -3700,7 +3698,7 @@ id: receives_input_from name: receives input from xref: RO:0002485 property_value: IAO:0000116 "See notes for inverse relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to inverse_of: sends_output_to ! sends output to @@ -3740,7 +3738,7 @@ name: regulated by def: "inverse of regulates" [] subset: RO:0002259 xref: RO:0002334 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 range: BFO:0000015 @@ -3755,9 +3753,9 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Hill" xsd:string -property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 +property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string @@ -3774,7 +3772,7 @@ id: regulates_activity_of name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] xref: RO:0011002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3794,7 +3792,7 @@ id: regulates_in_other_organism name: regulates in other organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] xref: RO:0002010 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 range: BFO:0000015 is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -3805,7 +3803,7 @@ name: regulates levels of def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] xref: RO:0002332 property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 @@ -3817,7 +3815,7 @@ id: regulates_quantity_of name: regulates quantity of def: "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." [] xref: RO:0011003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3836,7 +3834,7 @@ id: related_via_localization_to name: related via localization to def: "A relationship that holds via some process of localization" [] xref: RO:0002337 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 range: BFO:0000002 @@ -3857,7 +3855,7 @@ id: represses_expression_of name: represses expression of def: "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." [] xref: RO:0003002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3871,7 +3869,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -3916,7 +3914,7 @@ name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] @@ -3936,7 +3934,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002348 property_value: IAO:0000112 "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3948,7 +3946,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002349 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3962,7 +3960,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3972,7 +3970,7 @@ id: results_in_developmental_induction_of name: results in developmental induction of def: "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." [] xref: RO:0002357 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3982,7 +3980,7 @@ def: "p results in the developmental progression of s iff p is a developmental p xref: RO:0002295 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 range: CARO:0000000 @@ -3994,7 +3992,7 @@ name: results in developmental regression of xref: RO:0002301 property_value: IAO:0000112 "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4004,7 +4002,7 @@ name: results in disappearance of xref: RO:0002300 property_value: IAO:0000112 "foramen ovale closure SubClassOf results in disappearance of foramen ovale" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4020,7 +4018,7 @@ id: results_in_ending_of name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4034,7 +4032,7 @@ xref: RO:0002297 property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4056,7 +4054,7 @@ id: results_in_growth_of name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4071,7 +4069,7 @@ xref: RO:0002299 property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4087,7 +4085,7 @@ xref: RO:0002298 property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4100,7 +4098,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002565 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4126,7 +4124,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002356 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4135,7 +4133,7 @@ id: results_in_structural_organization_of name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4151,7 +4149,7 @@ name: results in transport across def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002342 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: occurs_across ! occurs across is_a: results_in_transport_to_from_or_in ! results in transport to from or in @@ -4160,7 +4158,7 @@ id: results_in_transport_along name: results in transport along def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] xref: RO:0002341 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4168,7 +4166,7 @@ id: results_in_transport_to_from_or_in name: results in transport to from or in xref: RO:0002344 property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4183,7 +4181,7 @@ id: sends_output_to name: sends output to xref: RO:0002486 property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to [Typedef] @@ -4225,7 +4223,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcript" xsd:string property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -4235,7 +4233,7 @@ name: sequentially related to def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string @@ -4248,7 +4246,7 @@ name: skeleton of def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 is_a: part_of @@ -4259,7 +4257,7 @@ name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] xref: RO:0002379 property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: overlaps ! overlaps @@ -4271,7 +4269,7 @@ subset: ro-eco xref: RO:0002163 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 @@ -4285,7 +4283,7 @@ name: stabilizes quantity of def: "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." [] xref: RO:0011015 property_value: IAO:0000112 "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_quantity_of ! directly positively regulates quantity of @@ -4294,14 +4292,14 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates id: starts subset: ro-eco xref: RO:0002223 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: starts_with subset: ro-eco xref: RO:0002224 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -4317,7 +4315,7 @@ name: subcluster of def: "A relation between a group and another group it is part of but does not fully constitute." [] xref: RO:0015003 property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." xsd:string -property_value: IAO:0000117 "Shawn Tan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true is_a: part_of @@ -4326,7 +4324,7 @@ is_a: part_of id: subject_participant_in name: subject participant in xref: RO:0002462 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4345,7 +4343,7 @@ name: surrounded by def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] xref: RO:0002219 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to inverse_of: surrounds ! surrounds @@ -4357,7 +4355,7 @@ def: "inverse of surrounded by" [] subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to @@ -4367,7 +4365,7 @@ name: symbiotically interacts with def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] subset: ro-eco xref: RO:0002440 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true @@ -4380,8 +4378,8 @@ def: "Relation between an anatomical structure (including cells) and a neuron th xref: RO:0002103 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: receives_input_from ! receives input from inverse_of: synapsed_to ! synapsed to @@ -4406,8 +4404,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002108 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" [] @@ -4420,8 +4418,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002109 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4434,8 +4432,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002112 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4448,8 +4446,8 @@ comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part som xref: RO:0002120 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: sends_output_to ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -4473,8 +4471,8 @@ def: "A relation between a motor neuron and a muscle that it synapses to via a t comment: Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) xref: RO:0002107 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_II_bouton ! synapsed_by_via_type_II_bouton @@ -4488,8 +4486,8 @@ comment: Expands to: has_part some ('type Ib terminal button' that has_part some xref: RO:0002105 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Ib_bouton ! synapsed_by_via_type_Ib_bouton @@ -4503,8 +4501,8 @@ comment: Expands to: has_part some ('type Is terminal button' that has_part some xref: RO:0002106 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Is_bouton ! synapsed_by_via_type_Is_bouton @@ -4514,7 +4512,7 @@ expand_expression_to: "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that id: target_participant_in name: target participant in xref: RO:0002463 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4523,7 +4521,7 @@ id: temporally_related_to subset: ro-eco xref: RO:0002222 property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string [Typedef] @@ -4531,7 +4529,7 @@ id: transformation_of name: transformation of def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] xref: RO:0002494 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: develops_from ! develops from @@ -4541,7 +4539,7 @@ name: transitively provides input for def: "transitive form of directly_provides_input_for" [] xref: RO:0002414 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." xsd:string property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string domain: BFO:0000015 @@ -4556,7 +4554,7 @@ def: "A relationship that holds between a disease and organism" [] xref: RO:0002451 property_value: IAO:0000112 "all dengue disease transmitted by some mosquito" xsd:string property_value: IAO:0000116 "Add domain and range constraints" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -4576,7 +4574,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002313 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "regulates localization of" xsd:string is_a: related_via_localization_to ! related via localization to is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4590,7 +4588,7 @@ xref: RO:0002376 property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string @@ -4608,7 +4606,7 @@ name: trophically interacts with def: "An interaction relationship in which the partners are related via a feeding relationship." [] subset: ro-eco xref: RO:0002438 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4618,7 +4616,7 @@ name: ubiquitinates def: "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" [] xref: RO:0002480 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with [Typedef] diff --git a/subsets/ro-causal.owl b/subsets/ro-causal.owl index 7ef14d05..d6ac9788 100644 --- a/subsets/ro-causal.owl +++ b/subsets/ro-causal.owl @@ -409,7 +409,7 @@ - David Osumi-Sutherland + RO:0002002 has_2D_boundary @@ -421,7 +421,7 @@ A relation that holds between two neurons that are electrically coupled via gap junctions. - David Osumi-Sutherland + RO:0002003 electrically_synapsed_to @@ -435,7 +435,7 @@ - David Osumi-Sutherland + RO:0002006 has_synaptic_terminal_of @@ -469,7 +469,7 @@ has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland + RO:0002007 bounding_layer_of @@ -505,9 +505,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. + A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. Note from NCEAS meeting: consider changing primary label - David Osumi-Sutherland + RO:0002008 coincident_with @@ -524,7 +524,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - David Osumi-Sutherland + RO:0002010 regulates_in_other_organism regulates in other organism @@ -553,7 +553,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + dos 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -568,7 +568,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + dos 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -584,7 +584,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + dos 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -599,7 +599,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -613,7 +613,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -630,7 +630,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + dos 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -644,7 +644,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + dos 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -658,7 +658,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + dos 2017-07-20T17:11:08Z RO:0002020 transports @@ -672,7 +672,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + dos 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -686,7 +686,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -697,7 +697,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + GOC:dos @@ -708,7 +708,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + dos 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -718,7 +718,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + GOC:dos @@ -729,7 +729,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + dos 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -739,7 +739,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + GOC:dos @@ -750,7 +750,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + dos 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -761,7 +761,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + GOC:dos @@ -780,7 +780,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + dos 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -797,7 +797,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + GOC:dos @@ -814,7 +814,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + RO:0002090 @@ -831,7 +831,7 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure that its soma is part of. - David Osumi-Sutherland + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -852,9 +852,9 @@ Examples include: the relationship between two channels collected simultaneously relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - David Osumi-Sutherland + fasciculates with - (forall (?x ?y) + (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) @@ -890,9 +890,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure its axon forms (chemical) synapses in. - Chris Mungall - David Osumi-Sutherland - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -924,8 +923,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -945,9 +944,9 @@ Examples include: the relationship between two channels collected simultaneously Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - Alexander Diehl - Chris Mungall - Lindsay Cowell + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) @@ -965,8 +964,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -985,8 +984,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -1005,8 +1004,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) RO:0002107 @@ -1023,8 +1022,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1043,8 +1042,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1064,8 +1063,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - Chris Mungall - David Osumi-Sutherland + + synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( @@ -1085,8 +1084,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1168,8 +1167,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -1196,8 +1195,8 @@ N1 SubclassOf ( Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -1218,7 +1217,7 @@ N1 SubclassOf ( A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - David Osumi-Sutherland + has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) @@ -1267,9 +1266,9 @@ N1 SubclassOf ( The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - David Osumi-Sutherland + has fasciculating component - (forall (?x ?y) + (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) @@ -1309,8 +1308,8 @@ N1 SubclassOf ( - X continuous_with Y if and only if X and Y share a fiat boundary. - David Osumi-Sutherland + X continuous_with Y if and only if X and Y share a fiat boundary. + connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) @@ -1329,8 +1328,8 @@ N1 SubclassOf ( x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom - proper overlaps - (forall (?x ?y) + proper overlaps + (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and @@ -1353,7 +1352,7 @@ N1 SubclassOf ( A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - Chris Mungall + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) @@ -1361,7 +1360,7 @@ N1 SubclassOf ( RO:0002163 spatially_disjoint_from - spatially disjoint from + spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern @@ -1498,7 +1497,7 @@ N1 SubclassOf ( A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - Chris Mungall + RO:0002200 has_phenotype @@ -1513,7 +1512,7 @@ N1 SubclassOf ( inverse of has phenotype - Chris Mungall + RO:0002201 @@ -1533,10 +1532,10 @@ N1 SubclassOf ( x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - Terry Meehan + + + + RO:0002202 develops_from This is the transitive form of the develops from relation @@ -1554,9 +1553,9 @@ N1 SubclassOf ( inverse of develops from - Chris Mungall - David Osumi-Sutherland - Terry Meehan + + + RO:0002203 develops_into @@ -1588,12 +1587,12 @@ N1 SubclassOf ( Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - Chris Mungall - David Osumi-Sutherland - has developmental precursor + + FBbt RO:0002207 + has developmental precursor directly_develops_from TODO - add child relations from DOS directly develops from @@ -1651,9 +1650,9 @@ N1 SubclassOf ( p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - Chris Mungall - David Hill - Tanya Berardini + + + GO Regulation precludes parthood; the regulatory process may not be within the regulated process. @@ -1676,7 +1675,7 @@ N1 SubclassOf ( p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - Chris Mungall + negatively regulates (process to process) @@ -1698,7 +1697,7 @@ N1 SubclassOf ( p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - Chris Mungall + positively regulates (process to process) @@ -1721,7 +1720,7 @@ N1 SubclassOf ( mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - Chris Mungall + has function realized in @@ -1740,7 +1739,7 @@ N1 SubclassOf ( c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - Chris Mungall + has function in RO:0002216 capable_of_part_of @@ -1757,7 +1756,7 @@ N1 SubclassOf ( x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - Chris Mungall + RO:0002219 surrounded_by @@ -1779,7 +1778,7 @@ N1 SubclassOf ( x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - Chris Mungall + RO:0002220 @@ -1803,7 +1802,7 @@ N1 SubclassOf ( inverse of surrounded by - Chris Mungall + RO:0002221 @@ -1816,7 +1815,7 @@ N1 SubclassOf ( - Chris Mungall + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 @@ -1830,7 +1829,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002223 starts @@ -1842,7 +1841,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002224 starts_with @@ -1856,7 +1855,7 @@ N1 SubclassOf ( x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - Chris Mungall + RO:0002225 develops_from_part_of develops from part of @@ -1871,7 +1870,7 @@ N1 SubclassOf ( x develops_in y if x is located in y whilst x is developing - Chris Mungall + EHDAA2 Jonathan Bard, EHDAA2 RO:0002226 @@ -1909,7 +1908,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002229 ends @@ -1921,7 +1920,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002230 ends_with @@ -1937,7 +1936,7 @@ N1 SubclassOf ( x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - Chris Mungall + starts with process that occurs in RO:0002231 @@ -1955,7 +1954,7 @@ N1 SubclassOf ( x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - Chris Mungall + ends with process that occurs in RO:0002232 @@ -1973,7 +1972,7 @@ N1 SubclassOf ( p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + consumes RO:0002233 @@ -1993,7 +1992,7 @@ N1 SubclassOf ( p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - Chris Mungall + produces RO:0002234 @@ -2047,7 +2046,7 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - Bill Duncan (https://orcid.org/0000-0001-9625-1899) + This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. @@ -2196,7 +2195,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y - Chris Mungall + RO:0002254 has_developmental_contribution_from has developmental contribution from @@ -2211,7 +2210,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho inverse of has developmental contribution from - Chris Mungall + RO:0002255 developmentally_contributes_to @@ -2229,9 +2228,9 @@ If you need an axiom that says 'has_participant min 2 object', you sho t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - Chris Mungall - David Osumi-Sutherland - Melissa Haendel + + + induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) @@ -2251,7 +2250,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally induced by - Chris Mungall + RO:0002257 developmentally_induces developmentally induces @@ -2269,7 +2268,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - Chris Mungall + In general you should not use this relation to make assertions - use one of the more specific relations below this one RO:0002258 developmentally_preceded_by @@ -2317,7 +2316,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - Chris Mungall + replaces RO:0002285 developmentally_replaces @@ -2332,7 +2331,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally preceded by - Chris Mungall + RO:0002286 developmentally_succeeded_by developmentally succeeded by @@ -2346,7 +2345,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - Chris Mungall + RO:0002287 part_of_developmental_precursor_of part of developmental precursor of @@ -2363,7 +2362,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - Chris Mungall + RO:0002295 results_in_developmental_progression_of results in developmental progression of @@ -2380,7 +2379,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - Chris Mungall + http://www.geneontology.org/GO.doc.development.shtml RO:0002296 @@ -2401,7 +2400,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002297 @@ -2422,7 +2421,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002298 @@ -2443,7 +2442,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002299 @@ -2461,7 +2460,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho foramen ovale closure SubClassOf results in disappearance of foramen ovale - Chris Mungall + May be merged into parent relation RO:0002300 results_in_disappearance_of @@ -2476,7 +2475,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) - Chris Mungall + May be merged into parent relation RO:0002301 results_in_developmental_regression_of @@ -2491,7 +2490,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of 'is substance that treats' - cjm + RO:0002302 is_treated_by_substance @@ -2511,7 +2510,7 @@ where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. - Pier Buttigieg + adapted for living in RO:0002303 @@ -2529,7 +2528,7 @@ where p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - cjm + RO:0002304 @@ -2547,7 +2546,7 @@ where p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - cjm + RO:0002305 @@ -2562,10 +2561,10 @@ where A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. - Austin Meier - Chris Mungall - Marie Angelique Laporte - cjm + + + + 2017-06-05T17:35:04Z RO:0002309 has_exposure_stimulus @@ -2580,7 +2579,7 @@ where Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. - Chris Mungall + regulates localization of RO:0002313 @@ -2600,7 +2599,7 @@ where an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002315 @@ -2617,7 +2616,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions RO:0002321 @@ -2633,7 +2632,7 @@ where An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. - Chris Mungall + adapted for RO:0002322 @@ -2647,7 +2646,7 @@ where A mereological relationship or a topological relationship - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships RO:0002323 @@ -2661,7 +2660,7 @@ where A relationship that holds between entities participating in some developmental process (GO:0032502) - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development RO:0002324 developmentally_related_to @@ -2678,9 +2677,8 @@ where Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. - Chris Mungall + In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - Gene Ontology Consortium RO:0002325 colocalizes_with @@ -2708,7 +2706,7 @@ then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. - Chris Mungall + In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 @@ -2725,7 +2723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - Chris Mungall + catalyzes executes has @@ -2744,7 +2742,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 functionally_related_to @@ -2758,7 +2756,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati this relation holds between c and p when c is part of some c', and c' is capable of p. - Chris Mungall + false RO:0002329 part_of_structure_that_is_capable_of @@ -2773,7 +2771,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati c involved_in p if and only if c enables some process p', and p' is part of p - Chris Mungall + actively involved in enables part of RO:0002331 @@ -2792,7 +2790,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - Chris Mungall + regulates levels of (process to entity) RO:0002332 @@ -2808,7 +2806,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables - Chris Mungall + RO:0002333 enabled_by @@ -2825,7 +2823,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of regulates - Chris Mungall + regulated by (processual) RO:0002334 @@ -2840,7 +2838,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of negatively regulates - Chris Mungall + RO:0002335 negatively_regulated_by @@ -2854,7 +2852,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of positively regulates - Chris Mungall + RO:0002336 positively_regulated_by @@ -2869,7 +2867,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds via some process of localization - Chris Mungall + Do not use this relation directly. It is a grouping relation. RO:0002337 related_via_localization_to @@ -2883,7 +2881,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - Chris Mungall + RO:0002338 @@ -2899,7 +2897,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - Chris Mungall + RO:0002339 @@ -2915,7 +2913,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. - Chris Mungall + RO:0002340 imports @@ -2929,7 +2927,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - Chris Mungall + RO:0002341 results_in_transport_along results in transport along @@ -2943,7 +2941,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - Chris Mungall + RO:0002342 results_in_transport_across @@ -2958,7 +2956,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'pollen tube growth' results_in growth_of some 'pollen tube' - Chris Mungall + RO:0002343 results_in_growth_of results in growth of @@ -2971,7 +2969,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - Chris Mungall + RO:0002344 results_in_transport_to_from_or_in results in transport to from or in @@ -2983,8 +2981,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. - Chris Mungall + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. + RO:0002345 exports @@ -3000,7 +2998,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - Chris Mungall + RO:0002348 @@ -3017,7 +3015,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - Chris Mungall + RO:0002349 @@ -3034,7 +3032,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has input - Chris Mungall + RO:0002352 @@ -3050,7 +3048,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has output - Chris Mungall + RO:0002353 @@ -3064,7 +3062,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002354 formed_as_result_of formed as result of @@ -3078,7 +3076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. - Chris Mungall + RO:0002355 results_in_structural_organization_of results in structural organization of @@ -3092,7 +3090,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - Chris Mungall + RO:0002356 @@ -3108,7 +3106,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. - Chris Mungall + RO:0002357 results_in_developmental_induction_of results in developmental induction of @@ -3120,7 +3118,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + http://neurolex.org/wiki/Property:DendriteLocation RO:0002360 has_dendrite_location @@ -3136,7 +3134,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - Chris Mungall + attached to (anatomical structure to anatomical structure) RO:0002371 @@ -3153,7 +3151,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002372 has_muscle_origin @@ -3176,7 +3174,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002373 has_muscle_insertion @@ -3200,7 +3198,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) @@ -3222,7 +3220,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - Chris Mungall + drains into drains to tributary channel of @@ -3247,7 +3245,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Deschutes River distributary_of Little Lava Lake x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - Chris Mungall + branch of distributary channel of http://en.wikipedia.org/wiki/Distributary @@ -3273,7 +3271,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. - Chris Mungall + anastomoses with RO:0002378 @@ -3289,7 +3287,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - Chris Mungall + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios RO:0002379 spatially_coextensive_with @@ -3312,7 +3310,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - Chris Mungall + RO:0002380 branching_part_of @@ -3331,7 +3329,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. - Chris Mungall + RO:0002381 main_stem_of @@ -3347,7 +3345,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_distributary_of y iff x distributary_of y and x does not flow back into y - Chris Mungall + RO:0002382 proper_distributary_of @@ -3362,7 +3360,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_tributary_of y iff x tributary_of y and x does not originate from y - Chris Mungall + RO:0002383 proper_tributary_of @@ -3379,7 +3377,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - Chris Mungall + RO:0002384 has_developmental_potential_involving has developmental potential involving @@ -3393,7 +3391,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - Chris Mungall + RO:0002385 has_potential_to_developmentally_contribute_to has potential to developmentally contribute to @@ -3407,7 +3405,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - Chris Mungall + RO:0002386 has_potential_to_developmentally_induce has potential to developmentally induce @@ -3421,7 +3419,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has the potential to develop into y iff x develops into y or if x is capable of developing into y - Chris Mungall + RO:0002387 has_potential_to_develop_into has potential to develop into @@ -3435,7 +3433,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - Chris Mungall + RO:0002388 has_potential_to_directly_develop_into has potential to directly develop into @@ -3450,7 +3448,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' RO:0002400 @@ -3468,7 +3466,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of upstream of - Chris Mungall + RO:0002404 causally_downstream_of causally downstream of @@ -3483,7 +3481,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002405 immediately_causally_downstream_of immediately causally downstream of @@ -3498,7 +3496,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - Chris Mungall + indirectly activates RO:0002407 @@ -3515,7 +3513,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - Chris Mungall + indirectly inhibits RO:0002409 @@ -3544,7 +3542,7 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002410 causally_related_to @@ -3566,7 +3564,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - Chris Mungall + RO:0002411 @@ -3582,7 +3580,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - Chris Mungall + RO:0002412 immediately_causally_upstream_of @@ -3598,7 +3596,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit - Chris Mungall + directly provides input for directly provides input for (process to process) @@ -3618,7 +3616,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different transitive form of directly_provides_input_for - Chris Mungall + This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. transitively provides input for (process to process) RO:0002414 @@ -3636,7 +3634,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall + influences (processual) RO:0002418 affects @@ -3652,7 +3650,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - Chris Mungall + RO:0002427 @@ -3668,7 +3666,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - Chris Mungall + RO:0002428 involved_in_regulation_of involved in regulation of @@ -3681,7 +3679,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - Chris Mungall + RO:0002429 involved_in_positive_regulation_of @@ -3695,7 +3693,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - Chris Mungall + RO:0002430 involved_in_negative_regulation_of @@ -3712,7 +3710,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - Chris Mungall + involved in or reguates RO:0002431 involved_in_or_involved_in_regulation_of @@ -3728,7 +3726,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall + executes activity in RO:0002432 enables activity in @@ -3740,8 +3738,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + GOC:cjm + GOC:dos @@ -3751,7 +3749,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - Chris Mungall + RO:0002433 contributes_to_morphology_of contributes to morphology of @@ -3768,7 +3766,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. - Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. RO:0002434 in pairwise interaction with @@ -3787,7 +3785,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) - Chris Mungall + RO:0002435 genetically_interacts_with genetically interacts with @@ -3803,7 +3801,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - Chris Mungall + binds molecularly binds with RO:0002436 @@ -3824,7 +3822,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - Chris Mungall + interacts with on organism level RO:0002437 @@ -3841,7 +3839,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the partners are related via a feeding relationship. - Chris Mungall + RO:0002438 trophically_interacts_with @@ -3859,9 +3857,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] Baleen whale preys on krill An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - Chris Mungall - Jorrit Poelen - Katja Shulz + + + is subject of predation interaction with preys upon RO:0002439 @@ -3880,7 +3878,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A biotic interaction in which the two organisms live together in more or less intimate association. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism RO:0002440 @@ -3896,7 +3894,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002441 @@ -3911,7 +3909,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002442 @@ -3926,7 +3924,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 This relation groups a pair of inverse relations, parasite of and parasitized by RO:0002443 @@ -3944,7 +3942,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human - Chris Mungall + parasitizes RO:0002444 direct parasite of @@ -3961,7 +3959,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + has parasite parasitised by RO:0002445 @@ -3980,7 +3978,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - Chris Mungall + RO:0002446 semibiotically interacts with @@ -3996,7 +3994,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. RO:0002447 phosphorylates @@ -4015,8 +4013,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - Chris Mungall - Vasundra Touré + + RO:0002448 molecularly controls directly_regulates_activity_of @@ -4033,8 +4031,8 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly inhibits RO:0002449 molecularly decreases activity of @@ -4052,8 +4050,8 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly activates RO:0002450 molecularly increases activity of @@ -4070,7 +4068,7 @@ For example, A and B may be gene products and binding of B by A positively regul all dengue disease transmitted by some mosquito A relationship that holds between a disease and organism Add domain and range constraints - Chris Mungall + RO:0002451 transmitted_by transmitted by @@ -4084,7 +4082,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between a disease or an organism and a phenotype - Chris Mungall + RO:0002452 has_symptom has symptom @@ -4096,7 +4094,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) RO:0002453 @@ -4111,7 +4109,7 @@ For example, A and B may be gene products and binding of B by A positively regul X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y - Chris Mungall + RO:0002454 has_host @@ -4128,7 +4126,7 @@ For example, A and B may be gene products and binding of B by A positively regul Bees pollinate Flowers This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - Chris Mungall + is subject of pollination interaction with RO:0002455 @@ -4143,7 +4141,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + has polinator is target of pollination interaction with RO:0002456 @@ -4160,7 +4158,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4175,7 +4173,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of preys on - Chris Mungall + has predator is target of predation interaction with RO:0002458 @@ -4195,7 +4193,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anopheles is a vector for Plasmodium - Chris Mungall + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism RO:0002459 @@ -4209,7 +4207,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002460 has_vector @@ -4222,7 +4220,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target RO:0002461 partner_in @@ -4235,7 +4233,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002462 subject_participant_in @@ -4248,7 +4246,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002463 target_participant_in @@ -4261,7 +4259,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002469 provides_nutrients_for @@ -4274,7 +4272,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is subject of eating interaction with RO:0002470 @@ -4288,7 +4286,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + eaten by is target of eating interaction with RO:0002471 @@ -4307,7 +4305,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - Chris Mungall + RO:0002473 @@ -4326,7 +4324,7 @@ For example, A and B may be gene products and binding of B by A positively regul ABal nucleus child nucleus of ABa nucleus (in C elegans) c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d - Chris Mungall + This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. RO:0002476 child_nucleus_of @@ -4340,7 +4338,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a hermaphroditic organism - Chris Mungall + RO:0002477 child_nucleus_of_in_hermaphrodite child nucleus of in hermaphrodite @@ -4353,7 +4351,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a male organism - Chris Mungall + RO:0002478 child_nucleus_of_in_male child nucleus of in male @@ -4367,7 +4365,7 @@ For example, A and B may be gene products and binding of B by A positively regul p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall + RO:0002479 has_part_that_occurs_in @@ -4382,7 +4380,7 @@ For example, A and B may be gene products and binding of B by A positively regul An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y Axiomatization to GO to be added later - Chris Mungall + RO:0002480 ubiquitinates ubiquitinates @@ -4396,7 +4394,7 @@ For example, A and B may be gene products and binding of B by A positively regul See notes for inverse relation - Chris Mungall + RO:0002485 receives_input_from receives input from @@ -4409,7 +4407,7 @@ For example, A and B may be gene products and binding of B by A positively regul This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - Chris Mungall + RO:0002486 sends_output_to sends output to @@ -4423,7 +4421,7 @@ For example, A and B may be gene products and binding of B by A positively regul x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - Chris Mungall + RO:0002494 transformation_of transformation of @@ -4437,7 +4435,7 @@ For example, A and B may be gene products and binding of B by A positively regul x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - Chris Mungall + RO:0002495 immediate_transformation_of @@ -4467,7 +4465,7 @@ For example, A and B may be gene products and binding of B by A positively regul p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002501 @@ -4483,7 +4481,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c - Chris Mungall + has intermediate product RO:0002505 @@ -4500,7 +4498,7 @@ For example, A and B may be gene products and binding of B by A positively regul The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002506 @@ -4522,11 +4520,11 @@ For example, A and B may be gene products and binding of B by A positively regul A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future - Chris Mungall + determined by (system to material entity) - Chris Mungall - Pier Buttigieg + + RO:0002507 determined_by @@ -4540,7 +4538,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of determined by - Chris Mungall + determines (material entity to system) RO:0002508 @@ -4559,7 +4557,7 @@ For example, A and B may be gene products and binding of B by A positively regul s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. - Chris Mungall + RO:0002509 determined_by_part_of @@ -4574,7 +4572,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between two entities that have the property of being sequences or having sequences. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. @@ -4594,7 +4592,7 @@ For example, A and B may be gene products and binding of B by A positively regul Two consecutive DNA residues are sequentially adjacent Two exons on a processed transcript that were previously connected by an intron are adjacent x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002515 @@ -4612,7 +4610,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as a start sequence the start codon for that transcript x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence - Chris Mungall + started by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4629,7 +4627,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has start sequence - Chris Mungall + starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4649,7 +4647,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence - Chris Mungall + ended by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4666,7 +4664,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has end sequence - Chris Mungall + ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4684,7 +4682,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. In the SO paper, this was defined as an instance-type relation - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002520 @@ -4701,7 +4699,7 @@ For example, A and B may be gene products and binding of B by A positively regul Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering - Chris Mungall + RO:0002521 is_sequentially_aligned_with @@ -4718,7 +4716,7 @@ For example, A and B may be gene products and binding of B by A positively regul The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y - Chris Mungall + RO:0002522 bounds_sequence_of @@ -4733,7 +4731,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of bounds sequence of - Chris Mungall + RO:0002523 @@ -4751,8 +4749,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x has subsequence y iff all of the sequence parts of x are sequence parts of y - Chris Mungall + x has subsequence y iff all of the sequence parts of y are sequence parts of x + contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4771,7 +4769,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has subsequence - Chris Mungall + contained by RO:0002525 @@ -4788,8 +4786,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. - Chris Mungall + x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. + RO:0002526 overlaps_sequence_of @@ -4803,8 +4801,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. - Chris Mungall + x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + disconnected from RO:0002527 @@ -4820,7 +4818,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of downstream of sequence of - Chris Mungall + RO:0002528 is_upstream_of_sequence_of @@ -4836,7 +4834,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. - Chris Mungall + RO:0002529 is_downstream_of_sequence_of @@ -4852,7 +4850,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y - Chris Mungall + RO:0002530 @@ -4869,7 +4867,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript inverse of immediately downstream of - Chris Mungall + RO:0002531 is_immediately_upstream_of_sequence_of @@ -4889,7 +4887,7 @@ For example, A and B may be gene products and binding of B by A positively regul Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - Chris Mungall + has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). RO:0002551 @@ -4911,7 +4909,7 @@ For example, A and B may be gene products and binding of B by A positively regul p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. - Chris Mungall + RO:0002552 results_in_ending_of results in ending of @@ -4926,7 +4924,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - Chris Mungall + http://eol.org/schema/terms/hyperparasitoidOf https://en.wikipedia.org/wiki/Hyperparasite RO:0002553 @@ -4944,7 +4942,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of hyperparasite of - Chris Mungall + RO:0002554 has epiparasite has hyperparasite @@ -4961,7 +4959,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + http://en.wikipedia.org/wiki/Allelopathy RO:0002555 @@ -4978,7 +4976,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002556 pathogen_of @@ -4991,7 +4989,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002557 has_pathogen @@ -5005,7 +5003,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + causally influenced by (entity-centric) RO:0002559 @@ -5020,7 +5018,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - Chris Mungall + RO:0002565 @@ -5039,8 +5037,8 @@ For example, A and B may be gene products and binding of B by A positively regul The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - Chris Mungall - Vasundra Touré + + causally influences (entity-centric) RO:0002566 @@ -5057,7 +5055,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between elements of a musculoskeletal system or its analogs. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. RO:0002567 biomechanically_related_to @@ -5071,7 +5069,7 @@ For example, A and B may be gene products and binding of B by A positively regul m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - Chris Mungall + Wikipedia:Antagonist_(muscle) RO:0002568 has_muscle_antagonist @@ -5087,7 +5085,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of branching part of - Chris Mungall + RO:0002569 @@ -5104,7 +5102,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - Chris Mungall + UBERON:cjm This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. RO:0002570 @@ -5121,7 +5119,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - Chris Mungall + GOC:cjm RO:0002571 @@ -5137,7 +5135,7 @@ For example, A and B may be gene products and binding of B by A positively regul s is luminal space of x iff s is lumen_of x and s is an immaterial entity - Chris Mungall + RO:0002572 luminal_space_of @@ -5152,7 +5150,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002574 participates_in_a_biotic-biotic_interaction_with @@ -5169,7 +5167,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has skeleton - Chris Mungall + RO:0002576 skeleton_of @@ -5184,7 +5182,7 @@ For example, A and B may be gene products and binding of B by A positively regul p directly regulates q iff p is immediately causally upstream of q and p regulates q. - Chris Mungall + directly regulates (processual) @@ -5205,7 +5203,7 @@ For example, A and B may be gene products and binding of B by A positively regul gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - Chris Mungall + RO:0002584 has_part_structure_that_is_capable_of has part structure that is capable of @@ -5320,7 +5318,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall + RO:0002595 causal_relation_between_material_entity_and_a_process @@ -5723,7 +5721,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. - Vasundra Touré + RO:0003002 represses_expression_of represses expression of @@ -5738,7 +5736,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. - Vasundra Touré + RO:0003003 increases_expression_of increases expression of @@ -5883,7 +5881,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:38:20Z RO:0004000 condition_has_genetic_basis_in @@ -5897,7 +5895,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:20Z RO:0004001 has_material_basis_in_gain_of_function_germline_mutation_in @@ -5913,7 +5911,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:37Z RO:0004002 has_material_basis_in_loss_of_function_germline_mutation_in @@ -5927,7 +5925,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:54Z RO:0004003 has_material_basis_in_germline_mutation_in @@ -5942,7 +5940,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:07Z RO:0004004 has_material_basis_in_somatic_mutation_in @@ -5957,7 +5955,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:26Z RO:0004005 has_major_susceptibility_factor @@ -5971,7 +5969,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:57Z RO:0004006 has_partial_material_basis_in_germline_mutation_in @@ -5985,7 +5983,7 @@ Environmental exposures include those imposed by natural environments, experimen p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - cjm + 2018-12-13T11:26:17Z RO:0004007 @@ -6001,7 +5999,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - cjm + 2018-12-13T11:26:32Z RO:0004008 @@ -6012,8 +6010,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6027,7 +6025,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - cjm + 2018-12-13T11:26:56Z RO:0004009 @@ -6038,8 +6036,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6053,7 +6051,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:53:08Z RO:0004010 is_genetic_basis_for_condition @@ -6067,7 +6065,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:55:51Z RO:0004011 is_causal_gain_of_function_germline_mutation_of_in @@ -6082,7 +6080,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:06Z RO:0004012 is_causal_loss_of_function_germline_mutation_of_in @@ -6098,7 +6096,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:40Z RO:0004013 is_causal_germline_mutation_in @@ -6114,7 +6112,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:57:07Z RO:0004014 is_causal_somatic_mutation_in @@ -6129,7 +6127,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. - cjm + 2017-11-05T02:57:43Z RO:0004015 is_causal_susceptibility_factor_for @@ -6145,7 +6143,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. - cjm + 2017-11-05T02:58:43Z RO:0004016 is_causal_germline_mutation_partially_giving_rise_to @@ -6160,7 +6158,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:01Z RO:0004017 realizable_has_basis_in @@ -6173,7 +6171,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:29Z RO:0004018 is_basis_for_realizable @@ -6188,7 +6186,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:26:47Z RO:0004019 disease_has_basis_in @@ -6204,7 +6202,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) - cjm + 2017-11-05T03:29:32Z RO:0004020 disease_has_basis_in_dysfunction_of @@ -6220,7 +6218,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. disease has basis in disruption of (disease to process) - cjm + 2017-11-05T03:37:52Z RO:0004021 disease_has_basis_in_disruption_of @@ -6244,7 +6242,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. - cjm + 2017-11-05T03:46:07Z RO:0004022 disease_has_basis_in_feature @@ -6260,7 +6258,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. - cjm + 2017-11-05T03:50:54Z RO:0004023 causal_relationship_with_disease_as_subject @@ -6277,7 +6275,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and a process where the disease process disrupts the execution of the process. disease causes disruption of (disease to process) - cjm + 2017-11-05T03:51:09Z RO:0004024 disease_causes_disruption_of @@ -6293,7 +6291,7 @@ Environmental exposures include those imposed by natural environments, experimen disease causes dysfunction of (disease to anatomical entity) - cjm + 2017-11-05T03:58:20Z RO:0004025 disease_causes_dysfunction_of @@ -6319,7 +6317,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. - cjm + 2017-11-05T04:06:02Z RO:0004026 disease_has_location @@ -6343,7 +6341,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity - cjm + 2017-12-26T19:37:31Z RO:0004027 disease_has_inflammation_site @@ -6359,7 +6357,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - cjm + 2017-12-26T19:45:49Z RO:0004028 realized_in_response_to_stimulus @@ -6382,7 +6380,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. - cjm + 2017-12-26T19:50:53Z RO:0004029 disease_has_feature @@ -6397,7 +6395,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. - cjm + 2017-12-26T19:58:44Z RO:0004030 disease_arises_from_alteration_in_structure @@ -6411,7 +6409,7 @@ Environmental exposures include those imposed by natural environments, experimen Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - cjm + 2018-01-25T23:20:13Z RO:0004031 enables_subfunction @@ -6425,7 +6423,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:30Z RO:0004032 @@ -6441,7 +6439,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:51Z RO:0004033 @@ -6458,7 +6456,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - cjm + 2018-01-26T23:53:14Z RO:0004034 @@ -6476,7 +6474,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - cjm + 2018-01-26T23:53:22Z RO:0004035 @@ -6492,7 +6490,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:05Z RO:0004046 causally_upstream_of_or_within,_negative_effect @@ -6506,7 +6504,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:19Z RO:0004047 causally_upstream_of_or_within,_positive_effect @@ -6633,10 +6631,10 @@ Environmental exposures include those imposed by natural environments, experimen An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - Austin Meier - Chris Mungall - David Osumi-Sutherland - Marie Angelique Laporte + + + + RO:0009501 triggered by process realized_in_response_to @@ -6659,7 +6657,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - Vasundra Touré + RO:0011002 regulates_activity_of regulates activity of @@ -6674,7 +6672,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. - Vasundra Touré + RO:0011003 regulates_quantity_of regulates quantity of @@ -6689,7 +6687,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. - Vasundra Touré + RO:0011004 indirectly_regulates_activity_of indirectly regulates activity of @@ -6706,7 +6704,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011007 decreases_by_repression_quantity_of decreases by repression quantity of @@ -6723,7 +6721,7 @@ For example, protein A (transcription factor) indirectly decreases by repression The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011008 increases_by_expression_quantity_of increases by expression quantity of @@ -6738,7 +6736,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly positively regulates the quantity of B. - Vasundra Touré + RO:0011009 directly_positively_regulates_quantity_of directly positively regulates quantity of @@ -6753,7 +6751,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly negatively regulates the quantity of B. - Vasundra Touré + RO:0011010 directly_negatively_regulates_quantity_of directly negatively regulates quantity of @@ -6768,7 +6766,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. - Vasundra Touré + indirectly activates RO:0011013 indirectly_positively_regulates_activity_of @@ -6785,7 +6783,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. - Vasundra Touré + RO:0011014 destabilizes_quantity_of destabilizes quantity of @@ -6801,7 +6799,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. - Vasundra Touré + RO:0011015 stabilizes_quantity_of stabilizes quantity of @@ -6814,7 +6812,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. - Vasundra Touré + indirectly inhibits RO:0011016 indirectly_negatively_regulates_activity_of @@ -6828,7 +6826,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. - Vasundra Touré + RO:0011021 directly_regulates_quantity_of directly regulates quantity of @@ -6841,7 +6839,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011022 indirectly_regulates_quantity_of indirectly regulates quantity of @@ -6854,7 +6852,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011023 indirectly_negatively_regulates_quantity_of indirectly negatively regulates quantity of @@ -6867,7 +6865,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011024 indirectly_positively_regulates_quantity_of indirectly positively regulates quantity of @@ -6880,8 +6878,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is regulated by the small molecule continuant + pg 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -6895,8 +6893,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is activated by the small molecule continuant + pg 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -6910,8 +6908,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant + pg 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -6924,8 +6922,8 @@ For example, protein A (transcription factor) indirectly increases by expression - p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + p acts on population of c iff c' is a collection, has members of type c, and p has participant c + pg 2020-06-08T17:21:33Z RO:0012003 @@ -6941,8 +6939,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process + pg 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -6956,8 +6954,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process + pg 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of @@ -6971,8 +6969,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process + pg 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of @@ -6985,8 +6983,8 @@ For example, protein A (transcription factor) indirectly increases by expression - The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. + pg 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -6999,7 +6997,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + pg 2021-02-26T07:28:29Z RO:0012008 @@ -7016,7 +7014,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + pg 2022-09-26T06:01:01Z RO:0012009 @@ -7032,7 +7030,7 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + pg 2022-09-26T06:06:20Z RO:0012010 @@ -7048,7 +7046,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + pg 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7063,7 +7061,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + pg 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7229,7 +7227,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relation between a group and another group it is part of but does not fully constitute. X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. - Shawn Tan + This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. RO:0015003 subcluster_of @@ -7301,7 +7299,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - http://orcid.org/0000-0002-7463-6306 + 2021-11-05T17:30:44Z RO:0016002 has_disease @@ -7457,7 +7455,7 @@ For example, protein A (transcription factor) indirectly increases by expression This relation groups relations between diseases and any other kind of entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. - cjm + 2018-09-26T00:00:32Z RO:0040035 disease_relationship @@ -7471,7 +7469,7 @@ For example, protein A (transcription factor) indirectly increases by expression p has anatomical participant c iff p has participant c, and c is an anatomical entity - cjm + 2018-09-26T01:08:58Z RO:0040036 results_in_changes_to_anatomical_or_cellular_structure diff --git a/subsets/ro-chado.obo b/subsets/ro-chado.obo index f0eedbec..300fa699 100644 --- a/subsets/ro-chado.obo +++ b/subsets/ro-chado.obo @@ -26,7 +26,7 @@ property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations O property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2023-01-04" xsd:string +property_value: owl:versionInfo "2023-02-19" xsd:string [Typedef] id: BFO:0000050 @@ -823,6 +823,7 @@ transitive_over: BFO:0000050 ! part of id: RO:0002207 name: directly_develops_from def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] +synonym: "has developmental precursor" EXACT [] is_a: RO:0002202 ! develops from inverse_of: RO:0002210 ! directly develops into @@ -2390,7 +2391,7 @@ is_a: RO:0002514 ! sequentially related to [Typedef] id: RO:0002524 name: has_subsequence -def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] is_transitive: true is_a: BFO:0000051 ! has part is_a: RO:0002522 ! bounds sequence of @@ -2409,7 +2410,7 @@ is_a: RO:0002526 ! overlaps sequence of [Typedef] id: RO:0002526 name: overlaps_sequence_of -def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] holds_over_chain: RO:0002524 RO:0002525 is_symmetric: true is_a: RO:0002131 ! overlaps @@ -2418,7 +2419,7 @@ is_a: RO:0002514 ! sequentially related to [Typedef] id: RO:0002527 name: does_not_overlap_sequence_of -def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] is_symmetric: true is_a: RO:0002514 ! sequentially related to diff --git a/subsets/ro-chado.obo.tmp b/subsets/ro-chado.obo.tmp index 7bd7cf91..1b4b78ac 100644 --- a/subsets/ro-chado.obo.tmp +++ b/subsets/ro-chado.obo.tmp @@ -25,7 +25,7 @@ property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations O property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2023-01-04" xsd:string +property_value: owl:versionInfo "2023-02-19" xsd:string owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: ()\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\n) [Typedef] @@ -823,6 +823,7 @@ transitive_over: BFO:0000050 ! part of id: RO:0002207 name: directly develops from def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] +synonym: "has developmental precursor" EXACT [] is_a: RO:0002202 ! develops from inverse_of: RO:0002210 ! directly develops into @@ -2390,7 +2391,7 @@ is_a: RO:0002514 ! sequentially related to [Typedef] id: RO:0002524 name: has subsequence -def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] is_transitive: true is_a: BFO:0000051 ! has part is_a: RO:0002522 ! bounds sequence of @@ -2409,7 +2410,7 @@ is_a: RO:0002526 ! overlaps sequence of [Typedef] id: RO:0002526 name: overlaps sequence of -def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] holds_over_chain: RO:0002524 RO:0002525 is_symmetric: true is_a: RO:0002131 ! overlaps @@ -2418,7 +2419,7 @@ is_a: RO:0002514 ! sequentially related to [Typedef] id: RO:0002527 name: does not overlap sequence of -def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] is_symmetric: true is_a: RO:0002514 ! sequentially related to diff --git a/subsets/ro-developmental.obo b/subsets/ro-developmental.obo index 3e95c217..0d29373a 100644 --- a/subsets/ro-developmental.obo +++ b/subsets/ro-developmental.obo @@ -13,7 +13,7 @@ id: acquires_nutrients_from name: acquires nutrients from subset: ro-eco xref: RO:0002457 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for @@ -58,7 +58,7 @@ property_value: RO:0004050 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:22Z [Typedef] @@ -71,7 +71,7 @@ property_value: RO:0004049 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:14Z [Typedef] @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z [Typedef] @@ -103,7 +103,7 @@ xref: RO:0004032 property_value: RO:0004049 RO:0002264 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z [Typedef] @@ -120,7 +120,7 @@ property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cy property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 domain: BFO:0000004 range: BFO:0000004 @@ -131,7 +131,7 @@ id: allelopath_of name: allelopath of subset: ro-eco xref: RO:0002555 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string @@ -153,7 +153,7 @@ def: "x anabranch_of y if x is a distributary of y (i.e. it channels a from a la subset: ro-eco xref: RO:0002378 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "anastomoses with" xsd:string is_a: distributary_of ! distributary of disjoint_from: proper_distributary_of ! proper distributary of @@ -165,7 +165,7 @@ name: attached to def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] subset: ro-eco xref: RO:0002371 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: attached_to_part_of ! attached to part of @@ -189,9 +189,8 @@ def: "Relation between a neuron and some structure its axon forms (chemical) syn xref: RO:0002102 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in @@ -202,7 +201,7 @@ id: biomechanically_related_to name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] xref: RO:0002567 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: CARO:0000003 range: CARO:0000003 @@ -214,7 +213,7 @@ name: biotically interacts with def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] subset: ro-eco xref: RO:0002437 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string @@ -231,7 +230,7 @@ def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\ comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco xref: RO:0002007 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 is_a: part_of @@ -242,7 +241,7 @@ def: "x bounds the sequence of y iff the upstream-most part of x is upstream of xref: RO:0002522 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to inverse_of: is_bound_by_sequence_of ! is bound by sequence of @@ -254,7 +253,7 @@ def: "x is a branching part of y if and only if x is part of y and x is connecte subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso FMA:85994 xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with @@ -269,7 +268,7 @@ subset: ro-eco xref: RO:0002215 property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 @@ -302,7 +301,7 @@ id: capable_of_part_of name: capable of part of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ is_a: causal_agent_in_process ! causal agent in process @@ -350,7 +349,7 @@ id: causal_relation_between_entities name: causal relation between entities xref: RO:0002506 property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000002 @@ -363,7 +362,7 @@ name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] xref: RO:0002595 property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 range: BFO:0000015 @@ -374,7 +373,7 @@ id: causal_relation_between_processes name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 @@ -389,7 +388,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: OGMS:0000031 is_a: causally_related_to ! causally related to is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:50:54Z [Typedef] @@ -398,7 +397,7 @@ name: causally downstream of def: "inverse of upstream of" [] xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within is_a: preceded_by inverse_of: causally_upstream_of ! causally upstream of @@ -409,7 +408,7 @@ name: causally downstream of or within def: "inverse of causally upstream of or within" [] subset: RO:0002259 xref: RO:0002427 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -418,7 +417,7 @@ is_a: causal_relation_between_processes ! causal relation between processes id: causally_influenced_by name: causally influenced by xref: RO:0002559 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: causal_relation_between_entities ! causal relation between entities @@ -429,8 +428,8 @@ id: causally_influences name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] xref: RO:0002566 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 @@ -443,7 +442,7 @@ name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] @@ -453,7 +452,7 @@ def: "p is causally upstream of q iff p is causally related to q, the end of p p subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes @@ -465,7 +464,7 @@ def: "p is causally upstream of, negative effect q iff p is casually upstream of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -478,7 +477,7 @@ comment: holds between x and y if and only if x is causally upstream of y and th subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -490,7 +489,7 @@ def: "p is 'causally upstream or within' q iff p is causally related to q, and t synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -502,7 +501,7 @@ name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -511,7 +510,7 @@ name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -537,7 +536,7 @@ name: child nucleus of def: "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" [] xref: RO:0002476 property_value: IAO:0000112 "ABal nucleus child nucleus of ABa nucleus (in C elegans)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." xsd:string domain: GO:0005634 range: GO:0005634 @@ -548,7 +547,7 @@ id: child_nucleus_of_in_hermaphrodite name: child nucleus of in hermaphrodite def: "A child nucleus relationship in which the cells are part of a hermaphroditic organism" [] xref: RO:0002477 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -556,7 +555,7 @@ id: child_nucleus_of_in_male name: child nucleus of in male def: "A child nucleus relationship in which the cells are part of a male organism" [] xref: RO:0002478 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -576,7 +575,7 @@ comment: Example: if we define region of chromosome as any subdivision of a chro subset: ro-eco xref: RO:0002008 property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -585,9 +584,8 @@ name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 -property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -599,7 +597,7 @@ name: commensually interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] subset: ro-eco xref: RO:0002441 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -610,7 +608,7 @@ def: "x composed_primarily_of y if and only if more than half of the mass of x i subset: ro-eco xref: RO:0002473 property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 @@ -639,7 +637,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: BFO:0000017 is_a: causally_related_to ! causally related to inverse_of: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:38:20Z [Typedef] @@ -648,7 +646,7 @@ name: conduit for def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] subset: ro-eco xref: RO:0002570 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 UBERON:cjm xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 @@ -661,7 +659,7 @@ name: confers advantage in subset: ro-eco xref: RO:0002322 property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "adapted for" xsd:string range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -727,7 +725,7 @@ name: continuous with def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 @@ -746,7 +744,7 @@ property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a het property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -771,7 +769,7 @@ id: contributes_to_morphology_of name: contributes to morphology of def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] xref: RO:0002433 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -796,7 +794,7 @@ id: decreases_by_repression_quantity_of name: decreases by repression quantity of def: "The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011007 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_negatively_regulates_quantity_of ! indirectly negatively regulates quantity of @@ -808,8 +806,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in wh xref: RO:0002121 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in @@ -821,7 +819,7 @@ name: destabilizes quantity of def: "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." [] xref: RO:0011014 property_value: IAO:0000112 "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_quantity_of ! directly negatively regulates quantity of @@ -832,11 +830,11 @@ name: determined by def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] subset: ro-eco xref: RO:0002507 -property_value: http://purl.org/dc/terms/creator "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/creator "Pier Buttigieg" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-4366-3088 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "A coral reef environment is determined by a particular coral reef" xsd:string property_value: IAO:0000116 "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602 property_value: IAO:0000589 "determined by (system to material entity)" xsd:string domain: RO:0002577 @@ -852,7 +850,7 @@ name: determined by part of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] subset: ro-eco xref: RO:0002509 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 range: BFO:0000040 is_a: causal_relation_between_entities ! causal relation between entities @@ -865,7 +863,7 @@ def: "inverse of determined by" [] subset: ro-eco subset: RO:0002259 xref: RO:0002508 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "determines (material entity to system)" xsd:string is_a: causally_influences ! causally influences @@ -876,7 +874,7 @@ def: "inverse of has developmental contribution from" [] subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to @@ -886,9 +884,9 @@ name: developmentally induced by def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] xref: RO:0002256 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string property_value: IAO:0000119 GO:0001759 xsd:string @@ -905,7 +903,7 @@ name: developmentally induces def: "Inverse of developmentally induced by" [] xref: RO:0002257 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_induce ! has potential to developmentally induce @@ -917,7 +915,7 @@ comment: This relation groups together various other developmental relations. It xref: RO:0002258 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string domain: BFO:0000002 range: BFO:0000002 @@ -929,7 +927,7 @@ id: developmentally_related_to name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] xref: RO:0002324 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] @@ -939,7 +937,7 @@ def: "x developmentally replaces y if and only if there is some developmental pr xref: RO:0002285 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "replaces" xsd:string is_a: developmentally_preceded_by ! developmentally preceded by @@ -949,7 +947,7 @@ name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] xref: RO:0002286 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -959,10 +957,10 @@ def: "x develops from y if and only if either (a) x directly develops from y or comment: This is the transitive form of the develops from relation xref: RO:0002202 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 domain: BFO:0000004 range: BFO:0000004 is_transitive: true @@ -975,7 +973,7 @@ name: develops from part of def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] xref: RO:0002225 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: develops_from ! develops from [Typedef] @@ -984,7 +982,7 @@ name: develops in def: "x develops_in y if x is located in y whilst x is developing" [] xref: RO:0002226 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string domain: CARO:0000000 @@ -997,9 +995,9 @@ def: "inverse of develops from" [] subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 is_transitive: true is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into @@ -1010,11 +1008,11 @@ id: directly_develops_from name: directly develops from def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] xref: RO:0002207 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "has developmental precursor" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000119 "FBbt" xsd:string property_value: RO:0002575 RO:0002202 is_a: develops_from ! develops from @@ -1060,8 +1058,8 @@ name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] xref: RO:0002449 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1072,7 +1070,7 @@ id: directly_negatively_regulates_quantity_of name: directly negatively regulates quantity of def: "The entity A has an activity that directly negatively regulates the quantity of B." [] xref: RO:0011010 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1107,8 +1105,8 @@ name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] xref: RO:0002450 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1119,7 +1117,7 @@ id: directly_positively_regulates_quantity_of name: directly positively regulates quantity of def: "The entity A has an activity that directly positively regulates the quantity of B." [] xref: RO:0011009 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1142,7 +1140,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002578 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string property_value: RO:0002575 RO:0002211 @@ -1155,8 +1153,8 @@ name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] xref: RO:0002448 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: molecularly_interacts_with ! molecularly interacts with @@ -1167,7 +1165,7 @@ id: directly_regulates_quantity_of name: directly regulates quantity of def: "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B." [] xref: RO:0011021 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -1177,7 +1175,7 @@ def: "A relationship between a disease and an anatomical structure where the mat xref: RO:0004030 range: CARO:0000003 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z [Typedef] @@ -1189,7 +1187,7 @@ property_value: IAO:0000589 "disease causes disruption of (disease to process)" domain: OGMS:0000031 range: BFO:0000015 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:51:09Z [Typedef] @@ -1200,7 +1198,7 @@ property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomica domain: OGMS:0000031 range: CARO:0000006 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z [Typedef] @@ -1210,7 +1208,7 @@ xref: RO:0004019 domain: OGMS:0000031 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject is_a: realizable_has_basis_in ! realizable has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:26:47Z [Typedef] @@ -1221,7 +1219,7 @@ xref: RO:0004021 property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:37:52Z [Typedef] @@ -1232,7 +1230,7 @@ xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string range: CARO:0000006 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z [Typedef] @@ -1243,7 +1241,7 @@ xref: RO:0004022 domain: OGMS:0000031 is_a: disease_has_basis_in ! disease has basis in is_a: has_phenotype ! has phenotype -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:46:07Z [Typedef] @@ -1253,7 +1251,7 @@ def: "A relationship between a disease and some feature of that disease, where t xref: RO:0004029 domain: OGMS:0000031 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:50:53Z [Typedef] @@ -1272,7 +1270,7 @@ xref: RO:0004027 domain: OGMS:0000031 range: BFO:0000004 is_a: disease_has_location ! disease has location -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:37:31Z [Typedef] @@ -1285,7 +1283,7 @@ property_value: IAO:0000232 "This relation is intentionally very general, and co domain: OGMS:0000031 range: BFO:0000004 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T04:06:02Z [Typedef] @@ -1294,7 +1292,7 @@ name: disease relationship def: "This relation groups relations between diseases and any other kind of entity." [] xref: RO:0040035 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z [Typedef] @@ -1306,7 +1304,7 @@ subset: ro-eco xref: RO:0002377 property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string @@ -1316,10 +1314,10 @@ is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: does_not_overlap_sequence_of name: does not overlap sequence of -def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] xref: RO:0002527 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "disconnected from" xsd:string is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -1338,7 +1336,7 @@ id: eats name: eats subset: ro-eco xref: RO:0002470 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -1359,7 +1357,7 @@ def: "A relationship that is mediated in some way by the environment or environm subset: ro-eco xref: RO:0002321 property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string [Typedef] @@ -1377,7 +1375,7 @@ name: electrically_synapsed_to def: "A relation that holds between two neurons that are electrically coupled via gap junctions." [] xref: RO:0002003 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: connected_to ! connected to [Typedef] @@ -1386,7 +1384,7 @@ name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: has_participant @@ -1397,7 +1395,7 @@ def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string property_value: IAO:0000118 "has" xsd:string @@ -1413,7 +1411,7 @@ name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] xref: RO:0004031 is_a: functionally_related_to ! functionally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z [Typedef] @@ -1430,14 +1428,14 @@ inverse_of: has_endoparasite ! has endoparasite id: ends subset: ro-eco xref: RO:0002229 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: ends_with subset: ro-eco xref: RO:0002230 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -1462,7 +1460,7 @@ name: exports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002345 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -1479,7 +1477,7 @@ def: "relationship between a neuron and a neuron projection bundle (e.g.- tract xref: RO:0002101 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 @@ -1492,7 +1490,7 @@ inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron proje id: formed_as_result_of name: formed as result of xref: RO:0002354 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of [Typedef] @@ -1500,7 +1498,7 @@ id: functionally_related_to name: functionally related to def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] xref: RO:0002328 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string [Typedef] @@ -1509,7 +1507,7 @@ name: genetically interacts with xref: RO:0002435 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with @@ -1517,7 +1515,7 @@ is_a: interacts_with ! interacts with [Typedef] id: has_2D_boundary xref: RO:0002002 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1557,7 +1555,7 @@ def: "inverse of branching part of" [] subset: ro-eco subset: RO:0002259 xref: RO:0002569 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: has_part is_a: in_branching_relationship_with ! in branching relationship with @@ -1593,7 +1591,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 "Bill Duncan (https://orcid.org/0000-0001-9625-1899)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant @@ -1622,7 +1620,7 @@ id: has_dendrite_location name: has dendrite location xref: RO:0002360 property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -1632,7 +1630,7 @@ def: "x has developmental contribution from y iff x has some part z such that z xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by @@ -1644,7 +1642,7 @@ name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to @@ -1656,7 +1654,7 @@ def: "p has direct input c iff c is a participant in p, c is present at the star xref: RO:0002400 property_value: IAO:0000112 "'protein catabolic process' SubClassOf has_direct_input some protein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly consumes" xsd:string property_value: IAO:0000232 "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" xsd:string is_a: has_input ! has input @@ -1666,7 +1664,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1711,7 +1709,7 @@ def: "x 'has end location' y if and only if there exists some process z such tha subset: ro-eco xref: RO:0002232 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -1724,7 +1722,7 @@ def: "x has end sequence y if the end of x is identical to the end of y, and x h xref: RO:0002518 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -1776,11 +1774,11 @@ id: has_exposure_stimulus name: has exposure stimulus def: "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002309 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 is_a: related_via_exposure_to ! related via exposure to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:35:04Z [Typedef] @@ -1806,7 +1804,7 @@ def: "The relation between a neuron projection bundle and a neuron projection th xref: RO:0002132 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 @@ -1828,7 +1826,7 @@ subset: ro-eco xref: RO:0002303 property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Pier Buttigieg" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string domain: CARO:0001010 range: ENVO:01000254 @@ -1851,7 +1849,7 @@ name: has host def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] subset: ro-eco xref: RO:0002454 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -1865,7 +1863,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 is_a: has_participant @@ -1886,7 +1884,7 @@ def: "p has intermediate c if and only if p has parts p1, p2 and p1 has output c subset: ro-eco xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string is_a: has_participant @@ -1924,7 +1922,7 @@ name: has major susceptibility factor xref: RO:0004005 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_susceptibility_factor_for ! is causal susceptibility factor for -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:26Z [Typedef] @@ -1935,7 +1933,7 @@ property_value: seeAlso Orphanet:410295 property_value: seeAlso Orphanet:410296 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_gain_of_function_germline_mutation_of_in ! is causal gain of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:20Z [Typedef] @@ -1945,7 +1943,7 @@ xref: RO:0004003 property_value: seeAlso Orphanet:317343 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_in ! is causal germline mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:54Z [Typedef] @@ -1954,7 +1952,7 @@ name: has material basis in loss of function germline mutation in xref: RO:0004002 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_loss_of_function_germline_mutation_of_in ! is causal loss of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:37Z [Typedef] @@ -1964,7 +1962,7 @@ xref: RO:0004004 property_value: seeAlso Orphanet:317344 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z [Typedef] @@ -1980,7 +1978,7 @@ id: has_muscle_antagonist name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string is_a: biomechanically_related_to ! biomechanically related to @@ -1989,7 +1987,7 @@ id: has_muscle_insertion name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} @@ -2001,7 +1999,7 @@ id: has_muscle_origin name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} @@ -2039,7 +2037,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string is_a: has_participant inverse_of: output_of ! output of @@ -2066,7 +2064,7 @@ name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] xref: RO:0002584 property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causal_relation_between_material_entity_and_a_process ! causal relation between material entity and a process is_a: functionally_related_to ! functionally related to @@ -2076,7 +2074,7 @@ name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco xref: RO:0002479 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 range: BFO:0000004 @@ -2086,7 +2084,7 @@ name: has partial material basis in germline mutation in xref: RO:0004006 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_partially_giving_rise_to ! is causal germline mutation partially giving rise to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:57Z [Typedef] @@ -2098,7 +2096,7 @@ id: has_pathogen name: has pathogen subset: ro-eco xref: RO:0002557 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2108,7 +2106,7 @@ def: "A relationship that holds between a biological entity and a phenotype. Her subset: ro-eco xref: RO:0002200 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: UPHENO:0001001 is_a: has_phenotype_or_disease ! has phenotype or disease inverse_of: phenotype_of ! phenotype of @@ -2129,9 +2127,9 @@ def: "Holds between a cell c and a protein complex or protein p if and only if t xref: RO:0002104 property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Alexander Diehl" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 @@ -2157,8 +2155,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in whi xref: RO:0002110 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "synapsed in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2172,7 +2170,7 @@ name: has potential to develop into def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] xref: RO:0002387 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2181,7 +2179,7 @@ name: has potential to developmentally contribute to def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] xref: RO:0002385 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2190,7 +2188,7 @@ name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] xref: RO:0002386 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2199,7 +2197,7 @@ name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] xref: RO:0002388 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_potential_to_develop_into ! has potential to develop into [Typedef] @@ -2223,7 +2221,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -2233,7 +2231,7 @@ def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c o subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -2244,7 +2242,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -2276,7 +2274,7 @@ name: has skeleton def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] xref: RO:0002551 property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 @@ -2321,7 +2319,7 @@ name: has soma location def: "Relation between a neuron and an anatomical structure that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 range: CARO:0000003 @@ -2335,7 +2333,7 @@ def: "x 'has starts location' y if and only if there exists some process z such subset: ro-eco xref: RO:0002231 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -2348,7 +2346,7 @@ def: "x has start sequence y if the start of x is identical to the start of y, a xref: RO:0002516 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2358,10 +2356,10 @@ inverse_of: is_start_sequence_of ! is start sequence of [Typedef] id: has_subsequence name: has subsequence -def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2375,7 +2373,7 @@ id: has_symptom name: has symptom def: "A relation that holds between a disease or an organism and a phenotype" [] xref: RO:0002452 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: OGMS:0000031 is_a: has_phenotype ! has phenotype @@ -2405,7 +2403,7 @@ def: "A general relation between a neuron and some structure in which it either xref: RO:0002130 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has synapse in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2417,7 +2415,7 @@ id: has_synaptic_terminal_of name: has synaptic terminal of xref: RO:0002006 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: overlaps ! overlaps inverse_of: has_synaptic_terminal_in ! has synaptic terminal in @@ -2429,7 +2427,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002339 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2440,7 +2438,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002338 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2448,7 +2446,7 @@ id: has_vector name: has vector subset: ro-eco xref: RO:0002460 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with [Typedef] @@ -2463,7 +2461,7 @@ id: host_of name: host of subset: ro-eco xref: RO:0002453 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2476,7 +2474,7 @@ synonym: "epiparasite of" RELATED [] synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string is_a: has_host ! has host @@ -2492,7 +2490,7 @@ synonym: "has epiparasite" RELATED [] synonym: "has hyperparasite" RELATED [] synonym: "hyperparasitoidized by" RELATED [] xref: RO:0002554 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2500,7 +2498,7 @@ id: immediate_transformation_of name: immediate transformation of def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] xref: RO:0002495 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002494 is_a: directly_develops_from ! directly develops from is_a: transformation_of ! transformation of @@ -2510,7 +2508,7 @@ id: immediately_causally_downstream_of name: immediately causally downstream of xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of is_a: immediately_preceded_by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of @@ -2520,7 +2518,7 @@ id: immediately_causally_upstream_of name: immediately causally upstream of def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: immediately_precedes @@ -2533,7 +2531,7 @@ xref: RO:0002087 id: immediately_precedes subset: ro-eco xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0002575 BFO:0000063 [Typedef] @@ -2542,7 +2540,7 @@ name: imports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002340 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -2551,7 +2549,7 @@ name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] xref: RO:0002375 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 @@ -2577,7 +2575,7 @@ id: increases_by_expression_quantity_of name: increases by expression quantity of def: "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011008 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_positively_regulates_quantity_of ! indirectly positively regulates quantity of @@ -2587,7 +2585,7 @@ id: increases_expression_of name: increases expression of def: "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." [] xref: RO:0003003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -2606,7 +2604,7 @@ id: indirectly_negatively_regulates name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true @@ -2618,7 +2616,7 @@ id: indirectly_negatively_regulates_activity_of name: indirectly negatively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B." [] xref: RO:0011016 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly inhibits" xsd:string is_a: indirectly_regulates_activity_of ! indirectly regulates activity of @@ -2627,7 +2625,7 @@ id: indirectly_negatively_regulates_quantity_of name: indirectly negatively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B." [] xref: RO:0011023 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2635,7 +2633,7 @@ id: indirectly_positively_regulates name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 is_transitive: true @@ -2647,7 +2645,7 @@ id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." [] xref: RO:0011013 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -2658,7 +2656,7 @@ id: indirectly_positively_regulates_quantity_of name: indirectly positively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B." [] xref: RO:0011024 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2676,7 +2674,7 @@ id: indirectly_regulates_activity_of name: indirectly regulates activity of def: "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." [] xref: RO:0011004 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: regulates_activity_of ! regulates activity of @@ -2686,7 +2684,7 @@ id: indirectly_regulates_quantity_of name: indirectly regulates quantity of def: "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B." [] xref: RO:0011022 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -2696,7 +2694,7 @@ def: "inverse of has input" [] subset: ro-eco subset: RO:0002259 xref: RO:0002352 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -2710,7 +2708,7 @@ xref: RO:0002434 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI domain: BFO:0000040 @@ -2723,7 +2721,7 @@ name: interacts with via parasite-host interaction def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] subset: ro-eco xref: RO:0002443 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2751,7 +2749,7 @@ id: involved_in name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] xref: RO:0002331 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in @@ -2763,7 +2761,7 @@ id: involved_in_negative_regulation_of name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] xref: RO:0002430 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2773,7 +2771,7 @@ name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in_process ! causal agent in process @@ -2784,7 +2782,7 @@ id: involved_in_positive_regulation_of name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] xref: RO:0002429 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2793,7 +2791,7 @@ id: involved_in_regulation_of name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] xref: RO:0002428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of @@ -2804,7 +2802,7 @@ def: "c executes activity in d if and only if c enables p and p occurs_in d. As synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -2853,7 +2851,7 @@ id: is_basis_for_realizable name: is basis for realizable xref: RO:0004018 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:29Z [Typedef] @@ -2863,7 +2861,7 @@ def: "inverse of bounds sequence of" [] subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to @@ -2874,7 +2872,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004011 property_value: seeAlso Orphanet:410296 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:55:51Z [Typedef] @@ -2885,7 +2883,7 @@ xref: RO:0004013 property_value: seeAlso Orphanet:317343 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:40Z [Typedef] @@ -2896,7 +2894,7 @@ xref: RO:0004016 property_value: seeAlso Orphanet:317346 is_a: contributes_to_condition ! contributes to condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:58:43Z [Typedef] @@ -2906,7 +2904,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004012 property_value: seeAlso Orphanet:410295 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:06Z [Typedef] @@ -2917,7 +2915,7 @@ xref: RO:0004014 property_value: seeAlso Orphanet:317344 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:07Z [Typedef] @@ -2927,7 +2925,7 @@ def: "Relates a gene to condition, such that a mutation in this gene predisposes xref: RO:0004015 property_value: seeAlso Orphanet:317345 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:43Z [Typedef] @@ -2937,7 +2935,7 @@ def: "x is a consecutive sequence of y iff x has subsequence y, and all the part xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: has_subsequence ! has subsequence @@ -2947,7 +2945,7 @@ name: is downstream of sequence of def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] xref: RO:0002529 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of @@ -2957,7 +2955,7 @@ id: is_eaten_by name: is eaten by subset: ro-eco xref: RO:0002471 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -2969,7 +2967,7 @@ def: "inverse of has end sequence" [] subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2982,7 +2980,7 @@ xref: RO:0004010 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string range: BFO:0000017 is_a: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:53:08Z [Typedef] @@ -2992,7 +2990,7 @@ def: "x is immediately downstream of the sequence of y iff either (1) x and y ha xref: RO:0002530 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002529 is_a: is_downstream_of_sequence_of ! is downstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3004,7 +3002,7 @@ def: "inverse of immediately downstream of" [] xref: RO:0002531 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: is_upstream_of_sequence_of ! is upstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3031,7 +3029,7 @@ def: "x is sequentially aligned with if a significant portion bases of x and y c xref: RO:0002521 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -3071,7 +3069,7 @@ def: "inverse of has start sequence" [] subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3084,7 +3082,7 @@ def: "inverse of has subsequence" [] subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of @@ -3107,7 +3105,7 @@ name: is treated by substance def: "Inverse of 'is substance that treats'" [] subset: RO:0002259 xref: RO:0002302 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 is_a: causally_related_to ! causally related to inverse_of: is_substance_that_treats ! is substance that treats @@ -3117,7 +3115,7 @@ name: is upstream of sequence of def: "inverse of downstream of sequence of" [] xref: RO:0002528 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -3127,7 +3125,7 @@ name: is vector for subset: ro-eco xref: RO:0002459 property_value: IAO:0000112 "Anopheles is a vector for Plasmodium" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: has_vector ! has vector @@ -3179,7 +3177,7 @@ name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco xref: RO:0002571 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:cjm xsd:string range: BFO:0000040 is_a: part_of @@ -3190,7 +3188,7 @@ name: luminal space of def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] subset: ro-eco xref: RO:0002572 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000141 is_a: lumen_of ! lumen of @@ -3202,7 +3200,7 @@ subset: ro-eco xref: RO:0002381 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with is_a: part_of @@ -3212,7 +3210,7 @@ id: mereotopologically_related_to name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] xref: RO:0002323 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string property_value: RO:0001900 RO:0001901 @@ -3230,7 +3228,7 @@ name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 @@ -3243,7 +3241,7 @@ name: mutualistically interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] subset: ro-eco xref: RO:0002442 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -3270,7 +3268,7 @@ name: negatively regulated by def: "inverse of negatively regulates" [] subset: RO:0002259 xref: RO:0002335 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3281,7 +3279,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 @@ -3330,7 +3328,7 @@ def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -3351,10 +3349,10 @@ expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://p [Typedef] id: overlaps_sequence_of name: overlaps sequence of -def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] xref: RO:0002526 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: overlaps ! overlaps is_a: sequentially_related_to ! sequentially related to @@ -3366,7 +3364,7 @@ subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string is_a: has_host ! has host @@ -3379,7 +3377,7 @@ name: parasitized by subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string @@ -3418,7 +3416,7 @@ name: part of developmental precursor of xref: RO:0002287 property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by [Typedef] @@ -3426,7 +3424,7 @@ id: part_of_structure_that_is_capable_of name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] xref: RO:0002329 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean is_a: functionally_related_to ! functionally related to @@ -3455,7 +3453,7 @@ subset: ro-eco synonym: "semibiotically interacts with" RELATED [] xref: RO:0002446 property_value: IAO:0000112 "Porifiera attaches to substrate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: biotically_interacts_with ! biotically interacts with @@ -3464,7 +3462,7 @@ id: participates_in_a_biotic-biotic_interaction_with name: participates in a biotic-biotic interaction with subset: ro-eco xref: RO:0002574 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 domain: CARO:0001010 range: CARO:0001010 @@ -3474,7 +3472,7 @@ is_a: biotically_interacts_with ! biotically interacts with id: partner_in name: partner in xref: RO:0002461 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string is_a: participates_in @@ -3483,7 +3481,7 @@ id: pathogen_of name: pathogen of subset: ro-eco xref: RO:0002556 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_host ! has host inverse_of: has_pathogen ! has pathogen @@ -3495,7 +3493,7 @@ subset: ro-eco subset: RO:0002259 xref: RO:0002201 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_functional: true [Typedef] @@ -3503,7 +3501,7 @@ id: phosphorylates name: phosphorylates xref: RO:0002447 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: molecularly_interacts_with ! molecularly interacts with @@ -3512,7 +3510,7 @@ id: pollinated_by name: pollinated by subset: ro-eco xref: RO:0002456 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string @@ -3525,7 +3523,7 @@ subset: ro-eco xref: RO:0002455 property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with @@ -3537,7 +3535,7 @@ name: positively regulated by def: "inverse of positively regulates" [] subset: RO:0002259 xref: RO:0002336 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3548,7 +3546,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002211 @@ -3583,7 +3581,7 @@ def: "inverse of preys on" [] subset: ro-eco subset: RO:0002259 xref: RO:0002458 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string @@ -3598,9 +3596,9 @@ subset: ro-eco xref: RO:0002439 property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Jorrit Poelen" xsd:string -property_value: IAO:0000117 "Katja Shulz" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7134-3324 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string @@ -3623,7 +3621,7 @@ def: "x proper_distributary_of y iff x distributary_of y and x does not flow bac subset: ro-eco xref: RO:0002382 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: distributary_of ! distributary of [Typedef] @@ -3633,7 +3631,7 @@ def: "x proper_tributary_of y iff x tributary_of y and x does not originate from subset: ro-eco xref: RO:0002383 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: tributary_of ! tributary of [Typedef] @@ -3642,7 +3640,7 @@ name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string @@ -3654,7 +3652,7 @@ id: provides_nutrients_for name: provides nutrients for subset: ro-eco xref: RO:0002469 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3663,7 +3661,7 @@ name: realizable has basis in xref: RO:0004017 is_a: causally_related_to ! causally related to inverse_of: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:01Z [Typedef] @@ -3672,10 +3670,10 @@ name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] synonym: "triggered by process" EXACT [RO:cjm] xref: RO:0009501 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "David Osumi-Sutherland" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string @@ -3692,7 +3690,7 @@ xref: RO:0004028 domain: BFO:0000017 range: BFO:0000040 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:45:49Z [Typedef] @@ -3700,7 +3698,7 @@ id: receives_input_from name: receives input from xref: RO:0002485 property_value: IAO:0000116 "See notes for inverse relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to inverse_of: sends_output_to ! sends output to @@ -3740,7 +3738,7 @@ name: regulated by def: "inverse of regulates" [] subset: RO:0002259 xref: RO:0002334 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 range: BFO:0000015 @@ -3755,9 +3753,9 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Hill" xsd:string -property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 +property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string @@ -3774,7 +3772,7 @@ id: regulates_activity_of name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] xref: RO:0011002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3794,7 +3792,7 @@ id: regulates_in_other_organism name: regulates in other organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] xref: RO:0002010 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 range: BFO:0000015 is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -3805,7 +3803,7 @@ name: regulates levels of def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] xref: RO:0002332 property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 @@ -3817,7 +3815,7 @@ id: regulates_quantity_of name: regulates quantity of def: "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." [] xref: RO:0011003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3836,7 +3834,7 @@ id: related_via_localization_to name: related via localization to def: "A relationship that holds via some process of localization" [] xref: RO:0002337 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 range: BFO:0000002 @@ -3857,7 +3855,7 @@ id: represses_expression_of name: represses expression of def: "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." [] xref: RO:0003002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3871,7 +3869,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -3916,7 +3914,7 @@ name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] @@ -3936,7 +3934,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002348 property_value: IAO:0000112 "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3948,7 +3946,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002349 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3962,7 +3960,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3972,7 +3970,7 @@ id: results_in_developmental_induction_of name: results in developmental induction of def: "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." [] xref: RO:0002357 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3982,7 +3980,7 @@ def: "p results in the developmental progression of s iff p is a developmental p xref: RO:0002295 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 range: CARO:0000000 @@ -3994,7 +3992,7 @@ name: results in developmental regression of xref: RO:0002301 property_value: IAO:0000112 "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4004,7 +4002,7 @@ name: results in disappearance of xref: RO:0002300 property_value: IAO:0000112 "foramen ovale closure SubClassOf results in disappearance of foramen ovale" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4020,7 +4018,7 @@ id: results_in_ending_of name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4034,7 +4032,7 @@ xref: RO:0002297 property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4056,7 +4054,7 @@ id: results_in_growth_of name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4071,7 +4069,7 @@ xref: RO:0002299 property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4087,7 +4085,7 @@ xref: RO:0002298 property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4100,7 +4098,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002565 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4126,7 +4124,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002356 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4135,7 +4133,7 @@ id: results_in_structural_organization_of name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4151,7 +4149,7 @@ name: results in transport across def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002342 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: occurs_across ! occurs across is_a: results_in_transport_to_from_or_in ! results in transport to from or in @@ -4160,7 +4158,7 @@ id: results_in_transport_along name: results in transport along def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] xref: RO:0002341 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4168,7 +4166,7 @@ id: results_in_transport_to_from_or_in name: results in transport to from or in xref: RO:0002344 property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4183,7 +4181,7 @@ id: sends_output_to name: sends output to xref: RO:0002486 property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to [Typedef] @@ -4225,7 +4223,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcript" xsd:string property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -4235,7 +4233,7 @@ name: sequentially related to def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string @@ -4248,7 +4246,7 @@ name: skeleton of def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 is_a: part_of @@ -4259,7 +4257,7 @@ name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] xref: RO:0002379 property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: overlaps ! overlaps @@ -4271,7 +4269,7 @@ subset: ro-eco xref: RO:0002163 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 @@ -4285,7 +4283,7 @@ name: stabilizes quantity of def: "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." [] xref: RO:0011015 property_value: IAO:0000112 "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_quantity_of ! directly positively regulates quantity of @@ -4294,14 +4292,14 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates id: starts subset: ro-eco xref: RO:0002223 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: starts_with subset: ro-eco xref: RO:0002224 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -4317,7 +4315,7 @@ name: subcluster of def: "A relation between a group and another group it is part of but does not fully constitute." [] xref: RO:0015003 property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." xsd:string -property_value: IAO:0000117 "Shawn Tan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true is_a: part_of @@ -4326,7 +4324,7 @@ is_a: part_of id: subject_participant_in name: subject participant in xref: RO:0002462 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4345,7 +4343,7 @@ name: surrounded by def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] xref: RO:0002219 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to inverse_of: surrounds ! surrounds @@ -4357,7 +4355,7 @@ def: "inverse of surrounded by" [] subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to @@ -4367,7 +4365,7 @@ name: symbiotically interacts with def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] subset: ro-eco xref: RO:0002440 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true @@ -4380,8 +4378,8 @@ def: "Relation between an anatomical structure (including cells) and a neuron th xref: RO:0002103 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: receives_input_from ! receives input from inverse_of: synapsed_to ! synapsed to @@ -4406,8 +4404,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002108 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" [] @@ -4420,8 +4418,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002109 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4434,8 +4432,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002112 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4448,8 +4446,8 @@ comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part som xref: RO:0002120 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: sends_output_to ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -4473,8 +4471,8 @@ def: "A relation between a motor neuron and a muscle that it synapses to via a t comment: Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) xref: RO:0002107 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_II_bouton ! synapsed_by_via_type_II_bouton @@ -4488,8 +4486,8 @@ comment: Expands to: has_part some ('type Ib terminal button' that has_part some xref: RO:0002105 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Ib_bouton ! synapsed_by_via_type_Ib_bouton @@ -4503,8 +4501,8 @@ comment: Expands to: has_part some ('type Is terminal button' that has_part some xref: RO:0002106 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Is_bouton ! synapsed_by_via_type_Is_bouton @@ -4514,7 +4512,7 @@ expand_expression_to: "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that id: target_participant_in name: target participant in xref: RO:0002463 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4523,7 +4521,7 @@ id: temporally_related_to subset: ro-eco xref: RO:0002222 property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string [Typedef] @@ -4531,7 +4529,7 @@ id: transformation_of name: transformation of def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] xref: RO:0002494 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: develops_from ! develops from @@ -4541,7 +4539,7 @@ name: transitively provides input for def: "transitive form of directly_provides_input_for" [] xref: RO:0002414 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." xsd:string property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string domain: BFO:0000015 @@ -4556,7 +4554,7 @@ def: "A relationship that holds between a disease and organism" [] xref: RO:0002451 property_value: IAO:0000112 "all dengue disease transmitted by some mosquito" xsd:string property_value: IAO:0000116 "Add domain and range constraints" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -4576,7 +4574,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002313 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "regulates localization of" xsd:string is_a: related_via_localization_to ! related via localization to is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4590,7 +4588,7 @@ xref: RO:0002376 property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string @@ -4608,7 +4606,7 @@ name: trophically interacts with def: "An interaction relationship in which the partners are related via a feeding relationship." [] subset: ro-eco xref: RO:0002438 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4618,7 +4616,7 @@ name: ubiquitinates def: "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" [] xref: RO:0002480 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with [Typedef] diff --git a/subsets/ro-developmental.owl b/subsets/ro-developmental.owl index bdb02d0a..27c2e134 100644 --- a/subsets/ro-developmental.owl +++ b/subsets/ro-developmental.owl @@ -409,7 +409,7 @@ - David Osumi-Sutherland + RO:0002002 has_2D_boundary @@ -421,7 +421,7 @@ A relation that holds between two neurons that are electrically coupled via gap junctions. - David Osumi-Sutherland + RO:0002003 electrically_synapsed_to @@ -435,7 +435,7 @@ - David Osumi-Sutherland + RO:0002006 has_synaptic_terminal_of @@ -469,7 +469,7 @@ has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland + RO:0002007 bounding_layer_of @@ -505,9 +505,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. + A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. Note from NCEAS meeting: consider changing primary label - David Osumi-Sutherland + RO:0002008 coincident_with @@ -524,7 +524,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - David Osumi-Sutherland + RO:0002010 regulates_in_other_organism regulates in other organism @@ -553,7 +553,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + dos 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -568,7 +568,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + dos 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -584,7 +584,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + dos 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -599,7 +599,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -613,7 +613,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -630,7 +630,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + dos 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -644,7 +644,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + dos 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -658,7 +658,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + dos 2017-07-20T17:11:08Z RO:0002020 transports @@ -672,7 +672,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + dos 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -686,7 +686,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -697,7 +697,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + GOC:dos @@ -708,7 +708,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + dos 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -718,7 +718,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + GOC:dos @@ -729,7 +729,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + dos 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -739,7 +739,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + GOC:dos @@ -750,7 +750,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + dos 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -761,7 +761,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + GOC:dos @@ -780,7 +780,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + dos 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -797,7 +797,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + GOC:dos @@ -814,7 +814,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + RO:0002090 @@ -831,7 +831,7 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure that its soma is part of. - David Osumi-Sutherland + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -852,9 +852,9 @@ Examples include: the relationship between two channels collected simultaneously relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - David Osumi-Sutherland + fasciculates with - (forall (?x ?y) + (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) @@ -890,9 +890,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure its axon forms (chemical) synapses in. - Chris Mungall - David Osumi-Sutherland - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -924,8 +923,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -945,9 +944,9 @@ Examples include: the relationship between two channels collected simultaneously Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - Alexander Diehl - Chris Mungall - Lindsay Cowell + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) @@ -965,8 +964,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -985,8 +984,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -1005,8 +1004,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) RO:0002107 @@ -1023,8 +1022,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1043,8 +1042,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1064,8 +1063,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - Chris Mungall - David Osumi-Sutherland + + synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( @@ -1085,8 +1084,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1168,8 +1167,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -1196,8 +1195,8 @@ N1 SubclassOf ( Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -1218,7 +1217,7 @@ N1 SubclassOf ( A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - David Osumi-Sutherland + has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) @@ -1267,9 +1266,9 @@ N1 SubclassOf ( The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - David Osumi-Sutherland + has fasciculating component - (forall (?x ?y) + (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) @@ -1309,8 +1308,8 @@ N1 SubclassOf ( - X continuous_with Y if and only if X and Y share a fiat boundary. - David Osumi-Sutherland + X continuous_with Y if and only if X and Y share a fiat boundary. + connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) @@ -1329,8 +1328,8 @@ N1 SubclassOf ( x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom - proper overlaps - (forall (?x ?y) + proper overlaps + (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and @@ -1353,7 +1352,7 @@ N1 SubclassOf ( A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - Chris Mungall + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) @@ -1361,7 +1360,7 @@ N1 SubclassOf ( RO:0002163 spatially_disjoint_from - spatially disjoint from + spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern @@ -1498,7 +1497,7 @@ N1 SubclassOf ( A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - Chris Mungall + RO:0002200 has_phenotype @@ -1513,7 +1512,7 @@ N1 SubclassOf ( inverse of has phenotype - Chris Mungall + RO:0002201 @@ -1533,10 +1532,10 @@ N1 SubclassOf ( x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - Terry Meehan + + + + RO:0002202 develops_from This is the transitive form of the develops from relation @@ -1554,9 +1553,9 @@ N1 SubclassOf ( inverse of develops from - Chris Mungall - David Osumi-Sutherland - Terry Meehan + + + RO:0002203 develops_into @@ -1588,12 +1587,12 @@ N1 SubclassOf ( Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - Chris Mungall - David Osumi-Sutherland - has developmental precursor + + FBbt RO:0002207 + has developmental precursor directly_develops_from TODO - add child relations from DOS directly develops from @@ -1651,9 +1650,9 @@ N1 SubclassOf ( p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - Chris Mungall - David Hill - Tanya Berardini + + + GO Regulation precludes parthood; the regulatory process may not be within the regulated process. @@ -1676,7 +1675,7 @@ N1 SubclassOf ( p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - Chris Mungall + negatively regulates (process to process) @@ -1698,7 +1697,7 @@ N1 SubclassOf ( p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - Chris Mungall + positively regulates (process to process) @@ -1721,7 +1720,7 @@ N1 SubclassOf ( mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - Chris Mungall + has function realized in @@ -1740,7 +1739,7 @@ N1 SubclassOf ( c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - Chris Mungall + has function in RO:0002216 capable_of_part_of @@ -1757,7 +1756,7 @@ N1 SubclassOf ( x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - Chris Mungall + RO:0002219 surrounded_by @@ -1779,7 +1778,7 @@ N1 SubclassOf ( x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - Chris Mungall + RO:0002220 @@ -1803,7 +1802,7 @@ N1 SubclassOf ( inverse of surrounded by - Chris Mungall + RO:0002221 @@ -1816,7 +1815,7 @@ N1 SubclassOf ( - Chris Mungall + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 @@ -1830,7 +1829,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002223 starts @@ -1842,7 +1841,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002224 starts_with @@ -1856,7 +1855,7 @@ N1 SubclassOf ( x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - Chris Mungall + RO:0002225 develops_from_part_of develops from part of @@ -1871,7 +1870,7 @@ N1 SubclassOf ( x develops_in y if x is located in y whilst x is developing - Chris Mungall + EHDAA2 Jonathan Bard, EHDAA2 RO:0002226 @@ -1909,7 +1908,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002229 ends @@ -1921,7 +1920,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002230 ends_with @@ -1937,7 +1936,7 @@ N1 SubclassOf ( x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - Chris Mungall + starts with process that occurs in RO:0002231 @@ -1955,7 +1954,7 @@ N1 SubclassOf ( x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - Chris Mungall + ends with process that occurs in RO:0002232 @@ -1973,7 +1972,7 @@ N1 SubclassOf ( p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + consumes RO:0002233 @@ -1993,7 +1992,7 @@ N1 SubclassOf ( p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - Chris Mungall + produces RO:0002234 @@ -2047,7 +2046,7 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - Bill Duncan (https://orcid.org/0000-0001-9625-1899) + This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. @@ -2196,7 +2195,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y - Chris Mungall + RO:0002254 has_developmental_contribution_from has developmental contribution from @@ -2211,7 +2210,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho inverse of has developmental contribution from - Chris Mungall + RO:0002255 developmentally_contributes_to @@ -2229,9 +2228,9 @@ If you need an axiom that says 'has_participant min 2 object', you sho t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - Chris Mungall - David Osumi-Sutherland - Melissa Haendel + + + induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) @@ -2251,7 +2250,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally induced by - Chris Mungall + RO:0002257 developmentally_induces developmentally induces @@ -2269,7 +2268,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - Chris Mungall + In general you should not use this relation to make assertions - use one of the more specific relations below this one RO:0002258 developmentally_preceded_by @@ -2317,7 +2316,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - Chris Mungall + replaces RO:0002285 developmentally_replaces @@ -2332,7 +2331,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally preceded by - Chris Mungall + RO:0002286 developmentally_succeeded_by developmentally succeeded by @@ -2346,7 +2345,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - Chris Mungall + RO:0002287 part_of_developmental_precursor_of part of developmental precursor of @@ -2363,7 +2362,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - Chris Mungall + RO:0002295 results_in_developmental_progression_of results in developmental progression of @@ -2380,7 +2379,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - Chris Mungall + http://www.geneontology.org/GO.doc.development.shtml RO:0002296 @@ -2401,7 +2400,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002297 @@ -2422,7 +2421,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002298 @@ -2443,7 +2442,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002299 @@ -2461,7 +2460,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho foramen ovale closure SubClassOf results in disappearance of foramen ovale - Chris Mungall + May be merged into parent relation RO:0002300 results_in_disappearance_of @@ -2476,7 +2475,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) - Chris Mungall + May be merged into parent relation RO:0002301 results_in_developmental_regression_of @@ -2491,7 +2490,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of 'is substance that treats' - cjm + RO:0002302 is_treated_by_substance @@ -2511,7 +2510,7 @@ where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. - Pier Buttigieg + adapted for living in RO:0002303 @@ -2529,7 +2528,7 @@ where p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - cjm + RO:0002304 @@ -2547,7 +2546,7 @@ where p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - cjm + RO:0002305 @@ -2562,10 +2561,10 @@ where A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. - Austin Meier - Chris Mungall - Marie Angelique Laporte - cjm + + + + 2017-06-05T17:35:04Z RO:0002309 has_exposure_stimulus @@ -2580,7 +2579,7 @@ where Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. - Chris Mungall + regulates localization of RO:0002313 @@ -2600,7 +2599,7 @@ where an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002315 @@ -2617,7 +2616,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions RO:0002321 @@ -2633,7 +2632,7 @@ where An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. - Chris Mungall + adapted for RO:0002322 @@ -2647,7 +2646,7 @@ where A mereological relationship or a topological relationship - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships RO:0002323 @@ -2661,7 +2660,7 @@ where A relationship that holds between entities participating in some developmental process (GO:0032502) - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development RO:0002324 developmentally_related_to @@ -2678,9 +2677,8 @@ where Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. - Chris Mungall + In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - Gene Ontology Consortium RO:0002325 colocalizes_with @@ -2708,7 +2706,7 @@ then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. - Chris Mungall + In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 @@ -2725,7 +2723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - Chris Mungall + catalyzes executes has @@ -2744,7 +2742,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 functionally_related_to @@ -2758,7 +2756,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati this relation holds between c and p when c is part of some c', and c' is capable of p. - Chris Mungall + false RO:0002329 part_of_structure_that_is_capable_of @@ -2773,7 +2771,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati c involved_in p if and only if c enables some process p', and p' is part of p - Chris Mungall + actively involved in enables part of RO:0002331 @@ -2792,7 +2790,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - Chris Mungall + regulates levels of (process to entity) RO:0002332 @@ -2808,7 +2806,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables - Chris Mungall + RO:0002333 enabled_by @@ -2825,7 +2823,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of regulates - Chris Mungall + regulated by (processual) RO:0002334 @@ -2840,7 +2838,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of negatively regulates - Chris Mungall + RO:0002335 negatively_regulated_by @@ -2854,7 +2852,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of positively regulates - Chris Mungall + RO:0002336 positively_regulated_by @@ -2869,7 +2867,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds via some process of localization - Chris Mungall + Do not use this relation directly. It is a grouping relation. RO:0002337 related_via_localization_to @@ -2883,7 +2881,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - Chris Mungall + RO:0002338 @@ -2899,7 +2897,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - Chris Mungall + RO:0002339 @@ -2915,7 +2913,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. - Chris Mungall + RO:0002340 imports @@ -2929,7 +2927,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - Chris Mungall + RO:0002341 results_in_transport_along results in transport along @@ -2943,7 +2941,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - Chris Mungall + RO:0002342 results_in_transport_across @@ -2958,7 +2956,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'pollen tube growth' results_in growth_of some 'pollen tube' - Chris Mungall + RO:0002343 results_in_growth_of results in growth of @@ -2971,7 +2969,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - Chris Mungall + RO:0002344 results_in_transport_to_from_or_in results in transport to from or in @@ -2983,8 +2981,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. - Chris Mungall + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. + RO:0002345 exports @@ -3000,7 +2998,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - Chris Mungall + RO:0002348 @@ -3017,7 +3015,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - Chris Mungall + RO:0002349 @@ -3034,7 +3032,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has input - Chris Mungall + RO:0002352 @@ -3050,7 +3048,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has output - Chris Mungall + RO:0002353 @@ -3064,7 +3062,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002354 formed_as_result_of formed as result of @@ -3078,7 +3076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. - Chris Mungall + RO:0002355 results_in_structural_organization_of results in structural organization of @@ -3092,7 +3090,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - Chris Mungall + RO:0002356 @@ -3108,7 +3106,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. - Chris Mungall + RO:0002357 results_in_developmental_induction_of results in developmental induction of @@ -3120,7 +3118,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + http://neurolex.org/wiki/Property:DendriteLocation RO:0002360 has_dendrite_location @@ -3136,7 +3134,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - Chris Mungall + attached to (anatomical structure to anatomical structure) RO:0002371 @@ -3153,7 +3151,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002372 has_muscle_origin @@ -3176,7 +3174,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002373 has_muscle_insertion @@ -3200,7 +3198,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) @@ -3222,7 +3220,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - Chris Mungall + drains into drains to tributary channel of @@ -3247,7 +3245,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Deschutes River distributary_of Little Lava Lake x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - Chris Mungall + branch of distributary channel of http://en.wikipedia.org/wiki/Distributary @@ -3273,7 +3271,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. - Chris Mungall + anastomoses with RO:0002378 @@ -3289,7 +3287,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - Chris Mungall + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios RO:0002379 spatially_coextensive_with @@ -3312,7 +3310,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - Chris Mungall + RO:0002380 branching_part_of @@ -3331,7 +3329,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. - Chris Mungall + RO:0002381 main_stem_of @@ -3347,7 +3345,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_distributary_of y iff x distributary_of y and x does not flow back into y - Chris Mungall + RO:0002382 proper_distributary_of @@ -3362,7 +3360,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_tributary_of y iff x tributary_of y and x does not originate from y - Chris Mungall + RO:0002383 proper_tributary_of @@ -3379,7 +3377,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - Chris Mungall + RO:0002384 has_developmental_potential_involving has developmental potential involving @@ -3393,7 +3391,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - Chris Mungall + RO:0002385 has_potential_to_developmentally_contribute_to has potential to developmentally contribute to @@ -3407,7 +3405,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - Chris Mungall + RO:0002386 has_potential_to_developmentally_induce has potential to developmentally induce @@ -3421,7 +3419,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has the potential to develop into y iff x develops into y or if x is capable of developing into y - Chris Mungall + RO:0002387 has_potential_to_develop_into has potential to develop into @@ -3435,7 +3433,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - Chris Mungall + RO:0002388 has_potential_to_directly_develop_into has potential to directly develop into @@ -3450,7 +3448,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' RO:0002400 @@ -3468,7 +3466,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of upstream of - Chris Mungall + RO:0002404 causally_downstream_of causally downstream of @@ -3483,7 +3481,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002405 immediately_causally_downstream_of immediately causally downstream of @@ -3498,7 +3496,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - Chris Mungall + indirectly activates RO:0002407 @@ -3515,7 +3513,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - Chris Mungall + indirectly inhibits RO:0002409 @@ -3544,7 +3542,7 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002410 causally_related_to @@ -3566,7 +3564,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - Chris Mungall + RO:0002411 @@ -3582,7 +3580,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - Chris Mungall + RO:0002412 immediately_causally_upstream_of @@ -3598,7 +3596,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit - Chris Mungall + directly provides input for directly provides input for (process to process) @@ -3618,7 +3616,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different transitive form of directly_provides_input_for - Chris Mungall + This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. transitively provides input for (process to process) RO:0002414 @@ -3636,7 +3634,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall + influences (processual) RO:0002418 affects @@ -3652,7 +3650,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - Chris Mungall + RO:0002427 @@ -3668,7 +3666,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - Chris Mungall + RO:0002428 involved_in_regulation_of involved in regulation of @@ -3681,7 +3679,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - Chris Mungall + RO:0002429 involved_in_positive_regulation_of @@ -3695,7 +3693,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - Chris Mungall + RO:0002430 involved_in_negative_regulation_of @@ -3712,7 +3710,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - Chris Mungall + involved in or reguates RO:0002431 involved_in_or_involved_in_regulation_of @@ -3728,7 +3726,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall + executes activity in RO:0002432 enables activity in @@ -3740,8 +3738,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + GOC:cjm + GOC:dos @@ -3751,7 +3749,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - Chris Mungall + RO:0002433 contributes_to_morphology_of contributes to morphology of @@ -3768,7 +3766,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. - Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. RO:0002434 in pairwise interaction with @@ -3787,7 +3785,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) - Chris Mungall + RO:0002435 genetically_interacts_with genetically interacts with @@ -3803,7 +3801,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - Chris Mungall + binds molecularly binds with RO:0002436 @@ -3824,7 +3822,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - Chris Mungall + interacts with on organism level RO:0002437 @@ -3841,7 +3839,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the partners are related via a feeding relationship. - Chris Mungall + RO:0002438 trophically_interacts_with @@ -3859,9 +3857,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] Baleen whale preys on krill An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - Chris Mungall - Jorrit Poelen - Katja Shulz + + + is subject of predation interaction with preys upon RO:0002439 @@ -3880,7 +3878,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A biotic interaction in which the two organisms live together in more or less intimate association. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism RO:0002440 @@ -3896,7 +3894,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002441 @@ -3911,7 +3909,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002442 @@ -3926,7 +3924,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 This relation groups a pair of inverse relations, parasite of and parasitized by RO:0002443 @@ -3944,7 +3942,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human - Chris Mungall + parasitizes RO:0002444 direct parasite of @@ -3961,7 +3959,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + has parasite parasitised by RO:0002445 @@ -3980,7 +3978,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - Chris Mungall + RO:0002446 semibiotically interacts with @@ -3996,7 +3994,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. RO:0002447 phosphorylates @@ -4015,8 +4013,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - Chris Mungall - Vasundra Touré + + RO:0002448 molecularly controls directly_regulates_activity_of @@ -4033,8 +4031,8 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly inhibits RO:0002449 molecularly decreases activity of @@ -4052,8 +4050,8 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly activates RO:0002450 molecularly increases activity of @@ -4070,7 +4068,7 @@ For example, A and B may be gene products and binding of B by A positively regul all dengue disease transmitted by some mosquito A relationship that holds between a disease and organism Add domain and range constraints - Chris Mungall + RO:0002451 transmitted_by transmitted by @@ -4084,7 +4082,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between a disease or an organism and a phenotype - Chris Mungall + RO:0002452 has_symptom has symptom @@ -4096,7 +4094,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) RO:0002453 @@ -4111,7 +4109,7 @@ For example, A and B may be gene products and binding of B by A positively regul X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y - Chris Mungall + RO:0002454 has_host @@ -4128,7 +4126,7 @@ For example, A and B may be gene products and binding of B by A positively regul Bees pollinate Flowers This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - Chris Mungall + is subject of pollination interaction with RO:0002455 @@ -4143,7 +4141,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + has polinator is target of pollination interaction with RO:0002456 @@ -4160,7 +4158,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4175,7 +4173,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of preys on - Chris Mungall + has predator is target of predation interaction with RO:0002458 @@ -4195,7 +4193,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anopheles is a vector for Plasmodium - Chris Mungall + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism RO:0002459 @@ -4209,7 +4207,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002460 has_vector @@ -4222,7 +4220,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target RO:0002461 partner_in @@ -4235,7 +4233,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002462 subject_participant_in @@ -4248,7 +4246,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002463 target_participant_in @@ -4261,7 +4259,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002469 provides_nutrients_for @@ -4274,7 +4272,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is subject of eating interaction with RO:0002470 @@ -4288,7 +4286,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + eaten by is target of eating interaction with RO:0002471 @@ -4307,7 +4305,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - Chris Mungall + RO:0002473 @@ -4326,7 +4324,7 @@ For example, A and B may be gene products and binding of B by A positively regul ABal nucleus child nucleus of ABa nucleus (in C elegans) c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d - Chris Mungall + This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. RO:0002476 child_nucleus_of @@ -4340,7 +4338,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a hermaphroditic organism - Chris Mungall + RO:0002477 child_nucleus_of_in_hermaphrodite child nucleus of in hermaphrodite @@ -4353,7 +4351,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a male organism - Chris Mungall + RO:0002478 child_nucleus_of_in_male child nucleus of in male @@ -4367,7 +4365,7 @@ For example, A and B may be gene products and binding of B by A positively regul p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall + RO:0002479 has_part_that_occurs_in @@ -4382,7 +4380,7 @@ For example, A and B may be gene products and binding of B by A positively regul An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y Axiomatization to GO to be added later - Chris Mungall + RO:0002480 ubiquitinates ubiquitinates @@ -4396,7 +4394,7 @@ For example, A and B may be gene products and binding of B by A positively regul See notes for inverse relation - Chris Mungall + RO:0002485 receives_input_from receives input from @@ -4409,7 +4407,7 @@ For example, A and B may be gene products and binding of B by A positively regul This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - Chris Mungall + RO:0002486 sends_output_to sends output to @@ -4423,7 +4421,7 @@ For example, A and B may be gene products and binding of B by A positively regul x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - Chris Mungall + RO:0002494 transformation_of transformation of @@ -4437,7 +4435,7 @@ For example, A and B may be gene products and binding of B by A positively regul x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - Chris Mungall + RO:0002495 immediate_transformation_of @@ -4467,7 +4465,7 @@ For example, A and B may be gene products and binding of B by A positively regul p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002501 @@ -4483,7 +4481,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c - Chris Mungall + has intermediate product RO:0002505 @@ -4500,7 +4498,7 @@ For example, A and B may be gene products and binding of B by A positively regul The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002506 @@ -4522,11 +4520,11 @@ For example, A and B may be gene products and binding of B by A positively regul A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future - Chris Mungall + determined by (system to material entity) - Chris Mungall - Pier Buttigieg + + RO:0002507 determined_by @@ -4540,7 +4538,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of determined by - Chris Mungall + determines (material entity to system) RO:0002508 @@ -4559,7 +4557,7 @@ For example, A and B may be gene products and binding of B by A positively regul s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. - Chris Mungall + RO:0002509 determined_by_part_of @@ -4574,7 +4572,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between two entities that have the property of being sequences or having sequences. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. @@ -4594,7 +4592,7 @@ For example, A and B may be gene products and binding of B by A positively regul Two consecutive DNA residues are sequentially adjacent Two exons on a processed transcript that were previously connected by an intron are adjacent x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002515 @@ -4612,7 +4610,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as a start sequence the start codon for that transcript x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence - Chris Mungall + started by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4629,7 +4627,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has start sequence - Chris Mungall + starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4649,7 +4647,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence - Chris Mungall + ended by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4666,7 +4664,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has end sequence - Chris Mungall + ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4684,7 +4682,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. In the SO paper, this was defined as an instance-type relation - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002520 @@ -4701,7 +4699,7 @@ For example, A and B may be gene products and binding of B by A positively regul Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering - Chris Mungall + RO:0002521 is_sequentially_aligned_with @@ -4718,7 +4716,7 @@ For example, A and B may be gene products and binding of B by A positively regul The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y - Chris Mungall + RO:0002522 bounds_sequence_of @@ -4733,7 +4731,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of bounds sequence of - Chris Mungall + RO:0002523 @@ -4751,8 +4749,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x has subsequence y iff all of the sequence parts of x are sequence parts of y - Chris Mungall + x has subsequence y iff all of the sequence parts of y are sequence parts of x + contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4771,7 +4769,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has subsequence - Chris Mungall + contained by RO:0002525 @@ -4788,8 +4786,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. - Chris Mungall + x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. + RO:0002526 overlaps_sequence_of @@ -4803,8 +4801,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. - Chris Mungall + x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + disconnected from RO:0002527 @@ -4820,7 +4818,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of downstream of sequence of - Chris Mungall + RO:0002528 is_upstream_of_sequence_of @@ -4836,7 +4834,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. - Chris Mungall + RO:0002529 is_downstream_of_sequence_of @@ -4852,7 +4850,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y - Chris Mungall + RO:0002530 @@ -4869,7 +4867,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript inverse of immediately downstream of - Chris Mungall + RO:0002531 is_immediately_upstream_of_sequence_of @@ -4889,7 +4887,7 @@ For example, A and B may be gene products and binding of B by A positively regul Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - Chris Mungall + has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). RO:0002551 @@ -4911,7 +4909,7 @@ For example, A and B may be gene products and binding of B by A positively regul p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. - Chris Mungall + RO:0002552 results_in_ending_of results in ending of @@ -4926,7 +4924,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - Chris Mungall + http://eol.org/schema/terms/hyperparasitoidOf https://en.wikipedia.org/wiki/Hyperparasite RO:0002553 @@ -4944,7 +4942,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of hyperparasite of - Chris Mungall + RO:0002554 has epiparasite has hyperparasite @@ -4961,7 +4959,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + http://en.wikipedia.org/wiki/Allelopathy RO:0002555 @@ -4978,7 +4976,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002556 pathogen_of @@ -4991,7 +4989,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002557 has_pathogen @@ -5005,7 +5003,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + causally influenced by (entity-centric) RO:0002559 @@ -5020,7 +5018,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - Chris Mungall + RO:0002565 @@ -5039,8 +5037,8 @@ For example, A and B may be gene products and binding of B by A positively regul The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - Chris Mungall - Vasundra Touré + + causally influences (entity-centric) RO:0002566 @@ -5057,7 +5055,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between elements of a musculoskeletal system or its analogs. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. RO:0002567 biomechanically_related_to @@ -5071,7 +5069,7 @@ For example, A and B may be gene products and binding of B by A positively regul m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - Chris Mungall + Wikipedia:Antagonist_(muscle) RO:0002568 has_muscle_antagonist @@ -5087,7 +5085,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of branching part of - Chris Mungall + RO:0002569 @@ -5104,7 +5102,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - Chris Mungall + UBERON:cjm This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. RO:0002570 @@ -5121,7 +5119,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - Chris Mungall + GOC:cjm RO:0002571 @@ -5137,7 +5135,7 @@ For example, A and B may be gene products and binding of B by A positively regul s is luminal space of x iff s is lumen_of x and s is an immaterial entity - Chris Mungall + RO:0002572 luminal_space_of @@ -5152,7 +5150,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002574 participates_in_a_biotic-biotic_interaction_with @@ -5169,7 +5167,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has skeleton - Chris Mungall + RO:0002576 skeleton_of @@ -5184,7 +5182,7 @@ For example, A and B may be gene products and binding of B by A positively regul p directly regulates q iff p is immediately causally upstream of q and p regulates q. - Chris Mungall + directly regulates (processual) @@ -5205,7 +5203,7 @@ For example, A and B may be gene products and binding of B by A positively regul gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - Chris Mungall + RO:0002584 has_part_structure_that_is_capable_of has part structure that is capable of @@ -5320,7 +5318,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall + RO:0002595 causal_relation_between_material_entity_and_a_process @@ -5723,7 +5721,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. - Vasundra Touré + RO:0003002 represses_expression_of represses expression of @@ -5738,7 +5736,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. - Vasundra Touré + RO:0003003 increases_expression_of increases expression of @@ -5883,7 +5881,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:38:20Z RO:0004000 condition_has_genetic_basis_in @@ -5897,7 +5895,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:20Z RO:0004001 has_material_basis_in_gain_of_function_germline_mutation_in @@ -5913,7 +5911,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:37Z RO:0004002 has_material_basis_in_loss_of_function_germline_mutation_in @@ -5927,7 +5925,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:54Z RO:0004003 has_material_basis_in_germline_mutation_in @@ -5942,7 +5940,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:07Z RO:0004004 has_material_basis_in_somatic_mutation_in @@ -5957,7 +5955,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:26Z RO:0004005 has_major_susceptibility_factor @@ -5971,7 +5969,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:57Z RO:0004006 has_partial_material_basis_in_germline_mutation_in @@ -5985,7 +5983,7 @@ Environmental exposures include those imposed by natural environments, experimen p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - cjm + 2018-12-13T11:26:17Z RO:0004007 @@ -6001,7 +5999,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - cjm + 2018-12-13T11:26:32Z RO:0004008 @@ -6012,8 +6010,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6027,7 +6025,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - cjm + 2018-12-13T11:26:56Z RO:0004009 @@ -6038,8 +6036,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6053,7 +6051,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:53:08Z RO:0004010 is_genetic_basis_for_condition @@ -6067,7 +6065,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:55:51Z RO:0004011 is_causal_gain_of_function_germline_mutation_of_in @@ -6082,7 +6080,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:06Z RO:0004012 is_causal_loss_of_function_germline_mutation_of_in @@ -6098,7 +6096,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:40Z RO:0004013 is_causal_germline_mutation_in @@ -6114,7 +6112,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:57:07Z RO:0004014 is_causal_somatic_mutation_in @@ -6129,7 +6127,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. - cjm + 2017-11-05T02:57:43Z RO:0004015 is_causal_susceptibility_factor_for @@ -6145,7 +6143,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. - cjm + 2017-11-05T02:58:43Z RO:0004016 is_causal_germline_mutation_partially_giving_rise_to @@ -6160,7 +6158,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:01Z RO:0004017 realizable_has_basis_in @@ -6173,7 +6171,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:29Z RO:0004018 is_basis_for_realizable @@ -6188,7 +6186,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:26:47Z RO:0004019 disease_has_basis_in @@ -6204,7 +6202,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) - cjm + 2017-11-05T03:29:32Z RO:0004020 disease_has_basis_in_dysfunction_of @@ -6220,7 +6218,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. disease has basis in disruption of (disease to process) - cjm + 2017-11-05T03:37:52Z RO:0004021 disease_has_basis_in_disruption_of @@ -6244,7 +6242,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. - cjm + 2017-11-05T03:46:07Z RO:0004022 disease_has_basis_in_feature @@ -6260,7 +6258,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. - cjm + 2017-11-05T03:50:54Z RO:0004023 causal_relationship_with_disease_as_subject @@ -6277,7 +6275,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and a process where the disease process disrupts the execution of the process. disease causes disruption of (disease to process) - cjm + 2017-11-05T03:51:09Z RO:0004024 disease_causes_disruption_of @@ -6293,7 +6291,7 @@ Environmental exposures include those imposed by natural environments, experimen disease causes dysfunction of (disease to anatomical entity) - cjm + 2017-11-05T03:58:20Z RO:0004025 disease_causes_dysfunction_of @@ -6319,7 +6317,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. - cjm + 2017-11-05T04:06:02Z RO:0004026 disease_has_location @@ -6343,7 +6341,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity - cjm + 2017-12-26T19:37:31Z RO:0004027 disease_has_inflammation_site @@ -6359,7 +6357,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - cjm + 2017-12-26T19:45:49Z RO:0004028 realized_in_response_to_stimulus @@ -6382,7 +6380,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. - cjm + 2017-12-26T19:50:53Z RO:0004029 disease_has_feature @@ -6397,7 +6395,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. - cjm + 2017-12-26T19:58:44Z RO:0004030 disease_arises_from_alteration_in_structure @@ -6411,7 +6409,7 @@ Environmental exposures include those imposed by natural environments, experimen Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - cjm + 2018-01-25T23:20:13Z RO:0004031 enables_subfunction @@ -6425,7 +6423,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:30Z RO:0004032 @@ -6441,7 +6439,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:51Z RO:0004033 @@ -6458,7 +6456,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - cjm + 2018-01-26T23:53:14Z RO:0004034 @@ -6476,7 +6474,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - cjm + 2018-01-26T23:53:22Z RO:0004035 @@ -6492,7 +6490,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:05Z RO:0004046 causally_upstream_of_or_within,_negative_effect @@ -6506,7 +6504,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:19Z RO:0004047 causally_upstream_of_or_within,_positive_effect @@ -6633,10 +6631,10 @@ Environmental exposures include those imposed by natural environments, experimen An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - Austin Meier - Chris Mungall - David Osumi-Sutherland - Marie Angelique Laporte + + + + RO:0009501 triggered by process realized_in_response_to @@ -6659,7 +6657,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - Vasundra Touré + RO:0011002 regulates_activity_of regulates activity of @@ -6674,7 +6672,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. - Vasundra Touré + RO:0011003 regulates_quantity_of regulates quantity of @@ -6689,7 +6687,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. - Vasundra Touré + RO:0011004 indirectly_regulates_activity_of indirectly regulates activity of @@ -6706,7 +6704,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011007 decreases_by_repression_quantity_of decreases by repression quantity of @@ -6723,7 +6721,7 @@ For example, protein A (transcription factor) indirectly decreases by repression The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011008 increases_by_expression_quantity_of increases by expression quantity of @@ -6738,7 +6736,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly positively regulates the quantity of B. - Vasundra Touré + RO:0011009 directly_positively_regulates_quantity_of directly positively regulates quantity of @@ -6753,7 +6751,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly negatively regulates the quantity of B. - Vasundra Touré + RO:0011010 directly_negatively_regulates_quantity_of directly negatively regulates quantity of @@ -6768,7 +6766,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. - Vasundra Touré + indirectly activates RO:0011013 indirectly_positively_regulates_activity_of @@ -6785,7 +6783,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. - Vasundra Touré + RO:0011014 destabilizes_quantity_of destabilizes quantity of @@ -6801,7 +6799,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. - Vasundra Touré + RO:0011015 stabilizes_quantity_of stabilizes quantity of @@ -6814,7 +6812,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. - Vasundra Touré + indirectly inhibits RO:0011016 indirectly_negatively_regulates_activity_of @@ -6828,7 +6826,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. - Vasundra Touré + RO:0011021 directly_regulates_quantity_of directly regulates quantity of @@ -6841,7 +6839,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011022 indirectly_regulates_quantity_of indirectly regulates quantity of @@ -6854,7 +6852,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011023 indirectly_negatively_regulates_quantity_of indirectly negatively regulates quantity of @@ -6867,7 +6865,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011024 indirectly_positively_regulates_quantity_of indirectly positively regulates quantity of @@ -6880,8 +6878,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is regulated by the small molecule continuant + pg 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -6895,8 +6893,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is activated by the small molecule continuant + pg 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -6910,8 +6908,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant + pg 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -6924,8 +6922,8 @@ For example, protein A (transcription factor) indirectly increases by expression - p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + p acts on population of c iff c' is a collection, has members of type c, and p has participant c + pg 2020-06-08T17:21:33Z RO:0012003 @@ -6941,8 +6939,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process + pg 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -6956,8 +6954,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process + pg 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of @@ -6971,8 +6969,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process + pg 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of @@ -6985,8 +6983,8 @@ For example, protein A (transcription factor) indirectly increases by expression - The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. + pg 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -6999,7 +6997,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + pg 2021-02-26T07:28:29Z RO:0012008 @@ -7016,7 +7014,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + pg 2022-09-26T06:01:01Z RO:0012009 @@ -7032,7 +7030,7 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + pg 2022-09-26T06:06:20Z RO:0012010 @@ -7048,7 +7046,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + pg 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7063,7 +7061,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + pg 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7229,7 +7227,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relation between a group and another group it is part of but does not fully constitute. X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. - Shawn Tan + This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. RO:0015003 subcluster_of @@ -7301,7 +7299,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - http://orcid.org/0000-0002-7463-6306 + 2021-11-05T17:30:44Z RO:0016002 has_disease @@ -7457,7 +7455,7 @@ For example, protein A (transcription factor) indirectly increases by expression This relation groups relations between diseases and any other kind of entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. - cjm + 2018-09-26T00:00:32Z RO:0040035 disease_relationship @@ -7471,7 +7469,7 @@ For example, protein A (transcription factor) indirectly increases by expression p has anatomical participant c iff p has participant c, and c is an anatomical entity - cjm + 2018-09-26T01:08:58Z RO:0040036 results_in_changes_to_anatomical_or_cellular_structure diff --git a/subsets/ro-eco.obo b/subsets/ro-eco.obo index 59230f28..7f3fab39 100644 --- a/subsets/ro-eco.obo +++ b/subsets/ro-eco.obo @@ -58,7 +58,7 @@ def: "OBSOLETE A relation that holds between two neurons connected directly via comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_transitive: true is_obsolete: true @@ -70,7 +70,7 @@ def: "OBSOLETE A relation that holds between a neuron that is synapsed_to anothe comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_transitive: true is_obsolete: true @@ -82,7 +82,7 @@ def: "OBSOLETE A relation that holds between a neuron that is synapsed_by anothe comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_transitive: true is_obsolete: true @@ -150,13 +150,13 @@ id: RO:0002001 name: aligned with property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "May be obsoleted, see https://github.com/oborel/obo-relations/issues/260" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_transitive: true [Typedef] id: RO:0002002 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0002323 ! mereotopologically related to [Typedef] @@ -164,28 +164,28 @@ id: RO:0002003 name: electrically_synapsed_to def: "A relation that holds between two neurons that are electrically coupled via gap junctions." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0002170 ! connected to [Typedef] id: RO:0002004 name: tracheates def: "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to)." [] -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0001018 ! contained in [Typedef] id: RO:0002005 name: innervated_by property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 inverse_of: RO:0002134 ! innervates [Typedef] id: RO:0002006 name: has synaptic terminal of property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0002131 ! overlaps inverse_of: RO:0002130 ! has synaptic terminal in @@ -195,7 +195,7 @@ name: bounding layer of def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" [] comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: BFO:0000050 [Typedef] @@ -205,7 +205,7 @@ def: "A relation that holds between two linear structures that are approximately comment: Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. subset: ro-eco property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0002323 ! mereotopologically related to [Typedef] @@ -213,14 +213,14 @@ id: RO:0002009 name: cell expresses def: "A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g." [] property_value: http://purl.org/dc/terms/description "x 'cell expresses' y iff:\ncell(x)\nAND gene(y)\nAND exists some 'transcription, DNA templated (GO_0006351)'(t)\nAND t occurs_in x\nAND t has_input y" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0002292 ! expresses [Typedef] id: RO:0002010 name: regulates in other organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0002418 ! causally upstream of or within [Typedef] @@ -228,7 +228,7 @@ id: RO:0002011 name: regulates transport of def: "A relationship that holds between a process that regulates a transport process and the entity transported by that process." [] subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 holds_over_chain: RO:0002211 RO:0002313 [Typedef] @@ -364,13 +364,13 @@ creation_date: 2017-12-07T12:58:06Z [Typedef] id: RO:0002082 subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 [Typedef] id: RO:0002085 name: encompasses comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "di" xsd:string is_transitive: true is_a: RO:0002088 @@ -383,7 +383,7 @@ subset: ro-eco [Typedef] id: RO:0002090 subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0002575 BFO:0000063 holds_over_chain: RO:0002230 RO:0002224 @@ -404,7 +404,7 @@ id: RO:0002100 name: has soma location def: "Relation between a neuron and an anatomical structure that its soma is part of." [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002131 ! overlaps transitive_over: BFO:0000050 @@ -416,7 +416,7 @@ name: fasciculates with def: "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 @@ -429,9 +429,8 @@ name: axon synapses in def: "Relation between a neuron and some structure its axon forms (chemical) synapses in." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002113 ! has presynaptic terminal in transitive_over: BFO:0000050 @@ -443,8 +442,8 @@ name: synapsed by def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002485 ! receives input from inverse_of: RO:0002120 ! synapsed to @@ -456,9 +455,9 @@ name: has plasma membrane part def: "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." [] property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Alexander Diehl" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 is_a: BFO:0000051 @@ -471,8 +470,8 @@ def: "A relation between a motor neuron and a muscle that it synapses to via a t comment: Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002120 ! synapsed to inverse_of: RO:0002109 ! synapsed_by_via_type_Ib_bouton @@ -485,8 +484,8 @@ def: "A relation between a motor neuron and a muscle that it synapses to via a t comment: Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002120 ! synapsed to inverse_of: RO:0002112 ! synapsed_by_via_type_Is_bouton @@ -498,8 +497,8 @@ name: synapsed_via_type_II_bouton_to def: "A relation between a motor neuron and a muscle that it synapses to via a type II bouton." [] comment: Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002120 ! synapsed to inverse_of: RO:0002108 ! synapsed_by_via_type_II_bouton @@ -512,8 +511,8 @@ def: "Relation between a muscle and a motor neuron that synapses to it via a typ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002103 ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" [] @@ -525,8 +524,8 @@ def: "Relation between a muscle and a motor neuron that synapses to it via a typ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002103 ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -537,8 +536,8 @@ name: has postsynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "synapsed in" xsd:string property_value: RO:0001900 RO:0001901 is_a: RO:0002130 ! has synaptic terminal in @@ -559,8 +558,8 @@ def: "Relation between a muscle and a motor neuron that synapses to it via a typ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002103 ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -605,8 +604,8 @@ def: " Relation between a neuron and an anatomical structure (including cells) t comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n ‘synapse ; GO:0045202’ that has_part some (\n ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002486 ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -617,8 +616,8 @@ name: dendrite synapsed in def: "Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.\n\n " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002110 ! has postsynaptic terminal in transitive_over: BFO:0000050 @@ -630,7 +629,7 @@ name: has synaptic terminal in def: "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has synapse in" xsd:string property_value: RO:0001900 RO:0001901 is_a: RO:0002131 ! overlaps @@ -660,7 +659,7 @@ name: has fasciculating neuron projection def: "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 @@ -672,7 +671,7 @@ name: innervates def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 transitive_over: BFO:0000050 expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] @@ -682,7 +681,7 @@ id: RO:0002150 name: continuous with def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 @@ -749,7 +748,7 @@ def: "x only in taxon y if and only if x is in taxon y, and there is no other or property_value: IAO:0000112 "lactation SubClassOf 'only in taxon' some 'Mammalia'" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints @@ -762,8 +761,8 @@ def: "x is in taxon y if an only if y is an organism, and the relationship betwe comment: Connects a biological entity to its taxon of origin. subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Jennifer Deegan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints @@ -785,7 +784,7 @@ def: "A is spatially_disjoint_from B if and only if they have no parts in common subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 @@ -857,7 +856,7 @@ name: has phenotype def: "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0016001 ! has phenotype or disease inverse_of: RO:0002201 ! phenotype of @@ -868,7 +867,7 @@ def: "inverse of has phenotype" [] subset: ro-eco subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_functional: true [Typedef] @@ -877,10 +876,10 @@ name: develops from def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] comment: This is the transitive form of the develops from relation property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 is_transitive: true is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002203 ! develops into @@ -891,9 +890,9 @@ name: develops into def: "inverse of develops from" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 is_transitive: true is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002387 ! has potential to develop into @@ -905,7 +904,7 @@ name: gene product of def: "definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\"" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002512 RO:0002510 is_a: RO:0002330 ! genomically related to inverse_of: RO:0002205 ! has gene product @@ -917,7 +916,7 @@ def: "x has gene product y if and only if x is a gene (SO:0000704) that particip property_value: IAO:0000112 "every HOTAIR lncRNA is the gene product of some HOXC gene" xsd:string property_value: IAO:0000112 "every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002511 RO:0002513 is_a: RO:0002330 ! genomically related to @@ -927,7 +926,7 @@ name: expressed in def: "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" [] property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002330 ! genomically related to inverse_of: RO:0002292 ! expresses transitive_over: BFO:0000050 @@ -937,10 +936,10 @@ id: RO:0002207 name: directly develops from def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "has developmental precursor" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000119 "FBbt" xsd:string property_value: RO:0002575 RO:0002202 is_a: RO:0002202 ! develops from @@ -976,9 +975,9 @@ def: "p regulates q iff p is causally upstream of q, the execution of p is not c subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Hill" xsd:string -property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 +property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string @@ -998,7 +997,7 @@ def: "p negatively regulates q iff p regulates q, and p decreases the rate or ma subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 @@ -1014,7 +1013,7 @@ def: "p positively regulates q iff p regulates q, and p increases the rate or ma subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002211 @@ -1035,7 +1034,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" xsd:string property_value: IAO:0000116 "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants." xsd:string property_value: IAO:0000116 "TODO: add homeomorphy axiom" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 [Typedef] id: RO:0002215 @@ -1044,7 +1043,7 @@ def: "A relation between a material entity (such as a cell) and a process, in wh subset: ro-eco property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 @@ -1055,7 +1054,7 @@ is_a: RO:0002216 ! capable of part of id: RO:0002216 name: capable of part of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} @@ -1067,7 +1066,7 @@ id: RO:0002217 name: obsolete actively participates in def: "OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role" [] comment: Obsoleted as the inverse property was obsoleted. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "agent in" xsd:string is_obsolete: true replaced_by: RO:0002608 @@ -1076,7 +1075,7 @@ replaced_by: RO:0002608 id: RO:0002218 name: obsolete has active participant def: "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has agent" xsd:string is_obsolete: true replaced_by: RO:0002500 @@ -1086,7 +1085,7 @@ id: RO:0002219 name: surrounded by def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: RO:0002220 ! adjacent to inverse_of: RO:0002221 ! surrounds @@ -1104,7 +1103,7 @@ property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cy property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: RO:0002163 ! spatially disjoint from @@ -1114,7 +1113,7 @@ name: surrounds def: "inverse of surrounded by" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: RO:0002220 ! adjacent to @@ -1122,19 +1121,19 @@ is_a: RO:0002220 ! adjacent to id: RO:0002222 subset: ro-eco property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string [Typedef] id: RO:0002223 subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: BFO:0000050 [Typedef] id: RO:0002224 subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: BFO:0000051 [Typedef] @@ -1142,7 +1141,7 @@ id: RO:0002225 name: develops from part of def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002207 BFO:0000050 is_a: RO:0002202 ! develops from @@ -1151,7 +1150,7 @@ id: RO:0002226 name: develops in def: "x develops_in y if x is located in y whilst x is developing" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string holds_over_chain: RO:0002207 RO:0001025 @@ -1172,13 +1171,13 @@ is_a: RO:0002444 ! parasite of [Typedef] id: RO:0002229 subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: BFO:0000050 [Typedef] id: RO:0002230 subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: BFO:0000051 [Typedef] @@ -1187,7 +1186,7 @@ name: has start location def: "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts with process that occurs in" xsd:string holds_over_chain: RO:0002224 BFO:0000066 is_a: RO:0002479 ! has part that occurs in @@ -1198,7 +1197,7 @@ name: has end location def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends with process that occurs in" xsd:string holds_over_chain: RO:0002230 BFO:0000066 is_a: RO:0002479 ! has part that occurs in @@ -1212,7 +1211,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string holds_over_chain: RO:0002224 RO:0002233 inverse_of: RO:0002352 ! input of @@ -1226,7 +1225,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string holds_over_chain: RO:0002230 RO:0002234 inverse_of: RO:0002353 ! output of @@ -1253,7 +1252,7 @@ is_a: RO:0002444 ! parasite of id: RO:0002238 name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] -property_value: IAO:0000117 "Bill Duncan (https://orcid.org/0000-0001-9625-1899)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string [Typedef] @@ -1345,7 +1344,7 @@ name: has developmental contribution from def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000051 RO:0002202 is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002255 ! developmentally contributes to @@ -1356,7 +1355,7 @@ name: developmentally contributes to def: "inverse of has developmental contribution from" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002203 BFO:0000050 is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002385 ! has potential to developmentally contribute to @@ -1366,9 +1365,9 @@ id: RO:0002256 name: developmentally induced by def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string property_value: IAO:0000119 GO:0001759 xsd:string @@ -1382,7 +1381,7 @@ id: RO:0002257 name: developmentally induces def: "Inverse of developmentally induced by" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002386 ! has potential to developmentally induce @@ -1393,7 +1392,7 @@ def: "Candidate definition: x developmentally related to y if and only if there comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string is_a: RO:0002324 ! developmentally related to inverse_of: RO:0002286 ! developmentally succeeded by @@ -1425,7 +1424,7 @@ name: developmentally replaces def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "replaces" xsd:string is_a: RO:0002258 ! developmentally preceded by @@ -1434,7 +1433,7 @@ id: RO:0002286 name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] @@ -1442,7 +1441,7 @@ id: RO:0002287 name: part of developmental precursor of property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000050 RO:0002210 is_a: RO:0002286 ! developmentally succeeded by @@ -1452,7 +1451,7 @@ name: ubiquitously expressed in def: "x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002206 ! expressed in inverse_of: RO:0002293 ! ubiquitously expresses @@ -1461,7 +1460,7 @@ id: RO:0002292 name: expresses def: "Inverse of 'expressed in'" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002330 ! genomically related to [Typedef] @@ -1470,7 +1469,7 @@ name: ubiquitously expresses def: "inverse of ubiquiotously expressed in" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002292 ! expresses [Typedef] @@ -1479,7 +1478,7 @@ name: results in developmental progression of def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions is_a: RO:0002324 ! developmentally related to @@ -1492,7 +1491,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -1506,7 +1505,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: RO:0002234 ! has output is_a: RO:0002295 ! results in developmental progression of @@ -1522,7 +1521,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -1537,7 +1536,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -1547,7 +1546,7 @@ id: RO:0002300 name: results in disappearance of property_value: IAO:0000112 "foramen ovale closure SubClassOf results in disappearance of foramen ovale" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: RO:0002552 ! results in ending of @@ -1556,7 +1555,7 @@ id: RO:0002301 name: results in developmental regression of property_value: IAO:0000112 "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: RO:0002552 ! results in ending of @@ -1565,7 +1564,7 @@ id: RO:0002302 name: is treated by substance def: "Inverse of 'is substance that treats'" [] subset: RO:0002259 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 is_a: RO:0002410 ! causally related to inverse_of: RO:0002606 ! is substance that treats @@ -1577,7 +1576,7 @@ comment: A population of xs will possess adaptations (either evolved naturally o subset: ro-eco property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Pier Buttigieg" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string is_a: RO:0002321 ! ecologically related to @@ -1588,7 +1587,7 @@ def: "p is causally upstream of, positive effect q iff p is casually upstream of comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 is_a: RO:0002411 ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -1599,7 +1598,7 @@ name: causally upstream of, negative effect def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 is_a: RO:0002411 ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect @@ -1608,17 +1607,17 @@ is_a: RO:0004046 ! causally upstream of or within, negative effect id: RO:0002309 name: has exposure stimulus def: "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." [] -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 is_a: RO:0002244 ! related via exposure to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:35:04Z [Typedef] id: RO:0002312 name: evolutionary variant of -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002320 ! evolutionarily related to [Typedef] @@ -1628,7 +1627,7 @@ def: "Holds between p and c when p is a localization process (localization cover subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "regulates localization of" xsd:string is_a: RO:0002337 ! related via localization to is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -1638,7 +1637,7 @@ id: RO:0002314 name: characteristic of part of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 @@ -1654,7 +1653,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -1663,7 +1662,7 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure id: RO:0002320 name: evolutionarily related to def: "A relationship that holds via some environmental process" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." xsd:string [Typedef] @@ -1672,7 +1671,7 @@ name: ecologically related to def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] subset: ro-eco property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string [Typedef] @@ -1680,7 +1679,7 @@ id: RO:0002322 name: confers advantage in subset: ro-eco property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "adapted for" xsd:string is_a: RO:0002321 ! ecologically related to @@ -1688,7 +1687,7 @@ is_a: RO:0002321 ! ecologically related to id: RO:0002323 name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string property_value: RO:0001900 RO:0001901 @@ -1696,7 +1695,7 @@ property_value: RO:0001900 RO:0001901 id: RO:0002324 name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] @@ -1704,9 +1703,8 @@ id: RO:0002325 name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" xsd:string is_a: RO:0002323 ! mereotopologically related to @@ -1718,7 +1716,7 @@ property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a het property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string is_a: RO:0002216 ! capable of part of is_a: RO:0002329 ! part of structure that is capable of @@ -1729,7 +1727,7 @@ name: enables def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string property_value: IAO:0000118 "has" xsd:string @@ -1745,14 +1743,14 @@ transitive_over: RO:0002017 ! has component activity id: RO:0002328 name: functionally related to def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string [Typedef] id: RO:0002329 name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} is_a: RO:0002328 ! functionally related to @@ -1761,14 +1759,14 @@ is_a: RO:0002328 ! functionally related to id: RO:0002330 name: genomically related to def: "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" xsd:string [Typedef] id: RO:0002331 name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in @@ -1781,7 +1779,7 @@ id: RO:0002332 name: regulates levels of def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string is_a: RO:0002328 ! functionally related to @@ -1791,7 +1789,7 @@ id: RO:0002333 name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002328 ! functionally related to [Typedef] @@ -1799,7 +1797,7 @@ id: RO:0002334 name: regulated by def: "inverse of regulates" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "regulated by (processual)" xsd:string is_transitive: true is_a: RO:0002427 ! causally downstream of or within @@ -1809,7 +1807,7 @@ id: RO:0002335 name: negatively regulated by def: "inverse of negatively regulates" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002334 ! regulated by [Typedef] @@ -1817,14 +1815,14 @@ id: RO:0002336 name: positively regulated by def: "inverse of positively regulates" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002334 ! regulated by [Typedef] id: RO:0002337 name: related via localization to def: "A relationship that holds via some process of localization" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string [Typedef] @@ -1834,7 +1832,7 @@ def: "This relationship holds between p and l when p is a transport or localizat subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002344 ! results in transport to from or in transitive_over: BFO:0000050 @@ -1845,7 +1843,7 @@ def: "This relationship holds between p and l when p is a transport or localizat subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002344 ! results in transport to from or in transitive_over: BFO:0000050 @@ -1854,14 +1852,14 @@ id: RO:0002340 name: imports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002020 ! transports [Typedef] id: RO:0002341 name: results in transport along def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to [Typedef] @@ -1869,7 +1867,7 @@ id: RO:0002342 name: results in transport across def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002021 ! occurs across is_a: RO:0002344 ! results in transport to from or in @@ -1877,7 +1875,7 @@ is_a: RO:0002344 ! results in transport to from or in id: RO:0002343 name: results in growth of property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -1885,7 +1883,7 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure id: RO:0002344 name: results in transport to from or in property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to [Typedef] @@ -1893,7 +1891,7 @@ id: RO:0002345 name: exports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002020 ! transports [Typedef] @@ -1904,7 +1902,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of [Typedef] @@ -1914,7 +1912,7 @@ def: "p 'results in determination of' c if and only if p is a developmental proc subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of [Typedef] @@ -1923,7 +1921,7 @@ name: input of def: "inverse of has input" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002328 ! functionally related to [Typedef] @@ -1932,20 +1930,20 @@ name: output of def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002354 name: formed as result of -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002353 ! output of [Typedef] id: RO:0002355 name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -1956,21 +1954,21 @@ def: "The relationship linking a cell and its participation in a process that re subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of [Typedef] id: RO:0002357 name: results in developmental induction of def: "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of [Typedef] id: RO:0002360 name: has dendrite location property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002131 ! overlaps [Typedef] @@ -1978,7 +1976,7 @@ id: RO:0002371 name: attached to def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: RO:0002170 ! connected to @@ -1988,7 +1986,7 @@ is_a: RO:0002177 ! attached to part of id: RO:0002372 name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin is_a: RO:0002371 ! attached to @@ -1998,7 +1996,7 @@ is_a: RO:0002567 ! biomechanically related to id: RO:0002373 name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion is_a: RO:0002371 ! attached to @@ -2012,8 +2010,7 @@ comment: A has_fused_element B does not imply that A has_part some B: rather tha synonym: "has fused element" BROAD [] property_value: IAO:0000112 "false" xsd:boolean property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 is_a: RO:0002156 ! derived by descent from @@ -2022,7 +2019,7 @@ id: RO:0002375 name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 @@ -2038,7 +2035,7 @@ subset: ro-eco property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string @@ -2058,7 +2055,7 @@ comment: This is both a mereotopological relationship and a relationship defined subset: ro-eco property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string @@ -2071,7 +2068,7 @@ name: anabranch of def: "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." [] subset: ro-eco property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "anastomoses with" xsd:string is_a: RO:0002377 ! distributary of disjoint_from: RO:0002382 ! proper distributary of @@ -2082,7 +2079,7 @@ id: RO:0002379 name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: RO:0002131 ! overlaps @@ -2092,7 +2089,7 @@ name: branching part of def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] subset: ro-eco property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso FMA:85994 xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 holds_over_chain: RO:0002377 RO:0002381 @@ -2107,7 +2104,7 @@ def: "x main_stem_of y if y is a branching structure and x is a channel that tra subset: ro-eco property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: BFO:0000050 is_a: RO:0002375 ! in branching relationship with @@ -2118,7 +2115,7 @@ name: proper distributary of def: "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" [] subset: ro-eco property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002377 ! distributary of [Typedef] @@ -2127,7 +2124,7 @@ name: proper tributary of def: "x proper_tributary_of y iff x tributary_of y and x does not originate from y" [] subset: ro-eco property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002376 ! tributary of [Typedef] @@ -2135,7 +2132,7 @@ id: RO:0002384 name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002324 ! developmentally related to [Typedef] @@ -2143,7 +2140,7 @@ id: RO:0002385 name: has potential to developmentally contribute to def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] @@ -2151,7 +2148,7 @@ id: RO:0002386 name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] @@ -2159,7 +2156,7 @@ id: RO:0002387 name: has potential to develop into def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] @@ -2167,7 +2164,7 @@ id: RO:0002388 name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002387 ! has potential to develop into [Typedef] @@ -2176,7 +2173,7 @@ name: has direct input def: "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] property_value: IAO:0000112 "'protein catabolic process' SubClassOf has_direct_input some protein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly consumes" xsd:string property_value: IAO:0000232 "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" xsd:string holds_over_chain: RO:0002224 RO:0002400 @@ -2187,7 +2184,7 @@ id: RO:0002401 name: obsolete has indirect input comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_obsolete: true [Typedef] @@ -2196,7 +2193,7 @@ name: obsolete has direct output def: "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. " [] property_value: IAO:0000112 "translation SubClassOf has_direct_output some protein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly produces" xsd:string is_obsolete: true @@ -2205,7 +2202,7 @@ id: RO:0002403 name: obsolete has indirect output comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002411 RO:0002402 is_obsolete: true @@ -2214,7 +2211,7 @@ id: RO:0002404 name: causally downstream of def: "inverse of upstream of" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: BFO:0000062 is_a: RO:0002427 ! causally downstream of or within inverse_of: RO:0002411 ! causally upstream of @@ -2223,7 +2220,7 @@ inverse_of: RO:0002411 ! causally upstream of id: RO:0002405 name: immediately causally downstream of property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002404 ! causally downstream of inverse_of: RO:0002412 ! immediately causally upstream of @@ -2238,7 +2235,7 @@ replaced_by: RO:0002629 id: RO:0002407 name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 holds_over_chain: RO:0002409 RO:0002409 @@ -2260,7 +2257,7 @@ replaced_by: RO:0002630 id: RO:0002409 name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 holds_over_chain: RO:0002630 RO:0002409 @@ -2275,7 +2272,7 @@ id: RO:0002410 name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] @@ -2284,7 +2281,7 @@ name: causally upstream of def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: BFO:0000063 is_a: RO:0002418 ! causally upstream of or within @@ -2293,7 +2290,7 @@ is_a: RO:0002418 ! causally upstream of or within id: RO:0002412 name: immediately causally upstream of def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: RO:0002090 is_a: RO:0002411 ! causally upstream of @@ -2303,7 +2300,7 @@ id: RO:0002413 name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string @@ -2316,7 +2313,7 @@ id: RO:0002414 name: transitively provides input for def: "transitive form of directly_provides_input_for" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." xsd:string property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string is_transitive: true @@ -2328,7 +2325,7 @@ name: causally upstream of or within def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true is_a: RO:0002501 ! causal relation between processes @@ -2339,19 +2336,19 @@ id: RO:0002424 name: differs in comment: This is an exploratory relation property_value: IAO:0000116 "false" xsd:boolean -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions xsd:anyURI [Typedef] id: RO:0002425 name: differs in attribute of -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002424 ! differs in [Typedef] id: RO:0002426 name: differs in attribute -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002424 ! differs in [Typedef] @@ -2359,7 +2356,7 @@ id: RO:0002427 name: causally downstream of or within def: "inverse of causally upstream of or within" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: RO:0002501 ! causal relation between processes @@ -2368,7 +2365,7 @@ is_a: RO:0002501 ! causal relation between processes id: RO:0002428 name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002327 RO:0002211 holds_over_chain: RO:0002331 RO:0002211 is_a: RO:0002263 ! acts upstream of @@ -2378,7 +2375,7 @@ is_a: RO:0002431 ! involved in or involved in regulation of id: RO:0002429 name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002428 holds_over_chain: RO:0002327 RO:0002213 holds_over_chain: RO:0002331 RO:0002213 @@ -2388,7 +2385,7 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002430 name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 holds_over_chain: RO:0002327 RO:0002212 holds_over_chain: RO:0002331 RO:0002212 @@ -2399,7 +2396,7 @@ id: RO:0002431 name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: RO:0002264 ! acts upstream of or within is_a: RO:0002328 ! functionally related to @@ -2411,7 +2408,7 @@ name: is active in def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] synonym: "enables activity in" EXACT [] property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} is_a: RO:0002131 ! overlaps @@ -2421,7 +2418,7 @@ is_a: RO:0002328 ! functionally related to id: RO:0002433 name: contributes to morphology of def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002131 ! overlaps [Typedef] @@ -2433,7 +2430,7 @@ synonym: "in pairwise interaction with" EXACT [] property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI is_symmetric: true @@ -2443,7 +2440,7 @@ id: RO:0002435 name: genetically interacts with property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: RO:0002434 ! interacts with @@ -2453,7 +2450,7 @@ id: RO:0002436 name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 @@ -2465,7 +2462,7 @@ id: RO:0002437 name: biotically interacts with def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string @@ -2478,7 +2475,7 @@ id: RO:0002438 name: trophically interacts with def: "An interaction relationship in which the partners are related via a feeding relationship." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: RO:0002574 ! participates in a biotic-biotic interaction with @@ -2489,9 +2486,9 @@ def: "An interaction relationship involving a predation process, where the subje subset: ro-eco property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Jorrit Poelen" xsd:string -property_value: IAO:0000117 "Katja Shulz" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7134-3324 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string @@ -2504,7 +2501,7 @@ id: RO:0002440 name: symbiotically interacts with def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true @@ -2515,7 +2512,7 @@ id: RO:0002441 name: commensually interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: RO:0002440 ! symbiotically interacts with @@ -2524,7 +2521,7 @@ id: RO:0002442 name: mutualistically interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: RO:0002440 ! symbiotically interacts with @@ -2533,7 +2530,7 @@ id: RO:0002443 name: interacts with via parasite-host interaction def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: RO:0002440 ! symbiotically interacts with @@ -2544,7 +2541,7 @@ name: parasite of subset: ro-eco synonym: "direct parasite of" EXACT [] property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string is_a: RO:0002443 ! interacts with via parasite-host interaction @@ -2556,7 +2553,7 @@ id: RO:0002445 name: parasitized by subset: ro-eco synonym: "directly parasitized by" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string @@ -2570,7 +2567,7 @@ def: "A biotic interaction relationship in which one partner is an organism and subset: ro-eco synonym: "semibiotically interacts with" RELATED [] property_value: IAO:0000112 "Porifiera attaches to substrate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: RO:0002437 ! biotically interacts with @@ -2578,7 +2575,7 @@ is_a: RO:0002437 ! biotically interacts with id: RO:0002447 name: phosphorylates property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: RO:0002436 ! molecularly interacts with @@ -2587,8 +2584,8 @@ id: RO:0002448 name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0002436 ! molecularly interacts with is_a: RO:0011002 ! regulates activity of @@ -2597,8 +2594,8 @@ id: RO:0002449 name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly inhibits" xsd:string is_a: RO:0002448 ! directly regulates activity of @@ -2607,8 +2604,8 @@ id: RO:0002450 name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly activates" xsd:string is_a: RO:0002448 ! directly regulates activity of @@ -2618,21 +2615,21 @@ name: transmitted by def: "A relationship that holds between a disease and organism" [] property_value: IAO:0000112 "all dengue disease transmitted by some mosquito" xsd:string property_value: IAO:0000116 "Add domain and range constraints" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0002452 name: has symptom def: "A relation that holds between a disease or an organism and a phenotype" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002200 ! has phenotype [Typedef] id: RO:0002453 name: host of subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string is_a: RO:0002440 ! symbiotically interacts with @@ -2641,7 +2638,7 @@ id: RO:0002454 name: has host def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string is_a: RO:0002440 ! symbiotically interacts with @@ -2651,7 +2648,7 @@ name: pollinates subset: ro-eco property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string is_a: RO:0002442 ! mutualistically interacts with @@ -2661,7 +2658,7 @@ inverse_of: RO:0002456 ! pollinated by id: RO:0002456 name: pollinated by subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string @@ -2671,7 +2668,7 @@ is_a: RO:0002442 ! mutualistically interacts with id: RO:0002457 name: acquires nutrients from subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string is_a: RO:0002438 ! trophically interacts with inverse_of: RO:0002469 ! provides nutrients for @@ -2682,7 +2679,7 @@ name: preyed upon by def: "inverse of preys on" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string @@ -2694,7 +2691,7 @@ id: RO:0002459 name: is vector for subset: ro-eco property_value: IAO:0000112 "Anopheles is a vector for Plasmodium" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" xsd:string is_a: RO:0002574 ! participates in a biotic-biotic interaction with inverse_of: RO:0002460 ! has vector @@ -2703,71 +2700,71 @@ inverse_of: RO:0002460 ! has vector id: RO:0002460 name: has vector subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002461 name: partner in -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string [Typedef] id: RO:0002462 name: subject participant in -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: RO:0002461 ! partner in [Typedef] id: RO:0002463 name: target participant in -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: RO:0002461 ! partner in [Typedef] id: RO:0002464 name: helper property (not for use in curation) -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string [Typedef] id: RO:0002465 name: is symbiosis -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002563 ! interaction relation helper property [Typedef] id: RO:0002466 name: is commensalism -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002465 ! is symbiosis [Typedef] id: RO:0002467 name: is mutualism -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002465 ! is symbiosis [Typedef] id: RO:0002468 name: is parasitism -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002465 ! is symbiosis [Typedef] id: RO:0002469 name: provides nutrients for subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002438 ! trophically interacts with [Typedef] id: RO:0002470 name: eats subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: RO:0002438 ! trophically interacts with @@ -2775,7 +2772,7 @@ is_a: RO:0002438 ! trophically interacts with id: RO:0002471 name: is eaten by subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string is_a: RO:0002438 ! trophically interacts with @@ -2785,7 +2782,7 @@ id: RO:0002472 name: is evidence for def: "A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and \nthe a supports either the existence of b, or the truth value of b." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002616 ! related via evidence or inference to inverse_of: RO:0002558 ! has evidence @@ -2795,7 +2792,7 @@ name: composed primarily of def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] subset: ro-eco property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 is_a: BFO:0000051 @@ -2805,7 +2802,7 @@ id: RO:0002476 name: child nucleus of def: "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" [] property_value: IAO:0000112 "ABal nucleus child nucleus of ABa nucleus (in C elegans)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." xsd:string is_a: RO:0002258 ! developmentally preceded by @@ -2813,14 +2810,14 @@ is_a: RO:0002258 ! developmentally preceded by id: RO:0002477 name: child nucleus of in hermaphrodite def: "A child nucleus relationship in which the cells are part of a hermaphroditic organism" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002476 ! child nucleus of [Typedef] id: RO:0002478 name: child nucleus of in male def: "A child nucleus relationship in which the cells are part of a male organism" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002476 ! child nucleus of [Typedef] @@ -2828,7 +2825,7 @@ id: RO:0002479 name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} [Typedef] @@ -2836,26 +2833,26 @@ id: RO:0002480 name: ubiquitinates def: "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" [] property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002436 ! molecularly interacts with [Typedef] id: RO:0002481 name: is kinase activity -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002482 name: is ubiquitination -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002485 name: receives input from property_value: IAO:0000116 "See notes for inverse relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002170 ! connected to inverse_of: RO:0002486 ! sends output to @@ -2863,20 +2860,20 @@ inverse_of: RO:0002486 ! sends output to id: RO:0002486 name: sends output to property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002170 ! connected to [Typedef] id: RO:0002487 name: relation between physical entity and a process or stage -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." xsd:string [Typedef] id: RO:0002488 name: existence starts during def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002583 BFO:0000050 is_a: RO:0002490 ! existence overlaps is_a: RO:0002496 ! existence starts during or after @@ -2886,7 +2883,7 @@ transitive_over: BFO:0000050 id: RO:0002489 name: existence starts with def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002488 ! existence starts during [Typedef] @@ -2894,7 +2891,7 @@ id: RO:0002490 name: existence overlaps def: "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002487 ! relation between physical entity and a process or stage [Typedef] @@ -2903,7 +2900,7 @@ name: existence starts and ends during def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. synonym: "exists during" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002488 ! existence starts during is_a: RO:0002492 ! existence ends during @@ -2912,7 +2909,7 @@ id: RO:0002492 name: existence ends during def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002593 BFO:0000050 is_a: RO:0002490 ! existence overlaps is_a: RO:0002497 ! existence ends during or before @@ -2923,14 +2920,14 @@ id: RO:0002493 name: existence ends with def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002492 ! existence ends during [Typedef] id: RO:0002494 name: transformation of def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002202 ! develops from @@ -2938,7 +2935,7 @@ is_a: RO:0002202 ! develops from id: RO:0002495 name: immediate transformation of def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002494 is_a: RO:0002207 ! directly develops from is_a: RO:0002494 ! transformation of @@ -2948,7 +2945,7 @@ id: RO:0002496 name: existence starts during or after def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000050 RO:0002496 holds_over_chain: RO:0002258 RO:0002496 is_a: RO:0002487 ! relation between physical entity and a process or stage @@ -2961,7 +2958,7 @@ id: RO:0002497 name: existence ends during or before def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000050 RO:0002497 holds_over_chain: RO:0002286 RO:0002497 is_a: RO:0002487 ! relation between physical entity and a process or stage @@ -2981,7 +2978,7 @@ inverse_of: RO:0002608 ! process has causal agent id: RO:0002501 name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string is_a: RO:0002410 ! causally related to @@ -2989,7 +2986,7 @@ is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002502 name: depends on -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso BFO:0000169 [Typedef] @@ -2997,7 +2994,7 @@ id: RO:0002503 name: towards def: "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" [] property_value: IAO:0000116 "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 is_a: RO:0002502 ! depends on @@ -3007,14 +3004,14 @@ name: has intermediate def: "p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c" [] subset: ro-eco property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string [Typedef] id: RO:0002506 name: causal relation between entities property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string is_a: RO:0002410 ! causally related to @@ -3024,11 +3021,11 @@ id: RO:0002507 name: determined by def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] subset: ro-eco -property_value: http://purl.org/dc/terms/creator "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/creator "Pier Buttigieg" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-4366-3088 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "A coral reef environment is determined by a particular coral reef" xsd:string property_value: IAO:0000116 "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602 property_value: IAO:0000589 "determined by (system to material entity)" xsd:string is_a: BFO:0000050 @@ -3042,7 +3039,7 @@ name: determines def: "inverse of determined by" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "determines (material entity to system)" xsd:string is_a: RO:0002566 ! causally influences @@ -3051,7 +3048,7 @@ id: RO:0002509 name: determined by part of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002507 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002506 ! causal relation between entities @@ -3060,7 +3057,7 @@ is_a: RO:0002506 ! causal relation between entities id: RO:0002510 name: transcribed from def: "x is transcribed from y if and only if x is synthesized from template y" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to inverse_of: RO:0002511 ! transcribed to @@ -3070,7 +3067,7 @@ id: RO:0002511 name: transcribed to def: "inverse of transcribed from" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to @@ -3078,7 +3075,7 @@ is_a: RO:0002330 ! genomically related to id: RO:0002512 name: ribosomal translation of def: "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to inverse_of: RO:0002513 ! ribosomally translates to @@ -3087,7 +3084,7 @@ inverse_of: RO:0002513 ! ribosomally translates to id: RO:0002513 name: ribosomally translates to def: "inverse of ribosomal translation of" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to @@ -3096,7 +3093,7 @@ id: RO:0002514 name: sequentially related to def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string @@ -3109,7 +3106,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcript" xsd:string property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002527 ! does not overlap sequence of @@ -3119,7 +3116,7 @@ name: has start sequence def: "x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3132,7 +3129,7 @@ name: is start sequence of def: "inverse of has start sequence" [] subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3144,7 +3141,7 @@ name: has end sequence def: "x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3157,7 +3154,7 @@ name: is end sequence of def: "inverse of has end sequence" [] subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3169,7 +3166,7 @@ name: is consecutive sequence of def: "x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002524 ! has subsequence @@ -3179,7 +3176,7 @@ name: is sequentially aligned with def: "x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: RO:0002514 ! sequentially related to @@ -3189,7 +3186,7 @@ name: bounds sequence of def: "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002514 ! sequentially related to inverse_of: RO:0002523 ! is bound by sequence of @@ -3200,16 +3197,16 @@ name: is bound by sequence of def: "inverse of bounds sequence of" [] subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002514 ! sequentially related to [Typedef] id: RO:0002524 name: has subsequence -def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3224,7 +3221,7 @@ name: is subsequence of def: "inverse of has subsequence" [] subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: BFO:0000050 @@ -3234,9 +3231,9 @@ is_a: RO:0002526 ! overlaps sequence of [Typedef] id: RO:0002526 name: overlaps sequence of -def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002524 RO:0002525 is_symmetric: true is_a: RO:0002131 ! overlaps @@ -3245,9 +3242,9 @@ is_a: RO:0002514 ! sequentially related to [Typedef] id: RO:0002527 name: does not overlap sequence of -def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "disconnected from" xsd:string is_symmetric: true is_a: RO:0002514 ! sequentially related to @@ -3257,7 +3254,7 @@ id: RO:0002528 name: is upstream of sequence of def: "inverse of downstream of sequence of" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002527 ! does not overlap sequence of @@ -3266,7 +3263,7 @@ id: RO:0002529 name: is downstream of sequence of def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002527 ! does not overlap sequence of inverse_of: RO:0002529 ! is downstream of sequence of @@ -3277,7 +3274,7 @@ name: is immediately downstream of sequence of def: "x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002529 is_a: RO:0002515 ! sequentially adjacent to is_a: RO:0002529 ! is downstream of sequence of @@ -3288,7 +3285,7 @@ name: is immediately upstream of sequence of def: "inverse of immediately downstream of" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002515 ! sequentially adjacent to is_a: RO:0002528 ! is upstream of sequence of @@ -3297,7 +3294,7 @@ id: RO:0002551 name: has skeleton def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string is_a: BFO:0000051 @@ -3308,7 +3305,7 @@ is_asymmetric: true id: RO:0002552 name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -3320,7 +3317,7 @@ subset: ro-eco synonym: "epiparasite of" RELATED [] synonym: "hyperparasitoid of" NARROW [] property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string holds_over_chain: RO:0002444 RO:0002444 @@ -3336,7 +3333,7 @@ subset: RO:0002259 synonym: "has epiparasite" RELATED [] synonym: "has hyperparasite" RELATED [] synonym: "hyperparasitoidized by" RELATED [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002445 RO:0002445 is_a: RO:0002453 ! host of @@ -3344,7 +3341,7 @@ is_a: RO:0002453 ! host of id: RO:0002555 name: allelopath of subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string @@ -3354,7 +3351,7 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with id: RO:0002556 name: pathogen of subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002454 ! has host inverse_of: RO:0002557 ! has pathogen @@ -3362,7 +3359,7 @@ inverse_of: RO:0002557 ! has pathogen id: RO:0002557 name: has pathogen subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002453 ! host of [Typedef] @@ -3372,14 +3369,14 @@ def: "inverse of is evidence for" [] comment: x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/25052702 is_a: RO:0002616 ! related via evidence or inference to [Typedef] id: RO:0002559 name: causally influenced by -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: RO:0002506 ! causal relation between entities @@ -3388,7 +3385,7 @@ inverse_of: RO:0002566 ! causally influences [Typedef] id: RO:0002563 name: interaction relation helper property -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI is_a: RO:0002464 ! helper property (not for use in curation) @@ -3396,7 +3393,7 @@ is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 name: molecular interaction relation helper property -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002563 ! interaction relation helper property [Typedef] @@ -3406,7 +3403,7 @@ def: "Holds between p and c when p is locomotion process and the outcome of this subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "" xsd:string is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -3414,8 +3411,8 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure id: RO:0002566 name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string is_a: RO:0002506 ! causal relation between entities @@ -3424,7 +3421,7 @@ is_a: RO:0002506 ! causal relation between entities id: RO:0002567 name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string is_a: RO:0002328 ! functionally related to @@ -3432,7 +3429,7 @@ is_a: RO:0002328 ! functionally related to id: RO:0002568 name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string is_a: RO:0002567 ! biomechanically related to @@ -3442,7 +3439,7 @@ name: has branching part def: "inverse of branching part of" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: BFO:0000051 is_a: RO:0002375 ! in branching relationship with @@ -3452,7 +3449,7 @@ id: RO:0002570 name: conduit for def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 UBERON:cjm xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string is_a: RO:0002131 ! overlaps @@ -3462,7 +3459,7 @@ id: RO:0002571 name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:cjm xsd:string is_a: BFO:0000050 @@ -3471,7 +3468,7 @@ id: RO:0002572 name: luminal space of def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002571 ! lumen of [Typedef] @@ -3479,7 +3476,7 @@ id: RO:0002573 name: has modifier def: "A relation that holds between an attribute or a qualifier and another attribute." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." xsd:string @@ -3487,7 +3484,7 @@ property_value: IAO:0000232 "This relation is intended to be used in combination id: RO:0002574 name: participates in a biotic-biotic interaction with subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: RO:0002437 ! biotically interacts with @@ -3496,7 +3493,7 @@ id: RO:0002576 name: skeleton of def: "inverse of has skeleton" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: BFO:0000050 [Typedef] @@ -3506,7 +3503,7 @@ def: "p directly regulates q iff p is immediately causally upstream of q and p r subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string property_value: RO:0002575 RO:0002211 @@ -3524,7 +3521,7 @@ id: RO:0002584 name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000051 RO:0002215 is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process @@ -3591,7 +3588,7 @@ id: RO:0002595 name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002410 ! causally related to @@ -3857,7 +3854,7 @@ def: "a produces b if some process that occurs_in a has_output b, where a and b comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 inverse_of: RO:0003001 ! produced by [Typedef] @@ -3866,20 +3863,20 @@ name: produced by def: "a produced_by b iff some process that occurs_in b has_output a." [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 [Typedef] id: RO:0003002 name: represses expression of def: "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0002449 ! directly negatively regulates activity of [Typedef] id: RO:0003003 name: increases expression of def: "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0002450 ! directly positively regulates activity of [Typedef] @@ -3887,7 +3884,7 @@ id: RO:0003301 name: has role in modeling def: "A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." [] comment: The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate. -property_value: IAO:0000117 "Matthew Brush" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-1048-5019 property_value: IAO:0000118 "is used to study" xsd:string is_asymmetric: true @@ -3964,7 +3961,7 @@ name: condition has genetic basis in property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string is_a: RO:0002410 ! causally related to inverse_of: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:38:20Z [Typedef] @@ -3974,7 +3971,7 @@ property_value: seeAlso Orphanet:410295 property_value: seeAlso Orphanet:410296 is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004011 ! is causal gain of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:20Z [Typedef] @@ -3982,7 +3979,7 @@ id: RO:0004002 name: has material basis in loss of function germline mutation in is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004012 ! is causal loss of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:37Z [Typedef] @@ -3991,7 +3988,7 @@ name: has material basis in germline mutation in property_value: seeAlso Orphanet:317343 is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004013 ! is causal germline mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:54Z [Typedef] @@ -4000,7 +3997,7 @@ name: has material basis in somatic mutation in property_value: seeAlso Orphanet:317344 is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004014 ! is causal somatic mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z [Typedef] @@ -4008,7 +4005,7 @@ id: RO:0004005 name: has major susceptibility factor is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004015 ! is causal susceptibility factor for -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:26Z [Typedef] @@ -4016,7 +4013,7 @@ id: RO:0004006 name: has partial material basis in germline mutation in is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004016 ! is causal germline mutation partially giving rise to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:57Z [Typedef] @@ -4024,7 +4021,7 @@ id: RO:0004007 name: has primary input or output def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -4034,7 +4031,7 @@ def: "p has primary output c if (a) p has output c and (b) the goal of process i subset: http://purl.obolibrary.org/obo/valid_for_go_ontology is_a: RO:0002234 ! has output is_a: RO:0004007 ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -4044,7 +4041,7 @@ def: "p has primary input c if (a) p has input c and (b) the goal of process is subset: http://purl.obolibrary.org/obo/valid_for_go_ontology is_a: RO:0002233 ! has input is_a: RO:0004007 ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -4052,7 +4049,7 @@ id: RO:0004010 name: is genetic basis for condition property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string is_a: RO:0004018 ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:53:08Z [Typedef] @@ -4061,7 +4058,7 @@ name: is causal gain of function germline mutation of in def: "Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." [] property_value: seeAlso Orphanet:410296 is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:55:51Z [Typedef] @@ -4070,7 +4067,7 @@ name: is causal loss of function germline mutation of in def: "Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." [] property_value: seeAlso Orphanet:410295 is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:06Z [Typedef] @@ -4080,7 +4077,7 @@ def: "Relates a gene to condition, such that a mutation in this gene is sufficie property_value: seeAlso Orphanet:317343 is_a: RO:0003303 ! causes condition is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:40Z [Typedef] @@ -4090,7 +4087,7 @@ def: "Relates a gene to condition, such that a mutation in this gene is sufficie property_value: seeAlso Orphanet:317344 is_a: RO:0003303 ! causes condition is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:07Z [Typedef] @@ -4099,7 +4096,7 @@ name: is causal susceptibility factor for def: "Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]." [] property_value: seeAlso Orphanet:317345 is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:43Z [Typedef] @@ -4109,7 +4106,7 @@ def: "Relates a gene to condition, such that a mutation in this gene partially c property_value: seeAlso Orphanet:317346 is_a: RO:0003304 ! contributes to condition is_a: RO:0004010 ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:58:43Z [Typedef] @@ -4117,14 +4114,14 @@ id: RO:0004017 name: realizable has basis in is_a: RO:0002410 ! causally related to inverse_of: RO:0004018 ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:01Z [Typedef] id: RO:0004018 name: is basis for realizable is_a: RO:0002410 ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:29Z [Typedef] @@ -4132,7 +4129,7 @@ id: RO:0004019 name: disease has basis in is_a: RO:0004017 ! realizable has basis in is_a: RO:0004023 ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:26:47Z [Typedef] @@ -4141,7 +4138,7 @@ name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string is_a: RO:0004019 ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z [Typedef] @@ -4150,7 +4147,7 @@ name: disease has basis in disruption of def: "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." [] property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string is_a: RO:0004019 ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:37:52Z [Typedef] @@ -4159,7 +4156,7 @@ name: disease has basis in feature def: "A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature." [] is_a: RO:0002200 ! has phenotype is_a: RO:0004019 ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:46:07Z [Typedef] @@ -4168,7 +4165,7 @@ name: causal relationship with disease as subject property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." xsd:string is_a: RO:0002410 ! causally related to is_a: RO:0040035 ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:50:54Z [Typedef] @@ -4179,7 +4176,7 @@ property_value: IAO:0000589 "disease causes disruption of (disease to process)" holds_over_chain: RO:0004025 RO:0002215 is_a: RO:0004023 ! causal relationship with disease as subject transitive_over: BFO:0000050 -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:51:09Z [Typedef] @@ -4188,7 +4185,7 @@ name: disease causes dysfunction of property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string is_a: RO:0004023 ! causal relationship with disease as subject transitive_over: BFO:0000050 -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z [Typedef] @@ -4198,7 +4195,7 @@ def: "A relationship between a disease and an anatomical entity where the diseas property_value: IAO:0000116 "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" xsd:string property_value: IAO:0000232 "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." xsd:string is_a: RO:0040035 ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T04:06:02Z [Typedef] @@ -4206,7 +4203,7 @@ id: RO:0004027 name: disease has inflammation site def: "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" [] is_a: RO:0004026 ! disease has location -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:37:31Z [Typedef] @@ -4215,7 +4212,7 @@ name: realized in response to stimulus def: "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." [] holds_over_chain: RO:0009501 RO:0002233 is_a: RO:0002410 ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:45:49Z [Typedef] @@ -4223,7 +4220,7 @@ id: RO:0004029 name: disease has feature def: "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." [] is_a: RO:0040035 ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:50:53Z [Typedef] @@ -4231,7 +4228,7 @@ id: RO:0004030 name: disease arises from alteration in structure def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." [] is_a: RO:0004019 ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z [Typedef] @@ -4240,7 +4237,7 @@ name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] holds_over_chain: RO:0002327 BFO:0000051 is_a: RO:0002328 ! functionally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z [Typedef] @@ -4251,7 +4248,7 @@ property_value: RO:0004049 RO:0002264 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z [Typedef] @@ -4261,7 +4258,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002264 holds_over_chain: RO:0002327 RO:0004046 is_a: RO:0002264 ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z [Typedef] @@ -4274,7 +4271,7 @@ property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of, holds_over_chain: RO:0002327 RO:0002304 is_a: RO:0002263 ! acts upstream of is_a: RO:0004032 ! acts upstream of or within, positive effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:14Z [Typedef] @@ -4287,7 +4284,7 @@ property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of, holds_over_chain: RO:0002327 RO:0002305 is_a: RO:0002263 ! acts upstream of is_a: RO:0004033 ! acts upstream of or within, negative effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:22Z [Typedef] @@ -4295,7 +4292,7 @@ id: RO:0004046 name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 is_a: RO:0002418 ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -4303,7 +4300,7 @@ id: RO:0004047 name: causally upstream of or within, positive effect property_value: RO:0004049 RO:0002418 is_a: RO:0002418 ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -4384,7 +4381,7 @@ def: "\"has substance added\" is a relation existing between a (physical) entity property_value: IAO:0000112 "muffin 'has substance added' some 'baking soda'" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." xsd:string -property_value: IAO:0000117 "Damion Dooley" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 [Typedef] id: RO:0009002 @@ -4392,7 +4389,7 @@ name: has substance removed def: "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." [] property_value: IAO:0000112 "'egg white' 'has substance removed' some 'egg yolk'" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Damion Dooley" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 [Typedef] id: RO:0009003 @@ -4400,7 +4397,7 @@ name: immersed in def: "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." [] property_value: IAO:0000112 "sardines 'immersed in' some 'oil and mustard'" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Damion Dooley" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 [Typedef] id: RO:0009004 @@ -4408,7 +4405,7 @@ name: has consumer def: "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect." [] property_value: IAO:0000112 "sardine has consumer some homo sapiens" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Damion Dooley" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 [Typedef] id: RO:0009005 @@ -4416,7 +4413,7 @@ name: has primary substance added def: "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." [] property_value: IAO:0000112 "bread 'has primary substance added' some 'flour'" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Damion Dooley" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 is_a: RO:0009001 ! has substance added [Typedef] @@ -4424,10 +4421,10 @@ id: RO:0009501 name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] synonym: "triggered by process" EXACT [RO:cjm] -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "David Osumi-Sutherland" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string @@ -4460,56 +4457,56 @@ property_value: IAO:0000119 "[072-ISO]" xsd:string id: RO:0011002 name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0002566 ! causally influences [Typedef] id: RO:0011003 name: regulates quantity of def: "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0002566 ! causally influences [Typedef] id: RO:0011004 name: indirectly regulates activity of def: "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011002 ! regulates activity of [Typedef] id: RO:0011007 name: decreases by repression quantity of def: "The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011023 ! indirectly negatively regulates quantity of [Typedef] id: RO:0011008 name: increases by expression quantity of def: "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011024 ! indirectly positively regulates quantity of [Typedef] id: RO:0011009 name: directly positively regulates quantity of def: "The entity A has an activity that directly positively regulates the quantity of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011021 ! directly regulates quantity of [Typedef] id: RO:0011010 name: directly negatively regulates quantity of def: "The entity A has an activity that directly negatively regulates the quantity of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011021 ! directly regulates quantity of [Typedef] id: RO:0011013 name: indirectly positively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly activates" xsd:string is_a: RO:0011004 ! indirectly regulates activity of @@ -4518,7 +4515,7 @@ id: RO:0011014 name: destabilizes quantity of def: "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." [] property_value: IAO:0000112 "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011010 ! directly negatively regulates quantity of [Typedef] @@ -4526,14 +4523,14 @@ id: RO:0011015 name: stabilizes quantity of def: "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." [] property_value: IAO:0000112 "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011009 ! directly positively regulates quantity of [Typedef] id: RO:0011016 name: indirectly negatively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly inhibits" xsd:string is_a: RO:0011004 ! indirectly regulates activity of @@ -4541,28 +4538,28 @@ is_a: RO:0011004 ! indirectly regulates activity of id: RO:0011021 name: directly regulates quantity of def: "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011003 ! regulates quantity of [Typedef] id: RO:0011022 name: indirectly regulates quantity of def: "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011003 ! regulates quantity of [Typedef] id: RO:0011023 name: indirectly negatively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011022 ! indirectly regulates quantity of [Typedef] id: RO:0011024 name: indirectly positively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011022 ! indirectly regulates quantity of [Typedef] @@ -4781,7 +4778,7 @@ name: has exemplar data def: "A relation between a material entity and some data in which the data is taken as exemplifying the material entity." [] property_value: IAO:0000112 "transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data])" xsd:string property_value: IAO:0000116 "C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C." xsd:string -property_value: IAO:0000117 "Patrick Ray" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-5260-9315 property_value: IAO:0000232 "This relation is not meant to capture the relation between occurrents and data." xsd:string inverse_of: RO:0015002 ! exemplar data of transitive_over: RO:0015003 ! subcluster of @@ -4789,14 +4786,14 @@ transitive_over: RO:0015003 ! subcluster of [Typedef] id: RO:0015002 name: exemplar data of -property_value: IAO:0000117 "Patrick Ray" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-5260-9315 [Typedef] id: RO:0015003 name: subcluster of def: "A relation between a group and another group it is part of but does not fully constitute." [] property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." xsd:string -property_value: IAO:0000117 "Shawn Tan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true is_a: BFO:0000050 @@ -4883,7 +4880,7 @@ property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:s id: RO:0016002 name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string is_a: RO:0016001 ! has phenotype or disease @@ -4903,8 +4900,8 @@ name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 +property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string holds_over_chain: RO:0002215 RO:0002233 @@ -4996,13 +4993,13 @@ id: RO:0040035 name: disease relationship def: "This relation groups relations between diseases and any other kind of entity." [] property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z [Typedef] id: RO:0040036 name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z diff --git a/subsets/ro-eco.owl b/subsets/ro-eco.owl index 6f1e3fe7..f85e1f99 100644 --- a/subsets/ro-eco.owl +++ b/subsets/ro-eco.owl @@ -147,7 +147,7 @@ tooth SubClassOf 'never in taxon' value 'Aves' x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. - Chris Mungall + Class: ?X DisjointWith: RO_0002162 some ?Y @@ -242,7 +242,7 @@ WHERE { S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. - https://orcid.org/0000-0002-6601-2165 + This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost dubious for taxon @@ -256,7 +256,7 @@ WHERE { S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S - https://orcid.org/0000-0002-6601-2165 + PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> @@ -631,7 +631,7 @@ Where we have an annotation assertion "directly P" "is direct form of" "P" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' - Chris Mungall + is direct form of @@ -643,7 +643,7 @@ Where we have an annotation assertion relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y - Chris Mungall + is indirect form of @@ -791,7 +791,7 @@ Where we have an annotation assertion true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation. - cjm + nominally disjoint with @@ -802,7 +802,7 @@ Where we have an annotation assertion Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" - cjm + 2018-03-13T23:59:29Z is directional form of @@ -813,7 +813,7 @@ Where we have an annotation assertion - cjm + 2018-03-14T00:03:16Z is positive form of @@ -824,7 +824,7 @@ Where we have an annotation assertion - cjm + 2018-03-14T00:03:24Z is negative form of @@ -837,7 +837,7 @@ Where we have an annotation assertion part-of is homeomorphic for independent continuants. R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. - cjm + 2018-10-21T19:46:34Z R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. is homeomorphic for @@ -1161,7 +1161,7 @@ Where we have an annotation assertion OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. - David Osumi-Sutherland + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). @@ -1177,7 +1177,7 @@ Where we have an annotation assertion OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first. - David Osumi-Sutherland + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). @@ -1193,7 +1193,7 @@ Where we have an annotation assertion OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first. - David Osumi-Sutherland + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). @@ -1308,7 +1308,7 @@ range: spatial region or site (immaterial continuant) May be obsoleted, see https://github.com/oborel/obo-relations/issues/260 - David Osumi-Sutherland + aligned with @@ -1319,7 +1319,7 @@ range: spatial region or site (immaterial continuant) - David Osumi-Sutherland + @@ -1329,7 +1329,7 @@ range: spatial region or site (immaterial continuant) A relation that holds between two neurons that are electrically coupled via gap junctions. - David Osumi-Sutherland + electrically_synapsed_to @@ -1341,7 +1341,7 @@ range: spatial region or site (immaterial continuant) The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). - David Osumi-Sutherland + tracheates @@ -1351,7 +1351,7 @@ range: spatial region or site (immaterial continuant) - David Osumi-Sutherland + http://www.ncbi.nlm.nih.gov/pubmed/22402613 innervated_by @@ -1363,7 +1363,7 @@ range: spatial region or site (immaterial continuant) - David Osumi-Sutherland + has synaptic terminal of @@ -1383,7 +1383,7 @@ range: spatial region or site (immaterial continuant) has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland + A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. bounding layer of @@ -1397,7 +1397,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. Note from NCEAS meeting: consider changing primary label - David Osumi-Sutherland + Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. coincident with @@ -1410,7 +1410,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g. - David Osumi-Sutherland + x 'cell expresses' y iff: cell(x) AND gene(y) @@ -1427,7 +1427,7 @@ AND t has_input y x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - David Osumi-Sutherland + regulates in other organism @@ -1441,7 +1441,7 @@ AND t has_input y A relationship that holds between a process that regulates a transport process and the entity transported by that process. - David Osumi-Sutherland + regulates transport of @@ -1685,7 +1685,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + @@ -1697,7 +1697,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + di Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. encompasses @@ -1720,7 +1720,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + @@ -1757,7 +1757,7 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure that its soma is part of. - David Osumi-Sutherland + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -1774,7 +1774,7 @@ Examples include: the relationship between two channels collected simultaneously relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - David Osumi-Sutherland + fasciculates with (forall (?x ?y) (iff @@ -1813,9 +1813,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure its axon forms (chemical) synapses in. - Chris Mungall - David Osumi-Sutherland - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -1834,8 +1833,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -1851,9 +1850,9 @@ Examples include: the relationship between two channels collected simultaneously Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - Alexander Diehl - Chris Mungall - Lindsay Cowell + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) @@ -1869,8 +1868,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -1887,8 +1886,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -1905,8 +1904,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) @@ -1921,8 +1920,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1939,8 +1938,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1961,8 +1960,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - Chris Mungall - David Osumi-Sutherland + + synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( @@ -1990,8 +1989,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -2057,8 +2056,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -2086,8 +2085,8 @@ N1 SubclassOf ( Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -2109,7 +2108,7 @@ N1 SubclassOf ( A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - David Osumi-Sutherland + has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) @@ -2167,7 +2166,7 @@ N1 SubclassOf ( The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - David Osumi-Sutherland + has fasciculating component (forall (?x ?y) (iff @@ -2210,7 +2209,7 @@ N1 SubclassOf ( Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - David Osumi-Sutherland + <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -2226,7 +2225,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. X continuous_with Y if and only if X and Y share a fiat boundary. - David Osumi-Sutherland + connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) @@ -2327,7 +2326,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria - Chris Mungall + only in taxon @@ -2378,8 +2377,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - Chris Mungall - Jennifer Deegan + + @@ -2397,7 +2396,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - Chris Mungall + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) @@ -2516,7 +2515,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - Chris Mungall + has phenotype @@ -2529,7 +2528,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of has phenotype - Chris Mungall + phenotype of @@ -2545,10 +2544,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - Terry Meehan + + + + This is the transitive form of the develops from relation develops from @@ -2564,9 +2563,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of develops from - Chris Mungall - David Osumi-Sutherland - Terry Meehan + + + develops into @@ -2585,7 +2584,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x" We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g. - Chris Mungall + gene product of @@ -2603,7 +2602,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y - Chris Mungall + has gene product @@ -2621,7 +2620,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.'neural crest cell' SubClassOf expresses some 'Wnt1 gene' x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process - Chris Mungall + expressed in @@ -2634,11 +2633,11 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - Chris Mungall - David Osumi-Sutherland - has developmental precursor + + FBbt + has developmental precursor TODO - add child relations from DOS directly develops from @@ -2699,9 +2698,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - Chris Mungall - David Hill - Tanya Berardini + + + GO Regulation precludes parthood; the regulatory process may not be within the regulated process. @@ -2726,7 +2725,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - Chris Mungall + negatively regulates (process to process) @@ -2754,7 +2753,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - Chris Mungall + positively regulates (process to process) @@ -2776,7 +2775,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) TODO: add homeomorphy axiom This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. - Chris Mungall + has prototype @@ -2789,7 +2788,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - Chris Mungall + has function realized in @@ -2810,7 +2809,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - Chris Mungall + has function in capable of part of @@ -2831,7 +2830,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role - Chris Mungall + agent in Obsoleted as the inverse property was obsoleted. @@ -2845,7 +2844,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. OBSOLETE x has participant y if and only if x realizes some active role that inheres in y - Chris Mungall + has agent obsolete has active participant @@ -2861,7 +2860,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - Chris Mungall + surrounded by @@ -2879,7 +2878,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - Chris Mungall + @@ -2901,7 +2900,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of surrounded by - Chris Mungall + surrounds @@ -2912,7 +2911,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 @@ -2924,7 +2923,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Chris Mungall + @@ -2934,7 +2933,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Chris Mungall + @@ -2950,7 +2949,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - Chris Mungall + develops from part of @@ -2966,7 +2965,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x develops_in y if x is located in y whilst x is developing - Chris Mungall + EHDAA2 Jonathan Bard, EHDAA2 develops in @@ -2998,7 +2997,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Chris Mungall + @@ -3008,7 +3007,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Chris Mungall + @@ -3024,7 +3023,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - Chris Mungall + starts with process that occurs in has start location @@ -3042,7 +3041,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - Chris Mungall + ends with process that occurs in has end location @@ -3060,7 +3059,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + consumes @@ -3081,7 +3080,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - Chris Mungall + produces @@ -3126,7 +3125,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - Bill Duncan (https://orcid.org/0000-0001-9625-1899) + This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. @@ -3274,7 +3273,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y - Chris Mungall + has developmental contribution from @@ -3291,7 +3290,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho inverse of has developmental contribution from - Chris Mungall + developmentally contributes to @@ -3305,9 +3304,9 @@ If you need an axiom that says 'has_participant min 2 object', you sho t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - Chris Mungall - David Osumi-Sutherland - Melissa Haendel + + + induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) @@ -3325,7 +3324,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally induced by - Chris Mungall + developmentally induces @@ -3339,7 +3338,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - Chris Mungall + In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by @@ -3389,7 +3388,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - Chris Mungall + replaces developmentally replaces @@ -3402,7 +3401,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally preceded by - Chris Mungall + developmentally succeeded by @@ -3418,7 +3417,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - Chris Mungall + part of developmental precursor of @@ -3432,7 +3431,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part. - Chris Mungall + ubiquitously expressed in @@ -3444,7 +3443,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of 'expressed in' - Chris Mungall + expresses @@ -3456,7 +3455,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho inverse of ubiquiotously expressed in - Chris Mungall + ubiquitously expresses @@ -3470,7 +3469,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - Chris Mungall + results in developmental progression of @@ -3485,7 +3484,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - Chris Mungall + http://www.geneontology.org/GO.doc.development.shtml @@ -3504,7 +3503,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - Chris Mungall + GOC:mtg_berkeley_2013 @@ -3523,7 +3522,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - Chris Mungall + GOC:mtg_berkeley_2013 @@ -3542,7 +3541,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - Chris Mungall + GOC:mtg_berkeley_2013 @@ -3558,7 +3557,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho foramen ovale closure SubClassOf results in disappearance of foramen ovale - Chris Mungall + May be merged into parent relation results in disappearance of @@ -3571,7 +3570,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) - Chris Mungall + May be merged into parent relation results in developmental regression of @@ -3584,7 +3583,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of 'is substance that treats' - cjm + is treated by substance @@ -3600,7 +3599,7 @@ where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. - Pier Buttigieg + adapted for living in A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. @@ -3616,7 +3615,7 @@ where p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - cjm + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y @@ -3632,7 +3631,7 @@ where p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - cjm + causally upstream of, negative effect @@ -3645,10 +3644,10 @@ where A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. - Austin Meier - Chris Mungall - Marie Angelique Laporte - cjm + + + + 2017-06-05T17:35:04Z has exposure stimulus @@ -3659,7 +3658,7 @@ where - Chris Mungall + evolutionary variant of @@ -3671,7 +3670,7 @@ where Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. - Chris Mungall + regulates localization of @@ -3691,7 +3690,7 @@ where q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of - Chris Mungall + inheres in part of @@ -3708,7 +3707,7 @@ where an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - Chris Mungall + GOC:mtg_berkeley_2013 @@ -3722,7 +3721,7 @@ where A relationship that holds via some environmental process - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to @@ -3734,7 +3733,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions ecologically related to @@ -3747,7 +3746,7 @@ where An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. - Chris Mungall + adapted for confers advantage in @@ -3759,7 +3758,7 @@ where A mereological relationship or a topological relationship - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to @@ -3771,7 +3770,7 @@ where A relationship that holds between entities participating in some developmental process (GO:0032502) - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to @@ -3784,9 +3783,8 @@ where Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. - Chris Mungall + In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - Gene Ontology Consortium colocalizes with @@ -3812,7 +3810,7 @@ then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. - Chris Mungall + In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. contributes to @@ -3835,7 +3833,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - Chris Mungall + catalyzes executes has @@ -3852,7 +3850,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to @@ -3868,7 +3866,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati this relation holds between c and p when c is part of some c', and c' is capable of p. - Chris Mungall + false part of structure that is capable of @@ -3888,7 +3886,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism genomically related to @@ -3908,7 +3906,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati c involved_in p if and only if c enables some process p', and p' is part of p - Chris Mungall + actively involved in enables part of involved in @@ -3923,7 +3921,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - Chris Mungall + regulates levels of (process to entity) regulates levels of @@ -3936,7 +3934,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables - Chris Mungall + enabled by @@ -3949,7 +3947,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of regulates - Chris Mungall + regulated by (processual) regulated by @@ -3962,7 +3960,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of negatively regulates - Chris Mungall + negatively regulated by @@ -3974,7 +3972,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of positively regulates - Chris Mungall + positively regulated by @@ -3985,7 +3983,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds via some process of localization - Chris Mungall + Do not use this relation directly. It is a grouping relation. related via localization to @@ -4001,7 +3999,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - Chris Mungall + @@ -4019,7 +4017,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - Chris Mungall + @@ -4033,7 +4031,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. - Chris Mungall + imports @@ -4045,7 +4043,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - Chris Mungall + results in transport along @@ -4057,7 +4055,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - Chris Mungall + results in transport across @@ -4070,7 +4068,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'pollen tube growth' results_in growth_of some 'pollen tube' - Chris Mungall + results in growth of @@ -4081,7 +4079,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - Chris Mungall + results in transport to from or in @@ -4092,7 +4090,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. - Chris Mungall + exports @@ -4105,7 +4103,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - Chris Mungall + @@ -4119,7 +4117,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - Chris Mungall + @@ -4133,7 +4131,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has input - Chris Mungall + input of @@ -4146,7 +4144,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has output - Chris Mungall + output of @@ -4158,7 +4156,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + formed as result of @@ -4170,7 +4168,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. - Chris Mungall + results in structural organization of @@ -4181,7 +4179,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - Chris Mungall + @@ -4195,7 +4193,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. - Chris Mungall + results in developmental induction of @@ -4205,7 +4203,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + http://neurolex.org/wiki/Property:DendriteLocation has dendrite location @@ -4219,7 +4217,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - Chris Mungall + attached to (anatomical structure to anatomical structure) attached to @@ -4233,7 +4231,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - Chris Mungall + Wikipedia:Insertion_(anatomy) has muscle origin @@ -4247,7 +4245,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - Chris Mungall + Wikipedia:Insertion_(anatomy) has muscle insertion @@ -4262,8 +4260,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati false x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat - Chris Mungall - Chris Mungall + has fused element A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. @@ -4278,7 +4275,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) @@ -4298,7 +4295,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - Chris Mungall + drains into drains to tributary channel of @@ -4321,7 +4318,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Deschutes River distributary_of Little Lava Lake x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - Chris Mungall + branch of distributary channel of http://en.wikipedia.org/wiki/Distributary @@ -4345,7 +4342,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. - Chris Mungall + anastomoses with anabranch of @@ -4365,7 +4362,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - Chris Mungall + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with @@ -4384,7 +4381,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - Chris Mungall + branching part of @@ -4401,7 +4398,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. - Chris Mungall + main stem of @@ -4415,7 +4412,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_distributary_of y iff x distributary_of y and x does not flow back into y - Chris Mungall + proper distributary of @@ -4428,7 +4425,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_tributary_of y iff x tributary_of y and x does not originate from y - Chris Mungall + proper tributary of @@ -4441,7 +4438,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - Chris Mungall + has developmental potential involving @@ -4453,7 +4450,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - Chris Mungall + has potential to developmentally contribute to @@ -4465,7 +4462,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - Chris Mungall + has potential to developmentally induce @@ -4477,7 +4474,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has the potential to develop into y iff x develops into y or if x is capable of developing into y - Chris Mungall + has potential to develop into @@ -4489,7 +4486,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - Chris Mungall + has potential to directly develop into @@ -4506,7 +4503,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' has direct input @@ -4518,7 +4515,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit obsolete has indirect input @@ -4533,7 +4530,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ translation SubClassOf has_direct_output some protein p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. - Chris Mungall + directly produces obsolete has direct output true @@ -4549,7 +4546,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - Chris Mungall + Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit obsolete has indirect output @@ -4566,7 +4563,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ inverse of upstream of - Chris Mungall + causally downstream of @@ -4578,7 +4575,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - Chris Mungall + immediately causally downstream of @@ -4618,7 +4615,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - Chris Mungall + indirectly activates indirectly positively regulates @@ -4656,7 +4653,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - Chris Mungall + indirectly inhibits indirectly negatively regulates @@ -4683,7 +4680,7 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to @@ -4703,7 +4700,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - Chris Mungall + causally upstream of @@ -4717,7 +4714,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - Chris Mungall + immediately causally upstream of @@ -4735,7 +4732,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit - Chris Mungall + directly provides input for directly provides input for (process to process) @@ -4751,7 +4748,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different transitive form of directly_provides_input_for - Chris Mungall + This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. transitively provides input for (process to process) transitively provides input for @@ -4767,7 +4764,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall + influences (processual) affects causally upstream of or within @@ -4779,7 +4776,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different false - Chris Mungall + This is an exploratory relation differs in https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions @@ -4791,7 +4788,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + differs in attribute of @@ -4801,7 +4798,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + differs in attribute @@ -4813,7 +4810,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - Chris Mungall + causally downstream of or within @@ -4835,7 +4832,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - Chris Mungall + involved in regulation of @@ -4854,7 +4851,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - Chris Mungall + involved in positive regulation of @@ -4874,7 +4871,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - Chris Mungall + involved in negative regulation of @@ -4889,7 +4886,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - Chris Mungall + involved in or reguates involved in or involved in regulation of @@ -4907,7 +4904,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall + executes activity in enables activity in @@ -4937,7 +4934,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - Chris Mungall + contributes to morphology of @@ -4950,7 +4947,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. - Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with @@ -4967,7 +4964,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) - Chris Mungall + genetically interacts with http://purl.obolibrary.org/obo/MI_0208 @@ -4981,7 +4978,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - Chris Mungall + binds molecularly binds with molecularly interacts with @@ -4998,7 +4995,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - Chris Mungall + interacts with on organism level biotically interacts with @@ -5013,7 +5010,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the partners are related via a feeding relationship. - Chris Mungall + trophically interacts with @@ -5029,9 +5026,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] Baleen whale preys on krill An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - Chris Mungall - Jorrit Poelen - Katja Shulz + + + is subject of predation interaction with preys upon @@ -5055,7 +5052,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A biotic interaction in which the two organisms live together in more or less intimate association. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism @@ -5076,7 +5073,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 commensually interacts with @@ -5096,7 +5093,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 mutualistically interacts with @@ -5116,7 +5113,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 This relation groups a pair of inverse relations, parasite of and parasitized by @@ -5139,7 +5136,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human - Chris Mungall + parasitizes direct parasite of @@ -5154,7 +5151,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + has parasite parasitised by directly parasitized by @@ -5171,7 +5168,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - Chris Mungall + semibiotically interacts with participates in a abiotic-biotic interaction with @@ -5190,7 +5187,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates @@ -5210,8 +5207,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - Chris Mungall - Vasundra Touré + + molecularly controls directly regulates activity of @@ -5229,8 +5226,8 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly inhibits molecularly decreases activity of directly negatively regulates activity of @@ -5249,8 +5246,8 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly activates molecularly increases activity of directly positively regulates activity of @@ -5265,7 +5262,7 @@ For example, A and B may be gene products and binding of B by A positively regul all dengue disease transmitted by some mosquito A relationship that holds between a disease and organism Add domain and range constraints - Chris Mungall + transmitted by @@ -5276,7 +5273,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between a disease or an organism and a phenotype - Chris Mungall + has symptom @@ -5286,7 +5283,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) host of @@ -5299,7 +5296,7 @@ For example, A and B may be gene products and binding of B by A positively regul X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y - Chris Mungall + has host http://eol.org/schema/terms/hasHost @@ -5314,7 +5311,7 @@ For example, A and B may be gene products and binding of B by A positively regul Bees pollinate Flowers This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - Chris Mungall + is subject of pollination interaction with pollinates @@ -5327,7 +5324,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + has polinator is target of pollination interaction with @@ -5342,7 +5339,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. acquires nutrients from @@ -5355,7 +5352,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of preys on - Chris Mungall + has predator is target of predation interaction with @@ -5373,7 +5370,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anopheles is a vector for Plasmodium - Chris Mungall + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism is vector for @@ -5385,7 +5382,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + has vector @@ -5395,7 +5392,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target partner in @@ -5406,7 +5403,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. subject participant in @@ -5417,7 +5414,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. target participant in @@ -5427,7 +5424,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) @@ -5438,7 +5435,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is symbiosis @@ -5448,7 +5445,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is commensalism @@ -5458,7 +5455,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is mutualism @@ -5468,7 +5465,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is parasitism @@ -5478,7 +5475,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + provides nutrients for @@ -5489,7 +5486,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is subject of eating interaction with eats @@ -5501,7 +5498,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + eaten by is target of eating interaction with @@ -5517,7 +5514,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and the a supports either the existence of b, or the truth value of b. - Chris Mungall + is evidence for @@ -5530,7 +5527,7 @@ the a supports either the existence of b, or the truth value of b. 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - Chris Mungall + @@ -5545,7 +5542,7 @@ the a supports either the existence of b, or the truth value of b. ABal nucleus child nucleus of ABa nucleus (in C elegans) c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d - Chris Mungall + This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. child nucleus of @@ -5557,7 +5554,7 @@ the a supports either the existence of b, or the truth value of b. A child nucleus relationship in which the cells are part of a hermaphroditic organism - Chris Mungall + child nucleus of in hermaphrodite @@ -5568,7 +5565,7 @@ the a supports either the existence of b, or the truth value of b. A child nucleus relationship in which the cells are part of a male organism - Chris Mungall + child nucleus of in male @@ -5582,7 +5579,7 @@ the a supports either the existence of b, or the truth value of b. p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall + has part that occurs in @@ -5609,7 +5606,7 @@ the a supports either the existence of b, or the truth value of b. An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y Axiomatization to GO to be added later - Chris Mungall + ubiquitinates @@ -5619,7 +5616,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + is kinase activity @@ -5629,7 +5626,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + is ubiquitination @@ -5641,7 +5638,7 @@ the a supports either the existence of b, or the truth value of b. See notes for inverse relation - Chris Mungall + receives input from @@ -5652,7 +5649,7 @@ the a supports either the existence of b, or the truth value of b. This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - Chris Mungall + sends output to @@ -5661,7 +5658,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. relation between physical entity and a process or stage @@ -5682,7 +5679,7 @@ the a supports either the existence of b, or the truth value of b. x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). - Chris Mungall + existence starts during @@ -5693,7 +5690,7 @@ the a supports either the existence of b, or the truth value of b. x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). - Chris Mungall + existence starts with @@ -5704,7 +5701,7 @@ the a supports either the existence of b, or the truth value of b. x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) - Chris Mungall + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps @@ -5717,7 +5714,7 @@ the a supports either the existence of b, or the truth value of b. x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) - Chris Mungall + exists during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts and ends during @@ -5739,7 +5736,7 @@ the a supports either the existence of b, or the truth value of b. x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). - Chris Mungall + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during @@ -5751,7 +5748,7 @@ the a supports either the existence of b, or the truth value of b. x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). - Chris Mungall + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with @@ -5764,7 +5761,7 @@ the a supports either the existence of b, or the truth value of b. x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - Chris Mungall + transformation of @@ -5776,7 +5773,7 @@ the a supports either the existence of b, or the truth value of b. x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - Chris Mungall + immediate transformation of @@ -5815,7 +5812,7 @@ the a supports either the existence of b, or the truth value of b. x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). - Chris Mungall + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after @@ -5854,7 +5851,7 @@ the a supports either the existence of b, or the truth value of b. x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. - Chris Mungall + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before @@ -5878,7 +5875,7 @@ the a supports either the existence of b, or the truth value of b. p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes @@ -5889,7 +5886,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + depends on @@ -5902,7 +5899,7 @@ the a supports either the existence of b, or the truth value of b. q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. - Chris Mungall + towards @@ -5914,7 +5911,7 @@ the a supports either the existence of b, or the truth value of b. 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c - Chris Mungall + has intermediate product has intermediate @@ -5927,7 +5924,7 @@ the a supports either the existence of b, or the truth value of b. The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities @@ -5945,11 +5942,11 @@ the a supports either the existence of b, or the truth value of b.A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future - Chris Mungall + determined by (system to material entity) - Chris Mungall - Pier Buttigieg + + determined by @@ -5961,7 +5958,7 @@ the a supports either the existence of b, or the truth value of b. inverse of determined by - Chris Mungall + determines (material entity to system) @@ -5980,7 +5977,7 @@ the a supports either the existence of b, or the truth value of b. s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. - Chris Mungall + determined by part of @@ -6002,7 +5999,7 @@ the a supports either the existence of b, or the truth value of b. x is transcribed from y if and only if x is synthesized from template y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 transcribed from @@ -6014,7 +6011,7 @@ the a supports either the existence of b, or the truth value of b. inverse of transcribed from - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 transcribed to @@ -6028,7 +6025,7 @@ the a supports either the existence of b, or the truth value of b. x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 ribosomal translation of @@ -6040,7 +6037,7 @@ the a supports either the existence of b, or the truth value of b. inverse of ribosomal translation of - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 ribosomally translates to @@ -6051,7 +6048,7 @@ the a supports either the existence of b, or the truth value of b. A relation that holds between two entities that have the property of being sequences or having sequences. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. @@ -6069,7 +6066,7 @@ the a supports either the existence of b, or the truth value of b.Two consecutive DNA residues are sequentially adjacent Two exons on a processed transcript that were previously connected by an intron are adjacent x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 sequentially adjacent to @@ -6085,7 +6082,7 @@ the a supports either the existence of b, or the truth value of b. Every CDS has as a start sequence the start codon for that transcript x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence - Chris Mungall + started by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6100,7 +6097,7 @@ the a supports either the existence of b, or the truth value of b. inverse of has start sequence - Chris Mungall + starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6118,7 +6115,7 @@ the a supports either the existence of b, or the truth value of b. Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence - Chris Mungall + ended by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6133,7 +6130,7 @@ the a supports either the existence of b, or the truth value of b. inverse of has end sequence - Chris Mungall + ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6149,7 +6146,7 @@ the a supports either the existence of b, or the truth value of b. x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. In the SO paper, this was defined as an instance-type relation - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 is consecutive sequence of @@ -6164,7 +6161,7 @@ the a supports either the existence of b, or the truth value of b. Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering - Chris Mungall + is sequentially aligned with @@ -6179,7 +6176,7 @@ the a supports either the existence of b, or the truth value of b. The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y - Chris Mungall + bounds sequence of @@ -6192,7 +6189,7 @@ the a supports either the existence of b, or the truth value of b. inverse of bounds sequence of - Chris Mungall + is bound by sequence of @@ -6208,8 +6205,8 @@ the a supports either the existence of b, or the truth value of b. - x has subsequence y iff all of the sequence parts of x are sequence parts of y - Chris Mungall + x has subsequence y iff all of the sequence parts of y are sequence parts of x + contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6226,7 +6223,7 @@ the a supports either the existence of b, or the truth value of b. inverse of has subsequence - Chris Mungall + contained by @@ -6245,8 +6242,8 @@ the a supports either the existence of b, or the truth value of b. - x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. - Chris Mungall + x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. + overlaps sequence of @@ -6258,8 +6255,8 @@ the a supports either the existence of b, or the truth value of b. - x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. - Chris Mungall + x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + disconnected from does not overlap sequence of @@ -6273,7 +6270,7 @@ the a supports either the existence of b, or the truth value of b. inverse of downstream of sequence of - Chris Mungall + is upstream of sequence of @@ -6287,7 +6284,7 @@ the a supports either the existence of b, or the truth value of b. x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. - Chris Mungall + is downstream of sequence of @@ -6301,7 +6298,7 @@ the a supports either the existence of b, or the truth value of b. A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y - Chris Mungall + is immediately downstream of sequence of @@ -6316,7 +6313,7 @@ the a supports either the existence of b, or the truth value of b. A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript inverse of immediately downstream of - Chris Mungall + is immediately upstream of sequence of @@ -6332,7 +6329,7 @@ the a supports either the existence of b, or the truth value of b. Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - Chris Mungall + has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). has skeleton @@ -6346,7 +6343,7 @@ the a supports either the existence of b, or the truth value of b. p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. - Chris Mungall + results in ending of @@ -6363,7 +6360,7 @@ the a supports either the existence of b, or the truth value of b. x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - Chris Mungall + http://eol.org/schema/terms/hyperparasitoidOf https://en.wikipedia.org/wiki/Hyperparasite hyperparasitoid of @@ -6383,7 +6380,7 @@ the a supports either the existence of b, or the truth value of b. inverse of hyperparasite of - Chris Mungall + has epiparasite has hyperparasite hyperparasitoidized by @@ -6398,7 +6395,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + http://en.wikipedia.org/wiki/Allelopathy allelopath of @@ -6413,7 +6410,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + pathogen of @@ -6424,7 +6421,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + has pathogen @@ -6436,7 +6433,7 @@ the a supports either the existence of b, or the truth value of b. inverse of is evidence for - Chris Mungall + @@ -6451,7 +6448,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + causally influenced by (entity-centric) causally influenced by @@ -6463,7 +6460,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ @@ -6475,7 +6472,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + molecular interaction relation helper property @@ -6486,7 +6483,7 @@ the a supports either the existence of b, or the truth value of b. Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - Chris Mungall + @@ -6511,8 +6508,8 @@ the a supports either the existence of b, or the truth value of b. The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - Chris Mungall - Vasundra Touré + + causally influences (entity-centric) causally influences @@ -6525,7 +6522,7 @@ the a supports either the existence of b, or the truth value of b. A relation that holds between elements of a musculoskeletal system or its analogs. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. biomechanically related to @@ -6537,7 +6534,7 @@ the a supports either the existence of b, or the truth value of b. m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - Chris Mungall + Wikipedia:Antagonist_(muscle) has muscle antagonist @@ -6551,7 +6548,7 @@ the a supports either the existence of b, or the truth value of b. inverse of branching part of - Chris Mungall + has branching part @@ -6564,7 +6561,7 @@ the a supports either the existence of b, or the truth value of b. x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - Chris Mungall + UBERON:cjm This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. @@ -6578,7 +6575,7 @@ the a supports either the existence of b, or the truth value of b. x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - Chris Mungall + GOC:cjm lumen of @@ -6591,7 +6588,7 @@ the a supports either the existence of b, or the truth value of b. s is luminal space of x iff s is lumen_of x and s is an immaterial entity - Chris Mungall + luminal space of @@ -6602,7 +6599,7 @@ the a supports either the existence of b, or the truth value of b. A relation that holds between an attribute or a qualifier and another attribute. - Chris Mungall + This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. @@ -6615,7 +6612,7 @@ the a supports either the existence of b, or the truth value of b. - Chris Mungall + participates in a biotic-biotic interaction with @@ -6628,7 +6625,7 @@ the a supports either the existence of b, or the truth value of b. inverse of has skeleton - Chris Mungall + skeleton of @@ -6641,7 +6638,7 @@ the a supports either the existence of b, or the truth value of b. p directly regulates q iff p is immediately causally upstream of q and p regulates q. - Chris Mungall + directly regulates (processual) @@ -6674,7 +6671,7 @@ the a supports either the existence of b, or the truth value of b. gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - Chris Mungall + has part structure that is capable of @@ -6779,7 +6776,7 @@ the a supports either the existence of b, or the truth value of b. A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall + causal relation between material entity and a process @@ -7204,7 +7201,7 @@ the a supports either the existence of b, or the truth value of b. a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. - Melissa Haendel + Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces @@ -7217,7 +7214,7 @@ the a supports either the existence of b, or the truth value of b. a produced_by b iff some process that occurs_in b has_output a. - Melissa Haendel + produced by @@ -7229,7 +7226,7 @@ the a supports either the existence of b, or the truth value of b. Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. - Vasundra Touré + represses expression of @@ -7240,7 +7237,7 @@ the a supports either the existence of b, or the truth value of b. Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. - Vasundra Touré + increases expression of @@ -7252,7 +7249,7 @@ the a supports either the existence of b, or the truth value of b. A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. - Matthew Brush + is used to study The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate. has role in modeling @@ -7379,7 +7376,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:38:20Z condition has genetic basis in @@ -7391,7 +7388,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:20Z has material basis in gain of function germline mutation in @@ -7405,7 +7402,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:37Z has material basis in loss of function germline mutation in @@ -7417,7 +7414,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:54Z has material basis in germline mutation in @@ -7430,7 +7427,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:07Z has material basis in somatic mutation in @@ -7443,7 +7440,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:26Z has major susceptibility factor @@ -7455,7 +7452,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:57Z has partial material basis in germline mutation in @@ -7466,7 +7463,7 @@ Environmental exposures include those imposed by natural environments, experimen p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - cjm + 2018-12-13T11:26:17Z has primary input or output @@ -7480,7 +7477,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - cjm + 2018-12-13T11:26:32Z has primary output @@ -7504,7 +7501,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - cjm + 2018-12-13T11:26:56Z has primary input @@ -7527,7 +7524,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:53:08Z is genetic basis for condition @@ -7539,7 +7536,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:55:51Z is causal gain of function germline mutation of in @@ -7552,7 +7549,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:06Z is causal loss of function germline mutation of in @@ -7566,7 +7563,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:40Z is causal germline mutation in @@ -7580,7 +7577,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:57:07Z is causal somatic mutation in @@ -7593,7 +7590,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. - cjm + 2017-11-05T02:57:43Z is causal susceptibility factor for @@ -7607,7 +7604,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. - cjm + 2017-11-05T02:58:43Z is causal germline mutation partially giving rise to @@ -7620,7 +7617,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:01Z realizable has basis in @@ -7631,7 +7628,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:29Z is basis for realizable @@ -7643,7 +7640,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:26:47Z disease has basis in @@ -7656,7 +7653,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) - cjm + 2017-11-05T03:29:32Z disease has basis in dysfunction of @@ -7669,7 +7666,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. disease has basis in disruption of (disease to process) - cjm + 2017-11-05T03:37:52Z disease has basis in disruption of @@ -7682,7 +7679,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. - cjm + 2017-11-05T03:46:07Z disease has basis in feature @@ -7695,7 +7692,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. - cjm + 2017-11-05T03:50:54Z causal relationship with disease as subject @@ -7716,7 +7713,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and a process where the disease process disrupts the execution of the process. disease causes disruption of (disease to process) - cjm + 2017-11-05T03:51:09Z disease causes disruption of @@ -7732,7 +7729,7 @@ Environmental exposures include those imposed by natural environments, experimen disease causes dysfunction of (disease to anatomical entity) - cjm + 2017-11-05T03:58:20Z disease causes dysfunction of @@ -7746,7 +7743,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. - cjm + 2017-11-05T04:06:02Z disease has location @@ -7758,7 +7755,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity - cjm + 2017-12-26T19:37:31Z disease has inflammation site @@ -7774,7 +7771,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - cjm + 2017-12-26T19:45:49Z realized in response to stimulus @@ -7786,7 +7783,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. - cjm + 2017-12-26T19:50:53Z disease has feature @@ -7798,7 +7795,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. - cjm + 2017-12-26T19:58:44Z disease arises from alteration in structure @@ -7814,7 +7811,7 @@ Environmental exposures include those imposed by natural environments, experimen Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - cjm + 2018-01-25T23:20:13Z enables subfunction @@ -7830,7 +7827,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:30Z acts upstream of or within, positive effect @@ -7848,7 +7845,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:51Z acts upstream of or within, negative effect @@ -7867,7 +7864,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - cjm + 2018-01-26T23:53:14Z acts upstream of, positive effect @@ -7887,7 +7884,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - cjm + 2018-01-26T23:53:22Z acts upstream of, negative effect @@ -7901,7 +7898,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:05Z causally upstream of or within, negative effect @@ -7913,7 +7910,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:19Z causally upstream of or within, positive effect @@ -8039,7 +8036,7 @@ Environmental exposures include those imposed by natural environments, experimen "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. - Damion Dooley + has substance added @@ -8052,7 +8049,7 @@ Environmental exposures include those imposed by natural environments, experimen 'egg white' 'has substance removed' some 'egg yolk' "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. - Damion Dooley + has substance removed @@ -8065,7 +8062,7 @@ Environmental exposures include those imposed by natural environments, experimen sardines 'immersed in' some 'oil and mustard' "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. - Damion Dooley + immersed in @@ -8077,7 +8074,7 @@ Environmental exposures include those imposed by natural environments, experimen sardine has consumer some homo sapiens 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. - Damion Dooley + has consumer @@ -8091,7 +8088,7 @@ Environmental exposures include those imposed by natural environments, experimen bread 'has primary substance added' some 'flour' 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance. - Damion Dooley + has primary substance added @@ -8105,10 +8102,10 @@ Environmental exposures include those imposed by natural environments, experimen An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - Austin Meier - Chris Mungall - David Osumi-Sutherland - Marie Angelique Laporte + + + + triggered by process realized in response to https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit @@ -8157,7 +8154,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - Vasundra Touré + regulates activity of @@ -8168,7 +8165,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. - Vasundra Touré + regulates quantity of @@ -8179,7 +8176,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. - Vasundra Touré + indirectly regulates activity of @@ -8192,7 +8189,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + decreases by repression quantity of @@ -8205,7 +8202,7 @@ For example, protein A (transcription factor) indirectly decreases by repression The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + increases by expression quantity of @@ -8216,7 +8213,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly positively regulates the quantity of B. - Vasundra Touré + directly positively regulates quantity of @@ -8227,7 +8224,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly negatively regulates the quantity of B. - Vasundra Touré + directly negatively regulates quantity of @@ -8238,7 +8235,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. - Vasundra Touré + indirectly activates indirectly positively regulates activity of @@ -8251,7 +8248,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. - Vasundra Touré + destabilizes quantity of @@ -8263,7 +8260,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. - Vasundra Touré + stabilizes quantity of @@ -8274,7 +8271,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. - Vasundra Touré + indirectly inhibits indirectly negatively regulates activity of @@ -8286,7 +8283,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. - Vasundra Touré + directly regulates quantity of @@ -8297,7 +8294,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. - Vasundra Touré + indirectly regulates quantity of @@ -8308,7 +8305,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. - Vasundra Touré + indirectly negatively regulates quantity of @@ -8319,7 +8316,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. - Vasundra Touré + indirectly positively regulates quantity of @@ -8650,7 +8647,7 @@ For example, protein A (transcription factor) indirectly increases by expression transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data]) A relation between a material entity and some data in which the data is taken as exemplifying the material entity. C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C. - Patrick Ray + This relation is not meant to capture the relation between occurrents and data. has exemplar data @@ -8660,7 +8657,7 @@ For example, protein A (transcription factor) indirectly increases by expression - Patrick Ray + exemplar data of @@ -8673,7 +8670,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relation between a group and another group it is part of but does not fully constitute. X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. - Shawn Tan + This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. subcluster of @@ -8855,7 +8852,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - http://orcid.org/0000-0002-7463-6306 + 2021-11-05T17:30:44Z has disease https://github.com/oborel/obo-relations/issues/478 @@ -8885,8 +8882,8 @@ For example, protein A (transcription factor) indirectly increases by expression A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - https://orcid.org/0000-0001-9625-1899 - https://orcid.org/0000-0003-2620-0345 + + A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z @@ -9039,7 +9036,7 @@ For example, protein A (transcription factor) indirectly increases by expression This relation groups relations between diseases and any other kind of entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. - cjm + 2018-09-26T00:00:32Z disease relationship @@ -9050,7 +9047,7 @@ For example, protein A (transcription factor) indirectly increases by expression p has anatomical participant c iff p has participant c, and c is an anatomical entity - cjm + 2018-09-26T01:08:58Z results in changes to anatomical or cellular structure diff --git a/subsets/ro-interaction.obo b/subsets/ro-interaction.obo index 31f6972d..521beb78 100644 --- a/subsets/ro-interaction.obo +++ b/subsets/ro-interaction.obo @@ -13,7 +13,7 @@ id: acquires_nutrients_from name: acquires nutrients from subset: ro-eco xref: RO:0002457 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for @@ -58,7 +58,7 @@ property_value: RO:0004050 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:22Z [Typedef] @@ -71,7 +71,7 @@ property_value: RO:0004049 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:14Z [Typedef] @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z [Typedef] @@ -103,7 +103,7 @@ xref: RO:0004032 property_value: RO:0004049 RO:0002264 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z [Typedef] @@ -120,7 +120,7 @@ property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cy property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 domain: BFO:0000004 range: BFO:0000004 @@ -131,7 +131,7 @@ id: allelopath_of name: allelopath of subset: ro-eco xref: RO:0002555 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string @@ -153,7 +153,7 @@ def: "x anabranch_of y if x is a distributary of y (i.e. it channels a from a la subset: ro-eco xref: RO:0002378 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "anastomoses with" xsd:string is_a: distributary_of ! distributary of disjoint_from: proper_distributary_of ! proper distributary of @@ -165,7 +165,7 @@ name: attached to def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] subset: ro-eco xref: RO:0002371 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: attached_to_part_of ! attached to part of @@ -189,9 +189,8 @@ def: "Relation between a neuron and some structure its axon forms (chemical) syn xref: RO:0002102 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in @@ -202,7 +201,7 @@ id: biomechanically_related_to name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] xref: RO:0002567 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: CARO:0000003 range: CARO:0000003 @@ -214,7 +213,7 @@ name: biotically interacts with def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] subset: ro-eco xref: RO:0002437 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string @@ -231,7 +230,7 @@ def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\ comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco xref: RO:0002007 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 is_a: part_of @@ -242,7 +241,7 @@ def: "x bounds the sequence of y iff the upstream-most part of x is upstream of xref: RO:0002522 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to inverse_of: is_bound_by_sequence_of ! is bound by sequence of @@ -254,7 +253,7 @@ def: "x is a branching part of y if and only if x is part of y and x is connecte subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso FMA:85994 xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with @@ -269,7 +268,7 @@ subset: ro-eco xref: RO:0002215 property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 @@ -302,7 +301,7 @@ id: capable_of_part_of name: capable of part of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ is_a: causal_agent_in_process ! causal agent in process @@ -350,7 +349,7 @@ id: causal_relation_between_entities name: causal relation between entities xref: RO:0002506 property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000002 @@ -363,7 +362,7 @@ name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] xref: RO:0002595 property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 range: BFO:0000015 @@ -374,7 +373,7 @@ id: causal_relation_between_processes name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 @@ -389,7 +388,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: OGMS:0000031 is_a: causally_related_to ! causally related to is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:50:54Z [Typedef] @@ -398,7 +397,7 @@ name: causally downstream of def: "inverse of upstream of" [] xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within is_a: preceded_by inverse_of: causally_upstream_of ! causally upstream of @@ -409,7 +408,7 @@ name: causally downstream of or within def: "inverse of causally upstream of or within" [] subset: RO:0002259 xref: RO:0002427 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -418,7 +417,7 @@ is_a: causal_relation_between_processes ! causal relation between processes id: causally_influenced_by name: causally influenced by xref: RO:0002559 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: causal_relation_between_entities ! causal relation between entities @@ -429,8 +428,8 @@ id: causally_influences name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] xref: RO:0002566 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 @@ -443,7 +442,7 @@ name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] @@ -453,7 +452,7 @@ def: "p is causally upstream of q iff p is causally related to q, the end of p p subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes @@ -465,7 +464,7 @@ def: "p is causally upstream of, negative effect q iff p is casually upstream of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -478,7 +477,7 @@ comment: holds between x and y if and only if x is causally upstream of y and th subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -490,7 +489,7 @@ def: "p is 'causally upstream or within' q iff p is causally related to q, and t synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -502,7 +501,7 @@ name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -511,7 +510,7 @@ name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -537,7 +536,7 @@ name: child nucleus of def: "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" [] xref: RO:0002476 property_value: IAO:0000112 "ABal nucleus child nucleus of ABa nucleus (in C elegans)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." xsd:string domain: GO:0005634 range: GO:0005634 @@ -548,7 +547,7 @@ id: child_nucleus_of_in_hermaphrodite name: child nucleus of in hermaphrodite def: "A child nucleus relationship in which the cells are part of a hermaphroditic organism" [] xref: RO:0002477 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -556,7 +555,7 @@ id: child_nucleus_of_in_male name: child nucleus of in male def: "A child nucleus relationship in which the cells are part of a male organism" [] xref: RO:0002478 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -576,7 +575,7 @@ comment: Example: if we define region of chromosome as any subdivision of a chro subset: ro-eco xref: RO:0002008 property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -585,9 +584,8 @@ name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 -property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -599,7 +597,7 @@ name: commensually interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] subset: ro-eco xref: RO:0002441 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -610,7 +608,7 @@ def: "x composed_primarily_of y if and only if more than half of the mass of x i subset: ro-eco xref: RO:0002473 property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 @@ -639,7 +637,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: BFO:0000017 is_a: causally_related_to ! causally related to inverse_of: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:38:20Z [Typedef] @@ -648,7 +646,7 @@ name: conduit for def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] subset: ro-eco xref: RO:0002570 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 UBERON:cjm xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 @@ -661,7 +659,7 @@ name: confers advantage in subset: ro-eco xref: RO:0002322 property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "adapted for" xsd:string range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -727,7 +725,7 @@ name: continuous with def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 @@ -746,7 +744,7 @@ property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a het property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -771,7 +769,7 @@ id: contributes_to_morphology_of name: contributes to morphology of def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] xref: RO:0002433 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -796,7 +794,7 @@ id: decreases_by_repression_quantity_of name: decreases by repression quantity of def: "The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011007 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_negatively_regulates_quantity_of ! indirectly negatively regulates quantity of @@ -808,8 +806,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in wh xref: RO:0002121 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in @@ -821,7 +819,7 @@ name: destabilizes quantity of def: "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." [] xref: RO:0011014 property_value: IAO:0000112 "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_quantity_of ! directly negatively regulates quantity of @@ -832,11 +830,11 @@ name: determined by def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] subset: ro-eco xref: RO:0002507 -property_value: http://purl.org/dc/terms/creator "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/creator "Pier Buttigieg" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-4366-3088 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "A coral reef environment is determined by a particular coral reef" xsd:string property_value: IAO:0000116 "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602 property_value: IAO:0000589 "determined by (system to material entity)" xsd:string domain: RO:0002577 @@ -852,7 +850,7 @@ name: determined by part of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] subset: ro-eco xref: RO:0002509 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 range: BFO:0000040 is_a: causal_relation_between_entities ! causal relation between entities @@ -865,7 +863,7 @@ def: "inverse of determined by" [] subset: ro-eco subset: RO:0002259 xref: RO:0002508 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "determines (material entity to system)" xsd:string is_a: causally_influences ! causally influences @@ -876,7 +874,7 @@ def: "inverse of has developmental contribution from" [] subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to @@ -886,9 +884,9 @@ name: developmentally induced by def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] xref: RO:0002256 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string property_value: IAO:0000119 GO:0001759 xsd:string @@ -905,7 +903,7 @@ name: developmentally induces def: "Inverse of developmentally induced by" [] xref: RO:0002257 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_induce ! has potential to developmentally induce @@ -917,7 +915,7 @@ comment: This relation groups together various other developmental relations. It xref: RO:0002258 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string domain: BFO:0000002 range: BFO:0000002 @@ -929,7 +927,7 @@ id: developmentally_related_to name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] xref: RO:0002324 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] @@ -939,7 +937,7 @@ def: "x developmentally replaces y if and only if there is some developmental pr xref: RO:0002285 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "replaces" xsd:string is_a: developmentally_preceded_by ! developmentally preceded by @@ -949,7 +947,7 @@ name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] xref: RO:0002286 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -959,10 +957,10 @@ def: "x develops from y if and only if either (a) x directly develops from y or comment: This is the transitive form of the develops from relation xref: RO:0002202 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 domain: BFO:0000004 range: BFO:0000004 is_transitive: true @@ -975,7 +973,7 @@ name: develops from part of def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] xref: RO:0002225 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: develops_from ! develops from [Typedef] @@ -984,7 +982,7 @@ name: develops in def: "x develops_in y if x is located in y whilst x is developing" [] xref: RO:0002226 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string domain: CARO:0000000 @@ -997,9 +995,9 @@ def: "inverse of develops from" [] subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 is_transitive: true is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into @@ -1010,11 +1008,11 @@ id: directly_develops_from name: directly develops from def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] xref: RO:0002207 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "has developmental precursor" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000119 "FBbt" xsd:string property_value: RO:0002575 RO:0002202 is_a: develops_from ! develops from @@ -1060,8 +1058,8 @@ name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] xref: RO:0002449 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1072,7 +1070,7 @@ id: directly_negatively_regulates_quantity_of name: directly negatively regulates quantity of def: "The entity A has an activity that directly negatively regulates the quantity of B." [] xref: RO:0011010 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1107,8 +1105,8 @@ name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] xref: RO:0002450 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1119,7 +1117,7 @@ id: directly_positively_regulates_quantity_of name: directly positively regulates quantity of def: "The entity A has an activity that directly positively regulates the quantity of B." [] xref: RO:0011009 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1142,7 +1140,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002578 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string property_value: RO:0002575 RO:0002211 @@ -1155,8 +1153,8 @@ name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] xref: RO:0002448 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: molecularly_interacts_with ! molecularly interacts with @@ -1167,7 +1165,7 @@ id: directly_regulates_quantity_of name: directly regulates quantity of def: "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B." [] xref: RO:0011021 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -1177,7 +1175,7 @@ def: "A relationship between a disease and an anatomical structure where the mat xref: RO:0004030 range: CARO:0000003 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z [Typedef] @@ -1189,7 +1187,7 @@ property_value: IAO:0000589 "disease causes disruption of (disease to process)" domain: OGMS:0000031 range: BFO:0000015 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:51:09Z [Typedef] @@ -1200,7 +1198,7 @@ property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomica domain: OGMS:0000031 range: CARO:0000006 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z [Typedef] @@ -1210,7 +1208,7 @@ xref: RO:0004019 domain: OGMS:0000031 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject is_a: realizable_has_basis_in ! realizable has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:26:47Z [Typedef] @@ -1221,7 +1219,7 @@ xref: RO:0004021 property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:37:52Z [Typedef] @@ -1232,7 +1230,7 @@ xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string range: CARO:0000006 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z [Typedef] @@ -1243,7 +1241,7 @@ xref: RO:0004022 domain: OGMS:0000031 is_a: disease_has_basis_in ! disease has basis in is_a: has_phenotype ! has phenotype -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:46:07Z [Typedef] @@ -1253,7 +1251,7 @@ def: "A relationship between a disease and some feature of that disease, where t xref: RO:0004029 domain: OGMS:0000031 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:50:53Z [Typedef] @@ -1272,7 +1270,7 @@ xref: RO:0004027 domain: OGMS:0000031 range: BFO:0000004 is_a: disease_has_location ! disease has location -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:37:31Z [Typedef] @@ -1285,7 +1283,7 @@ property_value: IAO:0000232 "This relation is intentionally very general, and co domain: OGMS:0000031 range: BFO:0000004 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T04:06:02Z [Typedef] @@ -1294,7 +1292,7 @@ name: disease relationship def: "This relation groups relations between diseases and any other kind of entity." [] xref: RO:0040035 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z [Typedef] @@ -1306,7 +1304,7 @@ subset: ro-eco xref: RO:0002377 property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string @@ -1316,10 +1314,10 @@ is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: does_not_overlap_sequence_of name: does not overlap sequence of -def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] xref: RO:0002527 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "disconnected from" xsd:string is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -1338,7 +1336,7 @@ id: eats name: eats subset: ro-eco xref: RO:0002470 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -1359,7 +1357,7 @@ def: "A relationship that is mediated in some way by the environment or environm subset: ro-eco xref: RO:0002321 property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string [Typedef] @@ -1377,7 +1375,7 @@ name: electrically_synapsed_to def: "A relation that holds between two neurons that are electrically coupled via gap junctions." [] xref: RO:0002003 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: connected_to ! connected to [Typedef] @@ -1386,7 +1384,7 @@ name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: has_participant @@ -1397,7 +1395,7 @@ def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string property_value: IAO:0000118 "has" xsd:string @@ -1413,7 +1411,7 @@ name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] xref: RO:0004031 is_a: functionally_related_to ! functionally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z [Typedef] @@ -1430,14 +1428,14 @@ inverse_of: has_endoparasite ! has endoparasite id: ends subset: ro-eco xref: RO:0002229 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: ends_with subset: ro-eco xref: RO:0002230 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -1462,7 +1460,7 @@ name: exports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002345 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -1479,7 +1477,7 @@ def: "relationship between a neuron and a neuron projection bundle (e.g.- tract xref: RO:0002101 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 @@ -1492,7 +1490,7 @@ inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron proje id: formed_as_result_of name: formed as result of xref: RO:0002354 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of [Typedef] @@ -1500,7 +1498,7 @@ id: functionally_related_to name: functionally related to def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] xref: RO:0002328 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string [Typedef] @@ -1509,7 +1507,7 @@ name: genetically interacts with xref: RO:0002435 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with @@ -1517,7 +1515,7 @@ is_a: interacts_with ! interacts with [Typedef] id: has_2D_boundary xref: RO:0002002 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1557,7 +1555,7 @@ def: "inverse of branching part of" [] subset: ro-eco subset: RO:0002259 xref: RO:0002569 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: has_part is_a: in_branching_relationship_with ! in branching relationship with @@ -1593,7 +1591,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 "Bill Duncan (https://orcid.org/0000-0001-9625-1899)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant @@ -1622,7 +1620,7 @@ id: has_dendrite_location name: has dendrite location xref: RO:0002360 property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -1632,7 +1630,7 @@ def: "x has developmental contribution from y iff x has some part z such that z xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by @@ -1644,7 +1642,7 @@ name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to @@ -1656,7 +1654,7 @@ def: "p has direct input c iff c is a participant in p, c is present at the star xref: RO:0002400 property_value: IAO:0000112 "'protein catabolic process' SubClassOf has_direct_input some protein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly consumes" xsd:string property_value: IAO:0000232 "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" xsd:string is_a: has_input ! has input @@ -1666,7 +1664,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1711,7 +1709,7 @@ def: "x 'has end location' y if and only if there exists some process z such tha subset: ro-eco xref: RO:0002232 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -1724,7 +1722,7 @@ def: "x has end sequence y if the end of x is identical to the end of y, and x h xref: RO:0002518 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -1776,11 +1774,11 @@ id: has_exposure_stimulus name: has exposure stimulus def: "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002309 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 is_a: related_via_exposure_to ! related via exposure to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:35:04Z [Typedef] @@ -1806,7 +1804,7 @@ def: "The relation between a neuron projection bundle and a neuron projection th xref: RO:0002132 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 @@ -1828,7 +1826,7 @@ subset: ro-eco xref: RO:0002303 property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Pier Buttigieg" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string domain: CARO:0001010 range: ENVO:01000254 @@ -1851,7 +1849,7 @@ name: has host def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] subset: ro-eco xref: RO:0002454 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -1865,7 +1863,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 is_a: has_participant @@ -1886,7 +1884,7 @@ def: "p has intermediate c if and only if p has parts p1, p2 and p1 has output c subset: ro-eco xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string is_a: has_participant @@ -1924,7 +1922,7 @@ name: has major susceptibility factor xref: RO:0004005 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_susceptibility_factor_for ! is causal susceptibility factor for -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:26Z [Typedef] @@ -1935,7 +1933,7 @@ property_value: seeAlso Orphanet:410295 property_value: seeAlso Orphanet:410296 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_gain_of_function_germline_mutation_of_in ! is causal gain of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:20Z [Typedef] @@ -1945,7 +1943,7 @@ xref: RO:0004003 property_value: seeAlso Orphanet:317343 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_in ! is causal germline mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:54Z [Typedef] @@ -1954,7 +1952,7 @@ name: has material basis in loss of function germline mutation in xref: RO:0004002 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_loss_of_function_germline_mutation_of_in ! is causal loss of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:37Z [Typedef] @@ -1964,7 +1962,7 @@ xref: RO:0004004 property_value: seeAlso Orphanet:317344 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z [Typedef] @@ -1980,7 +1978,7 @@ id: has_muscle_antagonist name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string is_a: biomechanically_related_to ! biomechanically related to @@ -1989,7 +1987,7 @@ id: has_muscle_insertion name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} @@ -2001,7 +1999,7 @@ id: has_muscle_origin name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} @@ -2039,7 +2037,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string is_a: has_participant inverse_of: output_of ! output of @@ -2066,7 +2064,7 @@ name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] xref: RO:0002584 property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causal_relation_between_material_entity_and_a_process ! causal relation between material entity and a process is_a: functionally_related_to ! functionally related to @@ -2076,7 +2074,7 @@ name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco xref: RO:0002479 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 range: BFO:0000004 @@ -2086,7 +2084,7 @@ name: has partial material basis in germline mutation in xref: RO:0004006 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_partially_giving_rise_to ! is causal germline mutation partially giving rise to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:57Z [Typedef] @@ -2098,7 +2096,7 @@ id: has_pathogen name: has pathogen subset: ro-eco xref: RO:0002557 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2108,7 +2106,7 @@ def: "A relationship that holds between a biological entity and a phenotype. Her subset: ro-eco xref: RO:0002200 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: UPHENO:0001001 is_a: has_phenotype_or_disease ! has phenotype or disease inverse_of: phenotype_of ! phenotype of @@ -2129,9 +2127,9 @@ def: "Holds between a cell c and a protein complex or protein p if and only if t xref: RO:0002104 property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Alexander Diehl" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 @@ -2157,8 +2155,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in whi xref: RO:0002110 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "synapsed in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2172,7 +2170,7 @@ name: has potential to develop into def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] xref: RO:0002387 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2181,7 +2179,7 @@ name: has potential to developmentally contribute to def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] xref: RO:0002385 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2190,7 +2188,7 @@ name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] xref: RO:0002386 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2199,7 +2197,7 @@ name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] xref: RO:0002388 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_potential_to_develop_into ! has potential to develop into [Typedef] @@ -2223,7 +2221,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -2233,7 +2231,7 @@ def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c o subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -2244,7 +2242,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -2276,7 +2274,7 @@ name: has skeleton def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] xref: RO:0002551 property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 @@ -2321,7 +2319,7 @@ name: has soma location def: "Relation between a neuron and an anatomical structure that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 range: CARO:0000003 @@ -2335,7 +2333,7 @@ def: "x 'has starts location' y if and only if there exists some process z such subset: ro-eco xref: RO:0002231 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -2348,7 +2346,7 @@ def: "x has start sequence y if the start of x is identical to the start of y, a xref: RO:0002516 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2358,10 +2356,10 @@ inverse_of: is_start_sequence_of ! is start sequence of [Typedef] id: has_subsequence name: has subsequence -def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2375,7 +2373,7 @@ id: has_symptom name: has symptom def: "A relation that holds between a disease or an organism and a phenotype" [] xref: RO:0002452 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: OGMS:0000031 is_a: has_phenotype ! has phenotype @@ -2405,7 +2403,7 @@ def: "A general relation between a neuron and some structure in which it either xref: RO:0002130 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has synapse in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2417,7 +2415,7 @@ id: has_synaptic_terminal_of name: has synaptic terminal of xref: RO:0002006 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: overlaps ! overlaps inverse_of: has_synaptic_terminal_in ! has synaptic terminal in @@ -2429,7 +2427,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002339 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2440,7 +2438,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002338 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2448,7 +2446,7 @@ id: has_vector name: has vector subset: ro-eco xref: RO:0002460 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with [Typedef] @@ -2463,7 +2461,7 @@ id: host_of name: host of subset: ro-eco xref: RO:0002453 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2476,7 +2474,7 @@ synonym: "epiparasite of" RELATED [] synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string is_a: has_host ! has host @@ -2492,7 +2490,7 @@ synonym: "has epiparasite" RELATED [] synonym: "has hyperparasite" RELATED [] synonym: "hyperparasitoidized by" RELATED [] xref: RO:0002554 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2500,7 +2498,7 @@ id: immediate_transformation_of name: immediate transformation of def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] xref: RO:0002495 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002494 is_a: directly_develops_from ! directly develops from is_a: transformation_of ! transformation of @@ -2510,7 +2508,7 @@ id: immediately_causally_downstream_of name: immediately causally downstream of xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of is_a: immediately_preceded_by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of @@ -2520,7 +2518,7 @@ id: immediately_causally_upstream_of name: immediately causally upstream of def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: immediately_precedes @@ -2533,7 +2531,7 @@ xref: RO:0002087 id: immediately_precedes subset: ro-eco xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0002575 BFO:0000063 [Typedef] @@ -2542,7 +2540,7 @@ name: imports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002340 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -2551,7 +2549,7 @@ name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] xref: RO:0002375 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 @@ -2577,7 +2575,7 @@ id: increases_by_expression_quantity_of name: increases by expression quantity of def: "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011008 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_positively_regulates_quantity_of ! indirectly positively regulates quantity of @@ -2587,7 +2585,7 @@ id: increases_expression_of name: increases expression of def: "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." [] xref: RO:0003003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -2606,7 +2604,7 @@ id: indirectly_negatively_regulates name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true @@ -2618,7 +2616,7 @@ id: indirectly_negatively_regulates_activity_of name: indirectly negatively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B." [] xref: RO:0011016 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly inhibits" xsd:string is_a: indirectly_regulates_activity_of ! indirectly regulates activity of @@ -2627,7 +2625,7 @@ id: indirectly_negatively_regulates_quantity_of name: indirectly negatively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B." [] xref: RO:0011023 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2635,7 +2633,7 @@ id: indirectly_positively_regulates name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 is_transitive: true @@ -2647,7 +2645,7 @@ id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." [] xref: RO:0011013 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -2658,7 +2656,7 @@ id: indirectly_positively_regulates_quantity_of name: indirectly positively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B." [] xref: RO:0011024 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2676,7 +2674,7 @@ id: indirectly_regulates_activity_of name: indirectly regulates activity of def: "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." [] xref: RO:0011004 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: regulates_activity_of ! regulates activity of @@ -2686,7 +2684,7 @@ id: indirectly_regulates_quantity_of name: indirectly regulates quantity of def: "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B." [] xref: RO:0011022 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -2696,7 +2694,7 @@ def: "inverse of has input" [] subset: ro-eco subset: RO:0002259 xref: RO:0002352 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -2710,7 +2708,7 @@ xref: RO:0002434 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI domain: BFO:0000040 @@ -2723,7 +2721,7 @@ name: interacts with via parasite-host interaction def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] subset: ro-eco xref: RO:0002443 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2751,7 +2749,7 @@ id: involved_in name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] xref: RO:0002331 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in @@ -2763,7 +2761,7 @@ id: involved_in_negative_regulation_of name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] xref: RO:0002430 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2773,7 +2771,7 @@ name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in_process ! causal agent in process @@ -2784,7 +2782,7 @@ id: involved_in_positive_regulation_of name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] xref: RO:0002429 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2793,7 +2791,7 @@ id: involved_in_regulation_of name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] xref: RO:0002428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of @@ -2804,7 +2802,7 @@ def: "c executes activity in d if and only if c enables p and p occurs_in d. As synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -2853,7 +2851,7 @@ id: is_basis_for_realizable name: is basis for realizable xref: RO:0004018 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:29Z [Typedef] @@ -2863,7 +2861,7 @@ def: "inverse of bounds sequence of" [] subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to @@ -2874,7 +2872,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004011 property_value: seeAlso Orphanet:410296 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:55:51Z [Typedef] @@ -2885,7 +2883,7 @@ xref: RO:0004013 property_value: seeAlso Orphanet:317343 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:40Z [Typedef] @@ -2896,7 +2894,7 @@ xref: RO:0004016 property_value: seeAlso Orphanet:317346 is_a: contributes_to_condition ! contributes to condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:58:43Z [Typedef] @@ -2906,7 +2904,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004012 property_value: seeAlso Orphanet:410295 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:06Z [Typedef] @@ -2917,7 +2915,7 @@ xref: RO:0004014 property_value: seeAlso Orphanet:317344 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:07Z [Typedef] @@ -2927,7 +2925,7 @@ def: "Relates a gene to condition, such that a mutation in this gene predisposes xref: RO:0004015 property_value: seeAlso Orphanet:317345 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:43Z [Typedef] @@ -2937,7 +2935,7 @@ def: "x is a consecutive sequence of y iff x has subsequence y, and all the part xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: has_subsequence ! has subsequence @@ -2947,7 +2945,7 @@ name: is downstream of sequence of def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] xref: RO:0002529 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of @@ -2957,7 +2955,7 @@ id: is_eaten_by name: is eaten by subset: ro-eco xref: RO:0002471 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -2969,7 +2967,7 @@ def: "inverse of has end sequence" [] subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2982,7 +2980,7 @@ xref: RO:0004010 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string range: BFO:0000017 is_a: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:53:08Z [Typedef] @@ -2992,7 +2990,7 @@ def: "x is immediately downstream of the sequence of y iff either (1) x and y ha xref: RO:0002530 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002529 is_a: is_downstream_of_sequence_of ! is downstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3004,7 +3002,7 @@ def: "inverse of immediately downstream of" [] xref: RO:0002531 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: is_upstream_of_sequence_of ! is upstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3031,7 +3029,7 @@ def: "x is sequentially aligned with if a significant portion bases of x and y c xref: RO:0002521 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -3071,7 +3069,7 @@ def: "inverse of has start sequence" [] subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3084,7 +3082,7 @@ def: "inverse of has subsequence" [] subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of @@ -3107,7 +3105,7 @@ name: is treated by substance def: "Inverse of 'is substance that treats'" [] subset: RO:0002259 xref: RO:0002302 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 is_a: causally_related_to ! causally related to inverse_of: is_substance_that_treats ! is substance that treats @@ -3117,7 +3115,7 @@ name: is upstream of sequence of def: "inverse of downstream of sequence of" [] xref: RO:0002528 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -3127,7 +3125,7 @@ name: is vector for subset: ro-eco xref: RO:0002459 property_value: IAO:0000112 "Anopheles is a vector for Plasmodium" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: has_vector ! has vector @@ -3179,7 +3177,7 @@ name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco xref: RO:0002571 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:cjm xsd:string range: BFO:0000040 is_a: part_of @@ -3190,7 +3188,7 @@ name: luminal space of def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] subset: ro-eco xref: RO:0002572 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000141 is_a: lumen_of ! lumen of @@ -3202,7 +3200,7 @@ subset: ro-eco xref: RO:0002381 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with is_a: part_of @@ -3212,7 +3210,7 @@ id: mereotopologically_related_to name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] xref: RO:0002323 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string property_value: RO:0001900 RO:0001901 @@ -3230,7 +3228,7 @@ name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 @@ -3243,7 +3241,7 @@ name: mutualistically interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] subset: ro-eco xref: RO:0002442 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -3270,7 +3268,7 @@ name: negatively regulated by def: "inverse of negatively regulates" [] subset: RO:0002259 xref: RO:0002335 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3281,7 +3279,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 @@ -3330,7 +3328,7 @@ def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -3351,10 +3349,10 @@ expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://p [Typedef] id: overlaps_sequence_of name: overlaps sequence of -def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] xref: RO:0002526 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: overlaps ! overlaps is_a: sequentially_related_to ! sequentially related to @@ -3366,7 +3364,7 @@ subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string is_a: has_host ! has host @@ -3379,7 +3377,7 @@ name: parasitized by subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string @@ -3418,7 +3416,7 @@ name: part of developmental precursor of xref: RO:0002287 property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by [Typedef] @@ -3426,7 +3424,7 @@ id: part_of_structure_that_is_capable_of name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] xref: RO:0002329 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean is_a: functionally_related_to ! functionally related to @@ -3455,7 +3453,7 @@ subset: ro-eco synonym: "semibiotically interacts with" RELATED [] xref: RO:0002446 property_value: IAO:0000112 "Porifiera attaches to substrate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: biotically_interacts_with ! biotically interacts with @@ -3464,7 +3462,7 @@ id: participates_in_a_biotic-biotic_interaction_with name: participates in a biotic-biotic interaction with subset: ro-eco xref: RO:0002574 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 domain: CARO:0001010 range: CARO:0001010 @@ -3474,7 +3472,7 @@ is_a: biotically_interacts_with ! biotically interacts with id: partner_in name: partner in xref: RO:0002461 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string is_a: participates_in @@ -3483,7 +3481,7 @@ id: pathogen_of name: pathogen of subset: ro-eco xref: RO:0002556 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_host ! has host inverse_of: has_pathogen ! has pathogen @@ -3495,7 +3493,7 @@ subset: ro-eco subset: RO:0002259 xref: RO:0002201 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_functional: true [Typedef] @@ -3503,7 +3501,7 @@ id: phosphorylates name: phosphorylates xref: RO:0002447 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: molecularly_interacts_with ! molecularly interacts with @@ -3512,7 +3510,7 @@ id: pollinated_by name: pollinated by subset: ro-eco xref: RO:0002456 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string @@ -3525,7 +3523,7 @@ subset: ro-eco xref: RO:0002455 property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with @@ -3537,7 +3535,7 @@ name: positively regulated by def: "inverse of positively regulates" [] subset: RO:0002259 xref: RO:0002336 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3548,7 +3546,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002211 @@ -3583,7 +3581,7 @@ def: "inverse of preys on" [] subset: ro-eco subset: RO:0002259 xref: RO:0002458 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string @@ -3598,9 +3596,9 @@ subset: ro-eco xref: RO:0002439 property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Jorrit Poelen" xsd:string -property_value: IAO:0000117 "Katja Shulz" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7134-3324 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string @@ -3623,7 +3621,7 @@ def: "x proper_distributary_of y iff x distributary_of y and x does not flow bac subset: ro-eco xref: RO:0002382 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: distributary_of ! distributary of [Typedef] @@ -3633,7 +3631,7 @@ def: "x proper_tributary_of y iff x tributary_of y and x does not originate from subset: ro-eco xref: RO:0002383 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: tributary_of ! tributary of [Typedef] @@ -3642,7 +3640,7 @@ name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string @@ -3654,7 +3652,7 @@ id: provides_nutrients_for name: provides nutrients for subset: ro-eco xref: RO:0002469 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3663,7 +3661,7 @@ name: realizable has basis in xref: RO:0004017 is_a: causally_related_to ! causally related to inverse_of: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:01Z [Typedef] @@ -3672,10 +3670,10 @@ name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] synonym: "triggered by process" EXACT [RO:cjm] xref: RO:0009501 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "David Osumi-Sutherland" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string @@ -3692,7 +3690,7 @@ xref: RO:0004028 domain: BFO:0000017 range: BFO:0000040 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:45:49Z [Typedef] @@ -3700,7 +3698,7 @@ id: receives_input_from name: receives input from xref: RO:0002485 property_value: IAO:0000116 "See notes for inverse relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to inverse_of: sends_output_to ! sends output to @@ -3740,7 +3738,7 @@ name: regulated by def: "inverse of regulates" [] subset: RO:0002259 xref: RO:0002334 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 range: BFO:0000015 @@ -3755,9 +3753,9 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Hill" xsd:string -property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 +property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string @@ -3774,7 +3772,7 @@ id: regulates_activity_of name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] xref: RO:0011002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3794,7 +3792,7 @@ id: regulates_in_other_organism name: regulates in other organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] xref: RO:0002010 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 range: BFO:0000015 is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -3805,7 +3803,7 @@ name: regulates levels of def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] xref: RO:0002332 property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 @@ -3817,7 +3815,7 @@ id: regulates_quantity_of name: regulates quantity of def: "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." [] xref: RO:0011003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3836,7 +3834,7 @@ id: related_via_localization_to name: related via localization to def: "A relationship that holds via some process of localization" [] xref: RO:0002337 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 range: BFO:0000002 @@ -3857,7 +3855,7 @@ id: represses_expression_of name: represses expression of def: "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." [] xref: RO:0003002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3871,7 +3869,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -3916,7 +3914,7 @@ name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] @@ -3936,7 +3934,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002348 property_value: IAO:0000112 "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3948,7 +3946,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002349 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3962,7 +3960,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3972,7 +3970,7 @@ id: results_in_developmental_induction_of name: results in developmental induction of def: "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." [] xref: RO:0002357 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3982,7 +3980,7 @@ def: "p results in the developmental progression of s iff p is a developmental p xref: RO:0002295 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 range: CARO:0000000 @@ -3994,7 +3992,7 @@ name: results in developmental regression of xref: RO:0002301 property_value: IAO:0000112 "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4004,7 +4002,7 @@ name: results in disappearance of xref: RO:0002300 property_value: IAO:0000112 "foramen ovale closure SubClassOf results in disappearance of foramen ovale" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4020,7 +4018,7 @@ id: results_in_ending_of name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4034,7 +4032,7 @@ xref: RO:0002297 property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4056,7 +4054,7 @@ id: results_in_growth_of name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4071,7 +4069,7 @@ xref: RO:0002299 property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4087,7 +4085,7 @@ xref: RO:0002298 property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4100,7 +4098,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002565 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4126,7 +4124,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002356 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4135,7 +4133,7 @@ id: results_in_structural_organization_of name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4151,7 +4149,7 @@ name: results in transport across def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002342 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: occurs_across ! occurs across is_a: results_in_transport_to_from_or_in ! results in transport to from or in @@ -4160,7 +4158,7 @@ id: results_in_transport_along name: results in transport along def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] xref: RO:0002341 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4168,7 +4166,7 @@ id: results_in_transport_to_from_or_in name: results in transport to from or in xref: RO:0002344 property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4183,7 +4181,7 @@ id: sends_output_to name: sends output to xref: RO:0002486 property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to [Typedef] @@ -4225,7 +4223,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcript" xsd:string property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -4235,7 +4233,7 @@ name: sequentially related to def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string @@ -4248,7 +4246,7 @@ name: skeleton of def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 is_a: part_of @@ -4259,7 +4257,7 @@ name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] xref: RO:0002379 property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: overlaps ! overlaps @@ -4271,7 +4269,7 @@ subset: ro-eco xref: RO:0002163 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 @@ -4285,7 +4283,7 @@ name: stabilizes quantity of def: "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." [] xref: RO:0011015 property_value: IAO:0000112 "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_quantity_of ! directly positively regulates quantity of @@ -4294,14 +4292,14 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates id: starts subset: ro-eco xref: RO:0002223 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: starts_with subset: ro-eco xref: RO:0002224 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -4317,7 +4315,7 @@ name: subcluster of def: "A relation between a group and another group it is part of but does not fully constitute." [] xref: RO:0015003 property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." xsd:string -property_value: IAO:0000117 "Shawn Tan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true is_a: part_of @@ -4326,7 +4324,7 @@ is_a: part_of id: subject_participant_in name: subject participant in xref: RO:0002462 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4345,7 +4343,7 @@ name: surrounded by def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] xref: RO:0002219 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to inverse_of: surrounds ! surrounds @@ -4357,7 +4355,7 @@ def: "inverse of surrounded by" [] subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to @@ -4367,7 +4365,7 @@ name: symbiotically interacts with def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] subset: ro-eco xref: RO:0002440 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true @@ -4380,8 +4378,8 @@ def: "Relation between an anatomical structure (including cells) and a neuron th xref: RO:0002103 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: receives_input_from ! receives input from inverse_of: synapsed_to ! synapsed to @@ -4406,8 +4404,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002108 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" [] @@ -4420,8 +4418,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002109 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4434,8 +4432,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002112 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4448,8 +4446,8 @@ comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part som xref: RO:0002120 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: sends_output_to ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -4473,8 +4471,8 @@ def: "A relation between a motor neuron and a muscle that it synapses to via a t comment: Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) xref: RO:0002107 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_II_bouton ! synapsed_by_via_type_II_bouton @@ -4488,8 +4486,8 @@ comment: Expands to: has_part some ('type Ib terminal button' that has_part some xref: RO:0002105 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Ib_bouton ! synapsed_by_via_type_Ib_bouton @@ -4503,8 +4501,8 @@ comment: Expands to: has_part some ('type Is terminal button' that has_part some xref: RO:0002106 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Is_bouton ! synapsed_by_via_type_Is_bouton @@ -4514,7 +4512,7 @@ expand_expression_to: "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that id: target_participant_in name: target participant in xref: RO:0002463 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4523,7 +4521,7 @@ id: temporally_related_to subset: ro-eco xref: RO:0002222 property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string [Typedef] @@ -4531,7 +4529,7 @@ id: transformation_of name: transformation of def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] xref: RO:0002494 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: develops_from ! develops from @@ -4541,7 +4539,7 @@ name: transitively provides input for def: "transitive form of directly_provides_input_for" [] xref: RO:0002414 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." xsd:string property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string domain: BFO:0000015 @@ -4556,7 +4554,7 @@ def: "A relationship that holds between a disease and organism" [] xref: RO:0002451 property_value: IAO:0000112 "all dengue disease transmitted by some mosquito" xsd:string property_value: IAO:0000116 "Add domain and range constraints" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -4576,7 +4574,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002313 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "regulates localization of" xsd:string is_a: related_via_localization_to ! related via localization to is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4590,7 +4588,7 @@ xref: RO:0002376 property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string @@ -4608,7 +4606,7 @@ name: trophically interacts with def: "An interaction relationship in which the partners are related via a feeding relationship." [] subset: ro-eco xref: RO:0002438 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4618,7 +4616,7 @@ name: ubiquitinates def: "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" [] xref: RO:0002480 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with [Typedef] diff --git a/subsets/ro-interaction.owl b/subsets/ro-interaction.owl index 717d6903..1f7b268f 100644 --- a/subsets/ro-interaction.owl +++ b/subsets/ro-interaction.owl @@ -409,7 +409,7 @@ - David Osumi-Sutherland + RO:0002002 has_2D_boundary @@ -421,7 +421,7 @@ A relation that holds between two neurons that are electrically coupled via gap junctions. - David Osumi-Sutherland + RO:0002003 electrically_synapsed_to @@ -435,7 +435,7 @@ - David Osumi-Sutherland + RO:0002006 has_synaptic_terminal_of @@ -469,7 +469,7 @@ has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland + RO:0002007 bounding_layer_of @@ -505,9 +505,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. + A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. Note from NCEAS meeting: consider changing primary label - David Osumi-Sutherland + RO:0002008 coincident_with @@ -524,7 +524,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - David Osumi-Sutherland + RO:0002010 regulates_in_other_organism regulates in other organism @@ -553,7 +553,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + dos 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -568,7 +568,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + dos 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -584,7 +584,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + dos 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -599,7 +599,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -613,7 +613,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -630,7 +630,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + dos 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -644,7 +644,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + dos 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -658,7 +658,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + dos 2017-07-20T17:11:08Z RO:0002020 transports @@ -672,7 +672,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + dos 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -686,7 +686,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -697,7 +697,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + GOC:dos @@ -708,7 +708,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + dos 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -718,7 +718,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + GOC:dos @@ -729,7 +729,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + dos 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -739,7 +739,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + GOC:dos @@ -750,7 +750,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + dos 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -761,7 +761,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + GOC:dos @@ -780,7 +780,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + dos 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -797,7 +797,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + GOC:dos @@ -814,7 +814,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + RO:0002090 @@ -831,7 +831,7 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure that its soma is part of. - David Osumi-Sutherland + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -852,9 +852,9 @@ Examples include: the relationship between two channels collected simultaneously relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - David Osumi-Sutherland + fasciculates with - (forall (?x ?y) + (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) @@ -890,9 +890,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure its axon forms (chemical) synapses in. - Chris Mungall - David Osumi-Sutherland - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -924,8 +923,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -945,9 +944,9 @@ Examples include: the relationship between two channels collected simultaneously Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - Alexander Diehl - Chris Mungall - Lindsay Cowell + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) @@ -965,8 +964,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -985,8 +984,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -1005,8 +1004,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) RO:0002107 @@ -1023,8 +1022,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1043,8 +1042,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1064,8 +1063,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - Chris Mungall - David Osumi-Sutherland + + synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( @@ -1085,8 +1084,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1168,8 +1167,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -1196,8 +1195,8 @@ N1 SubclassOf ( Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -1218,7 +1217,7 @@ N1 SubclassOf ( A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - David Osumi-Sutherland + has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) @@ -1267,9 +1266,9 @@ N1 SubclassOf ( The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - David Osumi-Sutherland + has fasciculating component - (forall (?x ?y) + (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) @@ -1309,8 +1308,8 @@ N1 SubclassOf ( - X continuous_with Y if and only if X and Y share a fiat boundary. - David Osumi-Sutherland + X continuous_with Y if and only if X and Y share a fiat boundary. + connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) @@ -1329,8 +1328,8 @@ N1 SubclassOf ( x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom - proper overlaps - (forall (?x ?y) + proper overlaps + (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and @@ -1353,7 +1352,7 @@ N1 SubclassOf ( A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - Chris Mungall + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) @@ -1361,7 +1360,7 @@ N1 SubclassOf ( RO:0002163 spatially_disjoint_from - spatially disjoint from + spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern @@ -1498,7 +1497,7 @@ N1 SubclassOf ( A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - Chris Mungall + RO:0002200 has_phenotype @@ -1513,7 +1512,7 @@ N1 SubclassOf ( inverse of has phenotype - Chris Mungall + RO:0002201 @@ -1533,10 +1532,10 @@ N1 SubclassOf ( x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - Terry Meehan + + + + RO:0002202 develops_from This is the transitive form of the develops from relation @@ -1554,9 +1553,9 @@ N1 SubclassOf ( inverse of develops from - Chris Mungall - David Osumi-Sutherland - Terry Meehan + + + RO:0002203 develops_into @@ -1588,12 +1587,12 @@ N1 SubclassOf ( Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - Chris Mungall - David Osumi-Sutherland - has developmental precursor + + FBbt RO:0002207 + has developmental precursor directly_develops_from TODO - add child relations from DOS directly develops from @@ -1651,9 +1650,9 @@ N1 SubclassOf ( p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - Chris Mungall - David Hill - Tanya Berardini + + + GO Regulation precludes parthood; the regulatory process may not be within the regulated process. @@ -1676,7 +1675,7 @@ N1 SubclassOf ( p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - Chris Mungall + negatively regulates (process to process) @@ -1698,7 +1697,7 @@ N1 SubclassOf ( p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - Chris Mungall + positively regulates (process to process) @@ -1721,7 +1720,7 @@ N1 SubclassOf ( mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - Chris Mungall + has function realized in @@ -1740,7 +1739,7 @@ N1 SubclassOf ( c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - Chris Mungall + has function in RO:0002216 capable_of_part_of @@ -1757,7 +1756,7 @@ N1 SubclassOf ( x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - Chris Mungall + RO:0002219 surrounded_by @@ -1779,7 +1778,7 @@ N1 SubclassOf ( x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - Chris Mungall + RO:0002220 @@ -1803,7 +1802,7 @@ N1 SubclassOf ( inverse of surrounded by - Chris Mungall + RO:0002221 @@ -1816,7 +1815,7 @@ N1 SubclassOf ( - Chris Mungall + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 @@ -1830,7 +1829,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002223 starts @@ -1842,7 +1841,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002224 starts_with @@ -1856,7 +1855,7 @@ N1 SubclassOf ( x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - Chris Mungall + RO:0002225 develops_from_part_of develops from part of @@ -1871,7 +1870,7 @@ N1 SubclassOf ( x develops_in y if x is located in y whilst x is developing - Chris Mungall + EHDAA2 Jonathan Bard, EHDAA2 RO:0002226 @@ -1909,7 +1908,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002229 ends @@ -1921,7 +1920,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002230 ends_with @@ -1937,7 +1936,7 @@ N1 SubclassOf ( x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - Chris Mungall + starts with process that occurs in RO:0002231 @@ -1955,7 +1954,7 @@ N1 SubclassOf ( x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - Chris Mungall + ends with process that occurs in RO:0002232 @@ -1973,7 +1972,7 @@ N1 SubclassOf ( p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + consumes RO:0002233 @@ -1993,7 +1992,7 @@ N1 SubclassOf ( p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - Chris Mungall + produces RO:0002234 @@ -2047,7 +2046,7 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - Bill Duncan (https://orcid.org/0000-0001-9625-1899) + This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. @@ -2196,7 +2195,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y - Chris Mungall + RO:0002254 has_developmental_contribution_from has developmental contribution from @@ -2211,7 +2210,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho inverse of has developmental contribution from - Chris Mungall + RO:0002255 developmentally_contributes_to @@ -2229,9 +2228,9 @@ If you need an axiom that says 'has_participant min 2 object', you sho t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - Chris Mungall - David Osumi-Sutherland - Melissa Haendel + + + induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) @@ -2251,7 +2250,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally induced by - Chris Mungall + RO:0002257 developmentally_induces developmentally induces @@ -2269,7 +2268,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - Chris Mungall + In general you should not use this relation to make assertions - use one of the more specific relations below this one RO:0002258 developmentally_preceded_by @@ -2317,7 +2316,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - Chris Mungall + replaces RO:0002285 developmentally_replaces @@ -2332,7 +2331,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally preceded by - Chris Mungall + RO:0002286 developmentally_succeeded_by developmentally succeeded by @@ -2346,7 +2345,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - Chris Mungall + RO:0002287 part_of_developmental_precursor_of part of developmental precursor of @@ -2363,7 +2362,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - Chris Mungall + RO:0002295 results_in_developmental_progression_of results in developmental progression of @@ -2380,7 +2379,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - Chris Mungall + http://www.geneontology.org/GO.doc.development.shtml RO:0002296 @@ -2401,7 +2400,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002297 @@ -2422,7 +2421,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002298 @@ -2443,7 +2442,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002299 @@ -2461,7 +2460,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho foramen ovale closure SubClassOf results in disappearance of foramen ovale - Chris Mungall + May be merged into parent relation RO:0002300 results_in_disappearance_of @@ -2476,7 +2475,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) - Chris Mungall + May be merged into parent relation RO:0002301 results_in_developmental_regression_of @@ -2491,7 +2490,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of 'is substance that treats' - cjm + RO:0002302 is_treated_by_substance @@ -2511,7 +2510,7 @@ where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. - Pier Buttigieg + adapted for living in RO:0002303 @@ -2529,7 +2528,7 @@ where p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - cjm + RO:0002304 @@ -2547,7 +2546,7 @@ where p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - cjm + RO:0002305 @@ -2562,10 +2561,10 @@ where A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. - Austin Meier - Chris Mungall - Marie Angelique Laporte - cjm + + + + 2017-06-05T17:35:04Z RO:0002309 has_exposure_stimulus @@ -2580,7 +2579,7 @@ where Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. - Chris Mungall + regulates localization of RO:0002313 @@ -2600,7 +2599,7 @@ where an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002315 @@ -2617,7 +2616,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions RO:0002321 @@ -2633,7 +2632,7 @@ where An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. - Chris Mungall + adapted for RO:0002322 @@ -2647,7 +2646,7 @@ where A mereological relationship or a topological relationship - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships RO:0002323 @@ -2661,7 +2660,7 @@ where A relationship that holds between entities participating in some developmental process (GO:0032502) - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development RO:0002324 developmentally_related_to @@ -2678,9 +2677,8 @@ where Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. - Chris Mungall + In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - Gene Ontology Consortium RO:0002325 colocalizes_with @@ -2708,7 +2706,7 @@ then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. - Chris Mungall + In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 @@ -2725,7 +2723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - Chris Mungall + catalyzes executes has @@ -2744,7 +2742,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 functionally_related_to @@ -2758,7 +2756,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati this relation holds between c and p when c is part of some c', and c' is capable of p. - Chris Mungall + false RO:0002329 part_of_structure_that_is_capable_of @@ -2773,7 +2771,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati c involved_in p if and only if c enables some process p', and p' is part of p - Chris Mungall + actively involved in enables part of RO:0002331 @@ -2792,7 +2790,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - Chris Mungall + regulates levels of (process to entity) RO:0002332 @@ -2808,7 +2806,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables - Chris Mungall + RO:0002333 enabled_by @@ -2825,7 +2823,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of regulates - Chris Mungall + regulated by (processual) RO:0002334 @@ -2840,7 +2838,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of negatively regulates - Chris Mungall + RO:0002335 negatively_regulated_by @@ -2854,7 +2852,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of positively regulates - Chris Mungall + RO:0002336 positively_regulated_by @@ -2869,7 +2867,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds via some process of localization - Chris Mungall + Do not use this relation directly. It is a grouping relation. RO:0002337 related_via_localization_to @@ -2883,7 +2881,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - Chris Mungall + RO:0002338 @@ -2899,7 +2897,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - Chris Mungall + RO:0002339 @@ -2915,7 +2913,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. - Chris Mungall + RO:0002340 imports @@ -2929,7 +2927,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - Chris Mungall + RO:0002341 results_in_transport_along results in transport along @@ -2943,7 +2941,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - Chris Mungall + RO:0002342 results_in_transport_across @@ -2958,7 +2956,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'pollen tube growth' results_in growth_of some 'pollen tube' - Chris Mungall + RO:0002343 results_in_growth_of results in growth of @@ -2971,7 +2969,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - Chris Mungall + RO:0002344 results_in_transport_to_from_or_in results in transport to from or in @@ -2983,8 +2981,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. - Chris Mungall + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. + RO:0002345 exports @@ -3000,7 +2998,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - Chris Mungall + RO:0002348 @@ -3017,7 +3015,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - Chris Mungall + RO:0002349 @@ -3034,7 +3032,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has input - Chris Mungall + RO:0002352 @@ -3050,7 +3048,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has output - Chris Mungall + RO:0002353 @@ -3064,7 +3062,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002354 formed_as_result_of formed as result of @@ -3078,7 +3076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. - Chris Mungall + RO:0002355 results_in_structural_organization_of results in structural organization of @@ -3092,7 +3090,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - Chris Mungall + RO:0002356 @@ -3108,7 +3106,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. - Chris Mungall + RO:0002357 results_in_developmental_induction_of results in developmental induction of @@ -3120,7 +3118,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + http://neurolex.org/wiki/Property:DendriteLocation RO:0002360 has_dendrite_location @@ -3136,7 +3134,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - Chris Mungall + attached to (anatomical structure to anatomical structure) RO:0002371 @@ -3153,7 +3151,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002372 has_muscle_origin @@ -3176,7 +3174,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002373 has_muscle_insertion @@ -3200,7 +3198,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) @@ -3222,7 +3220,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - Chris Mungall + drains into drains to tributary channel of @@ -3247,7 +3245,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Deschutes River distributary_of Little Lava Lake x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - Chris Mungall + branch of distributary channel of http://en.wikipedia.org/wiki/Distributary @@ -3273,7 +3271,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. - Chris Mungall + anastomoses with RO:0002378 @@ -3289,7 +3287,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - Chris Mungall + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios RO:0002379 spatially_coextensive_with @@ -3312,7 +3310,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - Chris Mungall + RO:0002380 branching_part_of @@ -3331,7 +3329,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. - Chris Mungall + RO:0002381 main_stem_of @@ -3347,7 +3345,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_distributary_of y iff x distributary_of y and x does not flow back into y - Chris Mungall + RO:0002382 proper_distributary_of @@ -3362,7 +3360,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_tributary_of y iff x tributary_of y and x does not originate from y - Chris Mungall + RO:0002383 proper_tributary_of @@ -3379,7 +3377,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - Chris Mungall + RO:0002384 has_developmental_potential_involving has developmental potential involving @@ -3393,7 +3391,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - Chris Mungall + RO:0002385 has_potential_to_developmentally_contribute_to has potential to developmentally contribute to @@ -3407,7 +3405,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - Chris Mungall + RO:0002386 has_potential_to_developmentally_induce has potential to developmentally induce @@ -3421,7 +3419,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has the potential to develop into y iff x develops into y or if x is capable of developing into y - Chris Mungall + RO:0002387 has_potential_to_develop_into has potential to develop into @@ -3435,7 +3433,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - Chris Mungall + RO:0002388 has_potential_to_directly_develop_into has potential to directly develop into @@ -3450,7 +3448,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' RO:0002400 @@ -3468,7 +3466,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of upstream of - Chris Mungall + RO:0002404 causally_downstream_of causally downstream of @@ -3483,7 +3481,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002405 immediately_causally_downstream_of immediately causally downstream of @@ -3498,7 +3496,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - Chris Mungall + indirectly activates RO:0002407 @@ -3515,7 +3513,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - Chris Mungall + indirectly inhibits RO:0002409 @@ -3544,7 +3542,7 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002410 causally_related_to @@ -3566,7 +3564,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - Chris Mungall + RO:0002411 @@ -3582,7 +3580,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - Chris Mungall + RO:0002412 immediately_causally_upstream_of @@ -3598,7 +3596,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit - Chris Mungall + directly provides input for directly provides input for (process to process) @@ -3618,7 +3616,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different transitive form of directly_provides_input_for - Chris Mungall + This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. transitively provides input for (process to process) RO:0002414 @@ -3636,7 +3634,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall + influences (processual) RO:0002418 affects @@ -3652,7 +3650,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - Chris Mungall + RO:0002427 @@ -3668,7 +3666,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - Chris Mungall + RO:0002428 involved_in_regulation_of involved in regulation of @@ -3681,7 +3679,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - Chris Mungall + RO:0002429 involved_in_positive_regulation_of @@ -3695,7 +3693,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - Chris Mungall + RO:0002430 involved_in_negative_regulation_of @@ -3712,7 +3710,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - Chris Mungall + involved in or reguates RO:0002431 involved_in_or_involved_in_regulation_of @@ -3728,7 +3726,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall + executes activity in RO:0002432 enables activity in @@ -3740,8 +3738,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + GOC:cjm + GOC:dos @@ -3751,7 +3749,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - Chris Mungall + RO:0002433 contributes_to_morphology_of contributes to morphology of @@ -3768,7 +3766,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. - Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. RO:0002434 in pairwise interaction with @@ -3787,7 +3785,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) - Chris Mungall + RO:0002435 genetically_interacts_with genetically interacts with @@ -3803,7 +3801,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - Chris Mungall + binds molecularly binds with RO:0002436 @@ -3824,7 +3822,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - Chris Mungall + interacts with on organism level RO:0002437 @@ -3841,7 +3839,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the partners are related via a feeding relationship. - Chris Mungall + RO:0002438 trophically_interacts_with @@ -3859,9 +3857,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] Baleen whale preys on krill An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - Chris Mungall - Jorrit Poelen - Katja Shulz + + + is subject of predation interaction with preys upon RO:0002439 @@ -3880,7 +3878,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A biotic interaction in which the two organisms live together in more or less intimate association. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism RO:0002440 @@ -3896,7 +3894,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002441 @@ -3911,7 +3909,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002442 @@ -3926,7 +3924,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 This relation groups a pair of inverse relations, parasite of and parasitized by RO:0002443 @@ -3944,7 +3942,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human - Chris Mungall + parasitizes RO:0002444 direct parasite of @@ -3961,7 +3959,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + has parasite parasitised by RO:0002445 @@ -3980,7 +3978,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - Chris Mungall + RO:0002446 semibiotically interacts with @@ -3996,7 +3994,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. RO:0002447 phosphorylates @@ -4015,8 +4013,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - Chris Mungall - Vasundra Touré + + RO:0002448 molecularly controls directly_regulates_activity_of @@ -4033,8 +4031,8 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly inhibits RO:0002449 molecularly decreases activity of @@ -4052,8 +4050,8 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly activates RO:0002450 molecularly increases activity of @@ -4070,7 +4068,7 @@ For example, A and B may be gene products and binding of B by A positively regul all dengue disease transmitted by some mosquito A relationship that holds between a disease and organism Add domain and range constraints - Chris Mungall + RO:0002451 transmitted_by transmitted by @@ -4084,7 +4082,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between a disease or an organism and a phenotype - Chris Mungall + RO:0002452 has_symptom has symptom @@ -4096,7 +4094,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) RO:0002453 @@ -4111,7 +4109,7 @@ For example, A and B may be gene products and binding of B by A positively regul X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y - Chris Mungall + RO:0002454 has_host @@ -4128,7 +4126,7 @@ For example, A and B may be gene products and binding of B by A positively regul Bees pollinate Flowers This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - Chris Mungall + is subject of pollination interaction with RO:0002455 @@ -4143,7 +4141,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + has polinator is target of pollination interaction with RO:0002456 @@ -4160,7 +4158,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4175,7 +4173,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of preys on - Chris Mungall + has predator is target of predation interaction with RO:0002458 @@ -4195,7 +4193,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anopheles is a vector for Plasmodium - Chris Mungall + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism RO:0002459 @@ -4209,7 +4207,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002460 has_vector @@ -4222,7 +4220,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target RO:0002461 partner_in @@ -4235,7 +4233,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002462 subject_participant_in @@ -4248,7 +4246,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002463 target_participant_in @@ -4261,7 +4259,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002469 provides_nutrients_for @@ -4274,7 +4272,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is subject of eating interaction with RO:0002470 @@ -4288,7 +4286,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + eaten by is target of eating interaction with RO:0002471 @@ -4307,7 +4305,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - Chris Mungall + RO:0002473 @@ -4326,7 +4324,7 @@ For example, A and B may be gene products and binding of B by A positively regul ABal nucleus child nucleus of ABa nucleus (in C elegans) c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d - Chris Mungall + This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. RO:0002476 child_nucleus_of @@ -4340,7 +4338,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a hermaphroditic organism - Chris Mungall + RO:0002477 child_nucleus_of_in_hermaphrodite child nucleus of in hermaphrodite @@ -4353,7 +4351,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a male organism - Chris Mungall + RO:0002478 child_nucleus_of_in_male child nucleus of in male @@ -4367,7 +4365,7 @@ For example, A and B may be gene products and binding of B by A positively regul p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall + RO:0002479 has_part_that_occurs_in @@ -4382,7 +4380,7 @@ For example, A and B may be gene products and binding of B by A positively regul An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y Axiomatization to GO to be added later - Chris Mungall + RO:0002480 ubiquitinates ubiquitinates @@ -4396,7 +4394,7 @@ For example, A and B may be gene products and binding of B by A positively regul See notes for inverse relation - Chris Mungall + RO:0002485 receives_input_from receives input from @@ -4409,7 +4407,7 @@ For example, A and B may be gene products and binding of B by A positively regul This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - Chris Mungall + RO:0002486 sends_output_to sends output to @@ -4423,7 +4421,7 @@ For example, A and B may be gene products and binding of B by A positively regul x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - Chris Mungall + RO:0002494 transformation_of transformation of @@ -4437,7 +4435,7 @@ For example, A and B may be gene products and binding of B by A positively regul x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - Chris Mungall + RO:0002495 immediate_transformation_of @@ -4467,7 +4465,7 @@ For example, A and B may be gene products and binding of B by A positively regul p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002501 @@ -4483,7 +4481,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c - Chris Mungall + has intermediate product RO:0002505 @@ -4500,7 +4498,7 @@ For example, A and B may be gene products and binding of B by A positively regul The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002506 @@ -4522,11 +4520,11 @@ For example, A and B may be gene products and binding of B by A positively regul A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future - Chris Mungall + determined by (system to material entity) - Chris Mungall - Pier Buttigieg + + RO:0002507 determined_by @@ -4540,7 +4538,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of determined by - Chris Mungall + determines (material entity to system) RO:0002508 @@ -4559,7 +4557,7 @@ For example, A and B may be gene products and binding of B by A positively regul s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. - Chris Mungall + RO:0002509 determined_by_part_of @@ -4574,7 +4572,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between two entities that have the property of being sequences or having sequences. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. @@ -4594,7 +4592,7 @@ For example, A and B may be gene products and binding of B by A positively regul Two consecutive DNA residues are sequentially adjacent Two exons on a processed transcript that were previously connected by an intron are adjacent x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002515 @@ -4612,7 +4610,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as a start sequence the start codon for that transcript x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence - Chris Mungall + started by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4629,7 +4627,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has start sequence - Chris Mungall + starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4649,7 +4647,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence - Chris Mungall + ended by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4666,7 +4664,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has end sequence - Chris Mungall + ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4684,7 +4682,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. In the SO paper, this was defined as an instance-type relation - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002520 @@ -4701,7 +4699,7 @@ For example, A and B may be gene products and binding of B by A positively regul Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering - Chris Mungall + RO:0002521 is_sequentially_aligned_with @@ -4718,7 +4716,7 @@ For example, A and B may be gene products and binding of B by A positively regul The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y - Chris Mungall + RO:0002522 bounds_sequence_of @@ -4733,7 +4731,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of bounds sequence of - Chris Mungall + RO:0002523 @@ -4751,8 +4749,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x has subsequence y iff all of the sequence parts of x are sequence parts of y - Chris Mungall + x has subsequence y iff all of the sequence parts of y are sequence parts of x + contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4771,7 +4769,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has subsequence - Chris Mungall + contained by RO:0002525 @@ -4788,8 +4786,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. - Chris Mungall + x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. + RO:0002526 overlaps_sequence_of @@ -4803,8 +4801,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. - Chris Mungall + x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + disconnected from RO:0002527 @@ -4820,7 +4818,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of downstream of sequence of - Chris Mungall + RO:0002528 is_upstream_of_sequence_of @@ -4836,7 +4834,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. - Chris Mungall + RO:0002529 is_downstream_of_sequence_of @@ -4852,7 +4850,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y - Chris Mungall + RO:0002530 @@ -4869,7 +4867,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript inverse of immediately downstream of - Chris Mungall + RO:0002531 is_immediately_upstream_of_sequence_of @@ -4889,7 +4887,7 @@ For example, A and B may be gene products and binding of B by A positively regul Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - Chris Mungall + has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). RO:0002551 @@ -4911,7 +4909,7 @@ For example, A and B may be gene products and binding of B by A positively regul p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. - Chris Mungall + RO:0002552 results_in_ending_of results in ending of @@ -4926,7 +4924,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - Chris Mungall + http://eol.org/schema/terms/hyperparasitoidOf https://en.wikipedia.org/wiki/Hyperparasite RO:0002553 @@ -4944,7 +4942,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of hyperparasite of - Chris Mungall + RO:0002554 has epiparasite has hyperparasite @@ -4961,7 +4959,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + http://en.wikipedia.org/wiki/Allelopathy RO:0002555 @@ -4978,7 +4976,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002556 pathogen_of @@ -4991,7 +4989,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002557 has_pathogen @@ -5005,7 +5003,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + causally influenced by (entity-centric) RO:0002559 @@ -5020,7 +5018,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - Chris Mungall + RO:0002565 @@ -5039,8 +5037,8 @@ For example, A and B may be gene products and binding of B by A positively regul The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - Chris Mungall - Vasundra Touré + + causally influences (entity-centric) RO:0002566 @@ -5057,7 +5055,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between elements of a musculoskeletal system or its analogs. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. RO:0002567 biomechanically_related_to @@ -5071,7 +5069,7 @@ For example, A and B may be gene products and binding of B by A positively regul m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - Chris Mungall + Wikipedia:Antagonist_(muscle) RO:0002568 has_muscle_antagonist @@ -5087,7 +5085,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of branching part of - Chris Mungall + RO:0002569 @@ -5104,7 +5102,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - Chris Mungall + UBERON:cjm This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. RO:0002570 @@ -5121,7 +5119,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - Chris Mungall + GOC:cjm RO:0002571 @@ -5137,7 +5135,7 @@ For example, A and B may be gene products and binding of B by A positively regul s is luminal space of x iff s is lumen_of x and s is an immaterial entity - Chris Mungall + RO:0002572 luminal_space_of @@ -5152,7 +5150,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002574 participates_in_a_biotic-biotic_interaction_with @@ -5169,7 +5167,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has skeleton - Chris Mungall + RO:0002576 skeleton_of @@ -5184,7 +5182,7 @@ For example, A and B may be gene products and binding of B by A positively regul p directly regulates q iff p is immediately causally upstream of q and p regulates q. - Chris Mungall + directly regulates (processual) @@ -5205,7 +5203,7 @@ For example, A and B may be gene products and binding of B by A positively regul gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - Chris Mungall + RO:0002584 has_part_structure_that_is_capable_of has part structure that is capable of @@ -5320,7 +5318,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall + RO:0002595 causal_relation_between_material_entity_and_a_process @@ -5723,7 +5721,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. - Vasundra Touré + RO:0003002 represses_expression_of represses expression of @@ -5738,7 +5736,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. - Vasundra Touré + RO:0003003 increases_expression_of increases expression of @@ -5883,7 +5881,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:38:20Z RO:0004000 condition_has_genetic_basis_in @@ -5897,7 +5895,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:20Z RO:0004001 has_material_basis_in_gain_of_function_germline_mutation_in @@ -5913,7 +5911,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:37Z RO:0004002 has_material_basis_in_loss_of_function_germline_mutation_in @@ -5927,7 +5925,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:54Z RO:0004003 has_material_basis_in_germline_mutation_in @@ -5942,7 +5940,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:07Z RO:0004004 has_material_basis_in_somatic_mutation_in @@ -5957,7 +5955,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:26Z RO:0004005 has_major_susceptibility_factor @@ -5971,7 +5969,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:57Z RO:0004006 has_partial_material_basis_in_germline_mutation_in @@ -5985,7 +5983,7 @@ Environmental exposures include those imposed by natural environments, experimen p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - cjm + 2018-12-13T11:26:17Z RO:0004007 @@ -6001,7 +5999,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - cjm + 2018-12-13T11:26:32Z RO:0004008 @@ -6012,8 +6010,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6027,7 +6025,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - cjm + 2018-12-13T11:26:56Z RO:0004009 @@ -6038,8 +6036,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6053,7 +6051,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:53:08Z RO:0004010 is_genetic_basis_for_condition @@ -6067,7 +6065,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:55:51Z RO:0004011 is_causal_gain_of_function_germline_mutation_of_in @@ -6082,7 +6080,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:06Z RO:0004012 is_causal_loss_of_function_germline_mutation_of_in @@ -6098,7 +6096,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:40Z RO:0004013 is_causal_germline_mutation_in @@ -6114,7 +6112,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:57:07Z RO:0004014 is_causal_somatic_mutation_in @@ -6129,7 +6127,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. - cjm + 2017-11-05T02:57:43Z RO:0004015 is_causal_susceptibility_factor_for @@ -6145,7 +6143,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. - cjm + 2017-11-05T02:58:43Z RO:0004016 is_causal_germline_mutation_partially_giving_rise_to @@ -6160,7 +6158,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:01Z RO:0004017 realizable_has_basis_in @@ -6173,7 +6171,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:29Z RO:0004018 is_basis_for_realizable @@ -6188,7 +6186,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:26:47Z RO:0004019 disease_has_basis_in @@ -6204,7 +6202,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) - cjm + 2017-11-05T03:29:32Z RO:0004020 disease_has_basis_in_dysfunction_of @@ -6220,7 +6218,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. disease has basis in disruption of (disease to process) - cjm + 2017-11-05T03:37:52Z RO:0004021 disease_has_basis_in_disruption_of @@ -6244,7 +6242,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. - cjm + 2017-11-05T03:46:07Z RO:0004022 disease_has_basis_in_feature @@ -6260,7 +6258,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. - cjm + 2017-11-05T03:50:54Z RO:0004023 causal_relationship_with_disease_as_subject @@ -6277,7 +6275,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and a process where the disease process disrupts the execution of the process. disease causes disruption of (disease to process) - cjm + 2017-11-05T03:51:09Z RO:0004024 disease_causes_disruption_of @@ -6293,7 +6291,7 @@ Environmental exposures include those imposed by natural environments, experimen disease causes dysfunction of (disease to anatomical entity) - cjm + 2017-11-05T03:58:20Z RO:0004025 disease_causes_dysfunction_of @@ -6319,7 +6317,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. - cjm + 2017-11-05T04:06:02Z RO:0004026 disease_has_location @@ -6343,7 +6341,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity - cjm + 2017-12-26T19:37:31Z RO:0004027 disease_has_inflammation_site @@ -6359,7 +6357,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - cjm + 2017-12-26T19:45:49Z RO:0004028 realized_in_response_to_stimulus @@ -6382,7 +6380,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. - cjm + 2017-12-26T19:50:53Z RO:0004029 disease_has_feature @@ -6397,7 +6395,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. - cjm + 2017-12-26T19:58:44Z RO:0004030 disease_arises_from_alteration_in_structure @@ -6411,7 +6409,7 @@ Environmental exposures include those imposed by natural environments, experimen Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - cjm + 2018-01-25T23:20:13Z RO:0004031 enables_subfunction @@ -6425,7 +6423,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:30Z RO:0004032 @@ -6441,7 +6439,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:51Z RO:0004033 @@ -6458,7 +6456,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - cjm + 2018-01-26T23:53:14Z RO:0004034 @@ -6476,7 +6474,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - cjm + 2018-01-26T23:53:22Z RO:0004035 @@ -6492,7 +6490,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:05Z RO:0004046 causally_upstream_of_or_within,_negative_effect @@ -6506,7 +6504,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:19Z RO:0004047 causally_upstream_of_or_within,_positive_effect @@ -6633,10 +6631,10 @@ Environmental exposures include those imposed by natural environments, experimen An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - Austin Meier - Chris Mungall - David Osumi-Sutherland - Marie Angelique Laporte + + + + RO:0009501 triggered by process realized_in_response_to @@ -6659,7 +6657,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - Vasundra Touré + RO:0011002 regulates_activity_of regulates activity of @@ -6674,7 +6672,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. - Vasundra Touré + RO:0011003 regulates_quantity_of regulates quantity of @@ -6689,7 +6687,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. - Vasundra Touré + RO:0011004 indirectly_regulates_activity_of indirectly regulates activity of @@ -6706,7 +6704,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011007 decreases_by_repression_quantity_of decreases by repression quantity of @@ -6723,7 +6721,7 @@ For example, protein A (transcription factor) indirectly decreases by repression The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011008 increases_by_expression_quantity_of increases by expression quantity of @@ -6738,7 +6736,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly positively regulates the quantity of B. - Vasundra Touré + RO:0011009 directly_positively_regulates_quantity_of directly positively regulates quantity of @@ -6753,7 +6751,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly negatively regulates the quantity of B. - Vasundra Touré + RO:0011010 directly_negatively_regulates_quantity_of directly negatively regulates quantity of @@ -6768,7 +6766,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. - Vasundra Touré + indirectly activates RO:0011013 indirectly_positively_regulates_activity_of @@ -6785,7 +6783,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. - Vasundra Touré + RO:0011014 destabilizes_quantity_of destabilizes quantity of @@ -6801,7 +6799,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. - Vasundra Touré + RO:0011015 stabilizes_quantity_of stabilizes quantity of @@ -6814,7 +6812,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. - Vasundra Touré + indirectly inhibits RO:0011016 indirectly_negatively_regulates_activity_of @@ -6828,7 +6826,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. - Vasundra Touré + RO:0011021 directly_regulates_quantity_of directly regulates quantity of @@ -6841,7 +6839,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011022 indirectly_regulates_quantity_of indirectly regulates quantity of @@ -6854,7 +6852,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011023 indirectly_negatively_regulates_quantity_of indirectly negatively regulates quantity of @@ -6867,7 +6865,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011024 indirectly_positively_regulates_quantity_of indirectly positively regulates quantity of @@ -6880,8 +6878,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is regulated by the small molecule continuant + pg 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -6895,8 +6893,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is activated by the small molecule continuant + pg 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -6910,8 +6908,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant + pg 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -6924,8 +6922,8 @@ For example, protein A (transcription factor) indirectly increases by expression - p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + p acts on population of c iff c' is a collection, has members of type c, and p has participant c + pg 2020-06-08T17:21:33Z RO:0012003 @@ -6941,8 +6939,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process + pg 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -6956,8 +6954,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process + pg 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of @@ -6971,8 +6969,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process + pg 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of @@ -6985,8 +6983,8 @@ For example, protein A (transcription factor) indirectly increases by expression - The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. + pg 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -6999,7 +6997,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + pg 2021-02-26T07:28:29Z RO:0012008 @@ -7016,7 +7014,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + pg 2022-09-26T06:01:01Z RO:0012009 @@ -7032,7 +7030,7 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + pg 2022-09-26T06:06:20Z RO:0012010 @@ -7048,7 +7046,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + pg 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7063,7 +7061,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + pg 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7229,7 +7227,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relation between a group and another group it is part of but does not fully constitute. X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. - Shawn Tan + This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. RO:0015003 subcluster_of @@ -7301,7 +7299,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - http://orcid.org/0000-0002-7463-6306 + 2021-11-05T17:30:44Z RO:0016002 has_disease @@ -7457,7 +7455,7 @@ For example, protein A (transcription factor) indirectly increases by expression This relation groups relations between diseases and any other kind of entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. - cjm + 2018-09-26T00:00:32Z RO:0040035 disease_relationship @@ -7471,7 +7469,7 @@ For example, protein A (transcription factor) indirectly increases by expression p has anatomical participant c iff p has participant c, and c is an anatomical entity - cjm + 2018-09-26T01:08:58Z RO:0040036 results_in_changes_to_anatomical_or_cellular_structure diff --git a/subsets/ro-mereotopology.obo b/subsets/ro-mereotopology.obo index 7945191a..33d6e97a 100644 --- a/subsets/ro-mereotopology.obo +++ b/subsets/ro-mereotopology.obo @@ -13,7 +13,7 @@ id: acquires_nutrients_from name: acquires nutrients from subset: ro-eco xref: RO:0002457 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for @@ -58,7 +58,7 @@ property_value: RO:0004050 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:22Z [Typedef] @@ -71,7 +71,7 @@ property_value: RO:0004049 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:14Z [Typedef] @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z [Typedef] @@ -103,7 +103,7 @@ xref: RO:0004032 property_value: RO:0004049 RO:0002264 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z [Typedef] @@ -120,7 +120,7 @@ property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cy property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 domain: BFO:0000004 range: BFO:0000004 @@ -131,7 +131,7 @@ id: allelopath_of name: allelopath of subset: ro-eco xref: RO:0002555 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string @@ -153,7 +153,7 @@ def: "x anabranch_of y if x is a distributary of y (i.e. it channels a from a la subset: ro-eco xref: RO:0002378 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "anastomoses with" xsd:string is_a: distributary_of ! distributary of disjoint_from: proper_distributary_of ! proper distributary of @@ -165,7 +165,7 @@ name: attached to def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] subset: ro-eco xref: RO:0002371 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: attached_to_part_of ! attached to part of @@ -189,9 +189,8 @@ def: "Relation between a neuron and some structure its axon forms (chemical) syn xref: RO:0002102 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in @@ -202,7 +201,7 @@ id: biomechanically_related_to name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] xref: RO:0002567 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: CARO:0000003 range: CARO:0000003 @@ -214,7 +213,7 @@ name: biotically interacts with def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] subset: ro-eco xref: RO:0002437 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string @@ -231,7 +230,7 @@ def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\ comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco xref: RO:0002007 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 is_a: part_of @@ -242,7 +241,7 @@ def: "x bounds the sequence of y iff the upstream-most part of x is upstream of xref: RO:0002522 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to inverse_of: is_bound_by_sequence_of ! is bound by sequence of @@ -254,7 +253,7 @@ def: "x is a branching part of y if and only if x is part of y and x is connecte subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso FMA:85994 xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with @@ -269,7 +268,7 @@ subset: ro-eco xref: RO:0002215 property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 @@ -302,7 +301,7 @@ id: capable_of_part_of name: capable of part of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ is_a: causal_agent_in_process ! causal agent in process @@ -350,7 +349,7 @@ id: causal_relation_between_entities name: causal relation between entities xref: RO:0002506 property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000002 @@ -363,7 +362,7 @@ name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] xref: RO:0002595 property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 range: BFO:0000015 @@ -374,7 +373,7 @@ id: causal_relation_between_processes name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 @@ -389,7 +388,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: OGMS:0000031 is_a: causally_related_to ! causally related to is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:50:54Z [Typedef] @@ -398,7 +397,7 @@ name: causally downstream of def: "inverse of upstream of" [] xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within is_a: preceded_by inverse_of: causally_upstream_of ! causally upstream of @@ -409,7 +408,7 @@ name: causally downstream of or within def: "inverse of causally upstream of or within" [] subset: RO:0002259 xref: RO:0002427 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -418,7 +417,7 @@ is_a: causal_relation_between_processes ! causal relation between processes id: causally_influenced_by name: causally influenced by xref: RO:0002559 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: causal_relation_between_entities ! causal relation between entities @@ -429,8 +428,8 @@ id: causally_influences name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] xref: RO:0002566 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 @@ -443,7 +442,7 @@ name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] @@ -453,7 +452,7 @@ def: "p is causally upstream of q iff p is causally related to q, the end of p p subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes @@ -465,7 +464,7 @@ def: "p is causally upstream of, negative effect q iff p is casually upstream of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -478,7 +477,7 @@ comment: holds between x and y if and only if x is causally upstream of y and th subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -490,7 +489,7 @@ def: "p is 'causally upstream or within' q iff p is causally related to q, and t synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -502,7 +501,7 @@ name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -511,7 +510,7 @@ name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -537,7 +536,7 @@ name: child nucleus of def: "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" [] xref: RO:0002476 property_value: IAO:0000112 "ABal nucleus child nucleus of ABa nucleus (in C elegans)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." xsd:string domain: GO:0005634 range: GO:0005634 @@ -548,7 +547,7 @@ id: child_nucleus_of_in_hermaphrodite name: child nucleus of in hermaphrodite def: "A child nucleus relationship in which the cells are part of a hermaphroditic organism" [] xref: RO:0002477 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -556,7 +555,7 @@ id: child_nucleus_of_in_male name: child nucleus of in male def: "A child nucleus relationship in which the cells are part of a male organism" [] xref: RO:0002478 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -576,7 +575,7 @@ comment: Example: if we define region of chromosome as any subdivision of a chro subset: ro-eco xref: RO:0002008 property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -585,9 +584,8 @@ name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 -property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -599,7 +597,7 @@ name: commensually interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] subset: ro-eco xref: RO:0002441 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -610,7 +608,7 @@ def: "x composed_primarily_of y if and only if more than half of the mass of x i subset: ro-eco xref: RO:0002473 property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 @@ -639,7 +637,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: BFO:0000017 is_a: causally_related_to ! causally related to inverse_of: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:38:20Z [Typedef] @@ -648,7 +646,7 @@ name: conduit for def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] subset: ro-eco xref: RO:0002570 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 UBERON:cjm xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 @@ -661,7 +659,7 @@ name: confers advantage in subset: ro-eco xref: RO:0002322 property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "adapted for" xsd:string range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -727,7 +725,7 @@ name: continuous with def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 @@ -746,7 +744,7 @@ property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a het property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -771,7 +769,7 @@ id: contributes_to_morphology_of name: contributes to morphology of def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] xref: RO:0002433 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -796,7 +794,7 @@ id: decreases_by_repression_quantity_of name: decreases by repression quantity of def: "The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011007 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_negatively_regulates_quantity_of ! indirectly negatively regulates quantity of @@ -808,8 +806,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in wh xref: RO:0002121 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in @@ -821,7 +819,7 @@ name: destabilizes quantity of def: "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." [] xref: RO:0011014 property_value: IAO:0000112 "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_quantity_of ! directly negatively regulates quantity of @@ -832,11 +830,11 @@ name: determined by def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] subset: ro-eco xref: RO:0002507 -property_value: http://purl.org/dc/terms/creator "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/creator "Pier Buttigieg" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-4366-3088 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "A coral reef environment is determined by a particular coral reef" xsd:string property_value: IAO:0000116 "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602 property_value: IAO:0000589 "determined by (system to material entity)" xsd:string domain: RO:0002577 @@ -852,7 +850,7 @@ name: determined by part of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] subset: ro-eco xref: RO:0002509 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 range: BFO:0000040 is_a: causal_relation_between_entities ! causal relation between entities @@ -865,7 +863,7 @@ def: "inverse of determined by" [] subset: ro-eco subset: RO:0002259 xref: RO:0002508 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "determines (material entity to system)" xsd:string is_a: causally_influences ! causally influences @@ -876,7 +874,7 @@ def: "inverse of has developmental contribution from" [] subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to @@ -886,9 +884,9 @@ name: developmentally induced by def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] xref: RO:0002256 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string property_value: IAO:0000119 GO:0001759 xsd:string @@ -905,7 +903,7 @@ name: developmentally induces def: "Inverse of developmentally induced by" [] xref: RO:0002257 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_induce ! has potential to developmentally induce @@ -917,7 +915,7 @@ comment: This relation groups together various other developmental relations. It xref: RO:0002258 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string domain: BFO:0000002 range: BFO:0000002 @@ -929,7 +927,7 @@ id: developmentally_related_to name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] xref: RO:0002324 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] @@ -939,7 +937,7 @@ def: "x developmentally replaces y if and only if there is some developmental pr xref: RO:0002285 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "replaces" xsd:string is_a: developmentally_preceded_by ! developmentally preceded by @@ -949,7 +947,7 @@ name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] xref: RO:0002286 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -959,10 +957,10 @@ def: "x develops from y if and only if either (a) x directly develops from y or comment: This is the transitive form of the develops from relation xref: RO:0002202 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 domain: BFO:0000004 range: BFO:0000004 is_transitive: true @@ -975,7 +973,7 @@ name: develops from part of def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] xref: RO:0002225 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: develops_from ! develops from [Typedef] @@ -984,7 +982,7 @@ name: develops in def: "x develops_in y if x is located in y whilst x is developing" [] xref: RO:0002226 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string domain: CARO:0000000 @@ -997,9 +995,9 @@ def: "inverse of develops from" [] subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 is_transitive: true is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into @@ -1010,11 +1008,11 @@ id: directly_develops_from name: directly develops from def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] xref: RO:0002207 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "has developmental precursor" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000119 "FBbt" xsd:string property_value: RO:0002575 RO:0002202 is_a: develops_from ! develops from @@ -1060,8 +1058,8 @@ name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] xref: RO:0002449 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1072,7 +1070,7 @@ id: directly_negatively_regulates_quantity_of name: directly negatively regulates quantity of def: "The entity A has an activity that directly negatively regulates the quantity of B." [] xref: RO:0011010 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1107,8 +1105,8 @@ name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] xref: RO:0002450 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1119,7 +1117,7 @@ id: directly_positively_regulates_quantity_of name: directly positively regulates quantity of def: "The entity A has an activity that directly positively regulates the quantity of B." [] xref: RO:0011009 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1142,7 +1140,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002578 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string property_value: RO:0002575 RO:0002211 @@ -1155,8 +1153,8 @@ name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] xref: RO:0002448 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: molecularly_interacts_with ! molecularly interacts with @@ -1167,7 +1165,7 @@ id: directly_regulates_quantity_of name: directly regulates quantity of def: "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B." [] xref: RO:0011021 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -1177,7 +1175,7 @@ def: "A relationship between a disease and an anatomical structure where the mat xref: RO:0004030 range: CARO:0000003 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z [Typedef] @@ -1189,7 +1187,7 @@ property_value: IAO:0000589 "disease causes disruption of (disease to process)" domain: OGMS:0000031 range: BFO:0000015 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:51:09Z [Typedef] @@ -1200,7 +1198,7 @@ property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomica domain: OGMS:0000031 range: CARO:0000006 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z [Typedef] @@ -1210,7 +1208,7 @@ xref: RO:0004019 domain: OGMS:0000031 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject is_a: realizable_has_basis_in ! realizable has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:26:47Z [Typedef] @@ -1221,7 +1219,7 @@ xref: RO:0004021 property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:37:52Z [Typedef] @@ -1232,7 +1230,7 @@ xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string range: CARO:0000006 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z [Typedef] @@ -1243,7 +1241,7 @@ xref: RO:0004022 domain: OGMS:0000031 is_a: disease_has_basis_in ! disease has basis in is_a: has_phenotype ! has phenotype -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:46:07Z [Typedef] @@ -1253,7 +1251,7 @@ def: "A relationship between a disease and some feature of that disease, where t xref: RO:0004029 domain: OGMS:0000031 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:50:53Z [Typedef] @@ -1272,7 +1270,7 @@ xref: RO:0004027 domain: OGMS:0000031 range: BFO:0000004 is_a: disease_has_location ! disease has location -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:37:31Z [Typedef] @@ -1285,7 +1283,7 @@ property_value: IAO:0000232 "This relation is intentionally very general, and co domain: OGMS:0000031 range: BFO:0000004 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T04:06:02Z [Typedef] @@ -1294,7 +1292,7 @@ name: disease relationship def: "This relation groups relations between diseases and any other kind of entity." [] xref: RO:0040035 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z [Typedef] @@ -1306,7 +1304,7 @@ subset: ro-eco xref: RO:0002377 property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string @@ -1316,10 +1314,10 @@ is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: does_not_overlap_sequence_of name: does not overlap sequence of -def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] xref: RO:0002527 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "disconnected from" xsd:string is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -1338,7 +1336,7 @@ id: eats name: eats subset: ro-eco xref: RO:0002470 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -1359,7 +1357,7 @@ def: "A relationship that is mediated in some way by the environment or environm subset: ro-eco xref: RO:0002321 property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string [Typedef] @@ -1377,7 +1375,7 @@ name: electrically_synapsed_to def: "A relation that holds between two neurons that are electrically coupled via gap junctions." [] xref: RO:0002003 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: connected_to ! connected to [Typedef] @@ -1386,7 +1384,7 @@ name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: has_participant @@ -1397,7 +1395,7 @@ def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string property_value: IAO:0000118 "has" xsd:string @@ -1413,7 +1411,7 @@ name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] xref: RO:0004031 is_a: functionally_related_to ! functionally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z [Typedef] @@ -1430,14 +1428,14 @@ inverse_of: has_endoparasite ! has endoparasite id: ends subset: ro-eco xref: RO:0002229 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: ends_with subset: ro-eco xref: RO:0002230 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -1462,7 +1460,7 @@ name: exports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002345 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -1479,7 +1477,7 @@ def: "relationship between a neuron and a neuron projection bundle (e.g.- tract xref: RO:0002101 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 @@ -1492,7 +1490,7 @@ inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron proje id: formed_as_result_of name: formed as result of xref: RO:0002354 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of [Typedef] @@ -1500,7 +1498,7 @@ id: functionally_related_to name: functionally related to def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] xref: RO:0002328 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string [Typedef] @@ -1509,7 +1507,7 @@ name: genetically interacts with xref: RO:0002435 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with @@ -1517,7 +1515,7 @@ is_a: interacts_with ! interacts with [Typedef] id: has_2D_boundary xref: RO:0002002 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1557,7 +1555,7 @@ def: "inverse of branching part of" [] subset: ro-eco subset: RO:0002259 xref: RO:0002569 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: has_part is_a: in_branching_relationship_with ! in branching relationship with @@ -1593,7 +1591,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 "Bill Duncan (https://orcid.org/0000-0001-9625-1899)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant @@ -1622,7 +1620,7 @@ id: has_dendrite_location name: has dendrite location xref: RO:0002360 property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -1632,7 +1630,7 @@ def: "x has developmental contribution from y iff x has some part z such that z xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by @@ -1644,7 +1642,7 @@ name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to @@ -1656,7 +1654,7 @@ def: "p has direct input c iff c is a participant in p, c is present at the star xref: RO:0002400 property_value: IAO:0000112 "'protein catabolic process' SubClassOf has_direct_input some protein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly consumes" xsd:string property_value: IAO:0000232 "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" xsd:string is_a: has_input ! has input @@ -1666,7 +1664,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1711,7 +1709,7 @@ def: "x 'has end location' y if and only if there exists some process z such tha subset: ro-eco xref: RO:0002232 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -1724,7 +1722,7 @@ def: "x has end sequence y if the end of x is identical to the end of y, and x h xref: RO:0002518 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -1776,11 +1774,11 @@ id: has_exposure_stimulus name: has exposure stimulus def: "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002309 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 is_a: related_via_exposure_to ! related via exposure to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:35:04Z [Typedef] @@ -1806,7 +1804,7 @@ def: "The relation between a neuron projection bundle and a neuron projection th xref: RO:0002132 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 @@ -1828,7 +1826,7 @@ subset: ro-eco xref: RO:0002303 property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Pier Buttigieg" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string domain: CARO:0001010 range: ENVO:01000254 @@ -1851,7 +1849,7 @@ name: has host def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] subset: ro-eco xref: RO:0002454 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -1865,7 +1863,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 is_a: has_participant @@ -1886,7 +1884,7 @@ def: "p has intermediate c if and only if p has parts p1, p2 and p1 has output c subset: ro-eco xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string is_a: has_participant @@ -1924,7 +1922,7 @@ name: has major susceptibility factor xref: RO:0004005 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_susceptibility_factor_for ! is causal susceptibility factor for -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:26Z [Typedef] @@ -1935,7 +1933,7 @@ property_value: seeAlso Orphanet:410295 property_value: seeAlso Orphanet:410296 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_gain_of_function_germline_mutation_of_in ! is causal gain of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:20Z [Typedef] @@ -1945,7 +1943,7 @@ xref: RO:0004003 property_value: seeAlso Orphanet:317343 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_in ! is causal germline mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:54Z [Typedef] @@ -1954,7 +1952,7 @@ name: has material basis in loss of function germline mutation in xref: RO:0004002 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_loss_of_function_germline_mutation_of_in ! is causal loss of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:37Z [Typedef] @@ -1964,7 +1962,7 @@ xref: RO:0004004 property_value: seeAlso Orphanet:317344 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z [Typedef] @@ -1980,7 +1978,7 @@ id: has_muscle_antagonist name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string is_a: biomechanically_related_to ! biomechanically related to @@ -1989,7 +1987,7 @@ id: has_muscle_insertion name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} @@ -2001,7 +1999,7 @@ id: has_muscle_origin name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} @@ -2039,7 +2037,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string is_a: has_participant inverse_of: output_of ! output of @@ -2066,7 +2064,7 @@ name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] xref: RO:0002584 property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causal_relation_between_material_entity_and_a_process ! causal relation between material entity and a process is_a: functionally_related_to ! functionally related to @@ -2076,7 +2074,7 @@ name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco xref: RO:0002479 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 range: BFO:0000004 @@ -2086,7 +2084,7 @@ name: has partial material basis in germline mutation in xref: RO:0004006 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_partially_giving_rise_to ! is causal germline mutation partially giving rise to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:57Z [Typedef] @@ -2098,7 +2096,7 @@ id: has_pathogen name: has pathogen subset: ro-eco xref: RO:0002557 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2108,7 +2106,7 @@ def: "A relationship that holds between a biological entity and a phenotype. Her subset: ro-eco xref: RO:0002200 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: UPHENO:0001001 is_a: has_phenotype_or_disease ! has phenotype or disease inverse_of: phenotype_of ! phenotype of @@ -2129,9 +2127,9 @@ def: "Holds between a cell c and a protein complex or protein p if and only if t xref: RO:0002104 property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Alexander Diehl" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 @@ -2157,8 +2155,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in whi xref: RO:0002110 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "synapsed in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2172,7 +2170,7 @@ name: has potential to develop into def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] xref: RO:0002387 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2181,7 +2179,7 @@ name: has potential to developmentally contribute to def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] xref: RO:0002385 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2190,7 +2188,7 @@ name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] xref: RO:0002386 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2199,7 +2197,7 @@ name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] xref: RO:0002388 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_potential_to_develop_into ! has potential to develop into [Typedef] @@ -2223,7 +2221,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -2233,7 +2231,7 @@ def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c o subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -2244,7 +2242,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -2276,7 +2274,7 @@ name: has skeleton def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] xref: RO:0002551 property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 @@ -2321,7 +2319,7 @@ name: has soma location def: "Relation between a neuron and an anatomical structure that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 range: CARO:0000003 @@ -2335,7 +2333,7 @@ def: "x 'has starts location' y if and only if there exists some process z such subset: ro-eco xref: RO:0002231 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -2348,7 +2346,7 @@ def: "x has start sequence y if the start of x is identical to the start of y, a xref: RO:0002516 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2358,10 +2356,10 @@ inverse_of: is_start_sequence_of ! is start sequence of [Typedef] id: has_subsequence name: has subsequence -def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2375,7 +2373,7 @@ id: has_symptom name: has symptom def: "A relation that holds between a disease or an organism and a phenotype" [] xref: RO:0002452 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: OGMS:0000031 is_a: has_phenotype ! has phenotype @@ -2405,7 +2403,7 @@ def: "A general relation between a neuron and some structure in which it either xref: RO:0002130 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has synapse in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2417,7 +2415,7 @@ id: has_synaptic_terminal_of name: has synaptic terminal of xref: RO:0002006 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: overlaps ! overlaps inverse_of: has_synaptic_terminal_in ! has synaptic terminal in @@ -2429,7 +2427,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002339 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2440,7 +2438,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002338 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2448,7 +2446,7 @@ id: has_vector name: has vector subset: ro-eco xref: RO:0002460 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with [Typedef] @@ -2463,7 +2461,7 @@ id: host_of name: host of subset: ro-eco xref: RO:0002453 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2476,7 +2474,7 @@ synonym: "epiparasite of" RELATED [] synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string is_a: has_host ! has host @@ -2492,7 +2490,7 @@ synonym: "has epiparasite" RELATED [] synonym: "has hyperparasite" RELATED [] synonym: "hyperparasitoidized by" RELATED [] xref: RO:0002554 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2500,7 +2498,7 @@ id: immediate_transformation_of name: immediate transformation of def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] xref: RO:0002495 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002494 is_a: directly_develops_from ! directly develops from is_a: transformation_of ! transformation of @@ -2510,7 +2508,7 @@ id: immediately_causally_downstream_of name: immediately causally downstream of xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of is_a: immediately_preceded_by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of @@ -2520,7 +2518,7 @@ id: immediately_causally_upstream_of name: immediately causally upstream of def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: immediately_precedes @@ -2533,7 +2531,7 @@ xref: RO:0002087 id: immediately_precedes subset: ro-eco xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0002575 BFO:0000063 [Typedef] @@ -2542,7 +2540,7 @@ name: imports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002340 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -2551,7 +2549,7 @@ name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] xref: RO:0002375 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 @@ -2577,7 +2575,7 @@ id: increases_by_expression_quantity_of name: increases by expression quantity of def: "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011008 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_positively_regulates_quantity_of ! indirectly positively regulates quantity of @@ -2587,7 +2585,7 @@ id: increases_expression_of name: increases expression of def: "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." [] xref: RO:0003003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -2606,7 +2604,7 @@ id: indirectly_negatively_regulates name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true @@ -2618,7 +2616,7 @@ id: indirectly_negatively_regulates_activity_of name: indirectly negatively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B." [] xref: RO:0011016 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly inhibits" xsd:string is_a: indirectly_regulates_activity_of ! indirectly regulates activity of @@ -2627,7 +2625,7 @@ id: indirectly_negatively_regulates_quantity_of name: indirectly negatively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B." [] xref: RO:0011023 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2635,7 +2633,7 @@ id: indirectly_positively_regulates name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 is_transitive: true @@ -2647,7 +2645,7 @@ id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." [] xref: RO:0011013 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -2658,7 +2656,7 @@ id: indirectly_positively_regulates_quantity_of name: indirectly positively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B." [] xref: RO:0011024 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2676,7 +2674,7 @@ id: indirectly_regulates_activity_of name: indirectly regulates activity of def: "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." [] xref: RO:0011004 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: regulates_activity_of ! regulates activity of @@ -2686,7 +2684,7 @@ id: indirectly_regulates_quantity_of name: indirectly regulates quantity of def: "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B." [] xref: RO:0011022 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -2696,7 +2694,7 @@ def: "inverse of has input" [] subset: ro-eco subset: RO:0002259 xref: RO:0002352 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -2710,7 +2708,7 @@ xref: RO:0002434 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI domain: BFO:0000040 @@ -2723,7 +2721,7 @@ name: interacts with via parasite-host interaction def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] subset: ro-eco xref: RO:0002443 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2751,7 +2749,7 @@ id: involved_in name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] xref: RO:0002331 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in @@ -2763,7 +2761,7 @@ id: involved_in_negative_regulation_of name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] xref: RO:0002430 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2773,7 +2771,7 @@ name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in_process ! causal agent in process @@ -2784,7 +2782,7 @@ id: involved_in_positive_regulation_of name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] xref: RO:0002429 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2793,7 +2791,7 @@ id: involved_in_regulation_of name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] xref: RO:0002428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of @@ -2804,7 +2802,7 @@ def: "c executes activity in d if and only if c enables p and p occurs_in d. As synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -2853,7 +2851,7 @@ id: is_basis_for_realizable name: is basis for realizable xref: RO:0004018 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:29Z [Typedef] @@ -2863,7 +2861,7 @@ def: "inverse of bounds sequence of" [] subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to @@ -2874,7 +2872,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004011 property_value: seeAlso Orphanet:410296 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:55:51Z [Typedef] @@ -2885,7 +2883,7 @@ xref: RO:0004013 property_value: seeAlso Orphanet:317343 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:40Z [Typedef] @@ -2896,7 +2894,7 @@ xref: RO:0004016 property_value: seeAlso Orphanet:317346 is_a: contributes_to_condition ! contributes to condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:58:43Z [Typedef] @@ -2906,7 +2904,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004012 property_value: seeAlso Orphanet:410295 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:06Z [Typedef] @@ -2917,7 +2915,7 @@ xref: RO:0004014 property_value: seeAlso Orphanet:317344 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:07Z [Typedef] @@ -2927,7 +2925,7 @@ def: "Relates a gene to condition, such that a mutation in this gene predisposes xref: RO:0004015 property_value: seeAlso Orphanet:317345 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:43Z [Typedef] @@ -2937,7 +2935,7 @@ def: "x is a consecutive sequence of y iff x has subsequence y, and all the part xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: has_subsequence ! has subsequence @@ -2947,7 +2945,7 @@ name: is downstream of sequence of def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] xref: RO:0002529 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of @@ -2957,7 +2955,7 @@ id: is_eaten_by name: is eaten by subset: ro-eco xref: RO:0002471 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -2969,7 +2967,7 @@ def: "inverse of has end sequence" [] subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2982,7 +2980,7 @@ xref: RO:0004010 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string range: BFO:0000017 is_a: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:53:08Z [Typedef] @@ -2992,7 +2990,7 @@ def: "x is immediately downstream of the sequence of y iff either (1) x and y ha xref: RO:0002530 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002529 is_a: is_downstream_of_sequence_of ! is downstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3004,7 +3002,7 @@ def: "inverse of immediately downstream of" [] xref: RO:0002531 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: is_upstream_of_sequence_of ! is upstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3031,7 +3029,7 @@ def: "x is sequentially aligned with if a significant portion bases of x and y c xref: RO:0002521 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -3071,7 +3069,7 @@ def: "inverse of has start sequence" [] subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3084,7 +3082,7 @@ def: "inverse of has subsequence" [] subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of @@ -3107,7 +3105,7 @@ name: is treated by substance def: "Inverse of 'is substance that treats'" [] subset: RO:0002259 xref: RO:0002302 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 is_a: causally_related_to ! causally related to inverse_of: is_substance_that_treats ! is substance that treats @@ -3117,7 +3115,7 @@ name: is upstream of sequence of def: "inverse of downstream of sequence of" [] xref: RO:0002528 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -3127,7 +3125,7 @@ name: is vector for subset: ro-eco xref: RO:0002459 property_value: IAO:0000112 "Anopheles is a vector for Plasmodium" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: has_vector ! has vector @@ -3179,7 +3177,7 @@ name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco xref: RO:0002571 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:cjm xsd:string range: BFO:0000040 is_a: part_of @@ -3190,7 +3188,7 @@ name: luminal space of def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] subset: ro-eco xref: RO:0002572 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000141 is_a: lumen_of ! lumen of @@ -3202,7 +3200,7 @@ subset: ro-eco xref: RO:0002381 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with is_a: part_of @@ -3212,7 +3210,7 @@ id: mereotopologically_related_to name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] xref: RO:0002323 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string property_value: RO:0001900 RO:0001901 @@ -3230,7 +3228,7 @@ name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 @@ -3243,7 +3241,7 @@ name: mutualistically interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] subset: ro-eco xref: RO:0002442 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -3270,7 +3268,7 @@ name: negatively regulated by def: "inverse of negatively regulates" [] subset: RO:0002259 xref: RO:0002335 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3281,7 +3279,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 @@ -3330,7 +3328,7 @@ def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -3351,10 +3349,10 @@ expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://p [Typedef] id: overlaps_sequence_of name: overlaps sequence of -def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] xref: RO:0002526 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: overlaps ! overlaps is_a: sequentially_related_to ! sequentially related to @@ -3366,7 +3364,7 @@ subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string is_a: has_host ! has host @@ -3379,7 +3377,7 @@ name: parasitized by subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string @@ -3418,7 +3416,7 @@ name: part of developmental precursor of xref: RO:0002287 property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by [Typedef] @@ -3426,7 +3424,7 @@ id: part_of_structure_that_is_capable_of name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] xref: RO:0002329 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean is_a: functionally_related_to ! functionally related to @@ -3455,7 +3453,7 @@ subset: ro-eco synonym: "semibiotically interacts with" RELATED [] xref: RO:0002446 property_value: IAO:0000112 "Porifiera attaches to substrate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: biotically_interacts_with ! biotically interacts with @@ -3464,7 +3462,7 @@ id: participates_in_a_biotic-biotic_interaction_with name: participates in a biotic-biotic interaction with subset: ro-eco xref: RO:0002574 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 domain: CARO:0001010 range: CARO:0001010 @@ -3474,7 +3472,7 @@ is_a: biotically_interacts_with ! biotically interacts with id: partner_in name: partner in xref: RO:0002461 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string is_a: participates_in @@ -3483,7 +3481,7 @@ id: pathogen_of name: pathogen of subset: ro-eco xref: RO:0002556 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_host ! has host inverse_of: has_pathogen ! has pathogen @@ -3495,7 +3493,7 @@ subset: ro-eco subset: RO:0002259 xref: RO:0002201 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_functional: true [Typedef] @@ -3503,7 +3501,7 @@ id: phosphorylates name: phosphorylates xref: RO:0002447 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: molecularly_interacts_with ! molecularly interacts with @@ -3512,7 +3510,7 @@ id: pollinated_by name: pollinated by subset: ro-eco xref: RO:0002456 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string @@ -3525,7 +3523,7 @@ subset: ro-eco xref: RO:0002455 property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with @@ -3537,7 +3535,7 @@ name: positively regulated by def: "inverse of positively regulates" [] subset: RO:0002259 xref: RO:0002336 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3548,7 +3546,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002211 @@ -3583,7 +3581,7 @@ def: "inverse of preys on" [] subset: ro-eco subset: RO:0002259 xref: RO:0002458 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string @@ -3598,9 +3596,9 @@ subset: ro-eco xref: RO:0002439 property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Jorrit Poelen" xsd:string -property_value: IAO:0000117 "Katja Shulz" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7134-3324 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string @@ -3623,7 +3621,7 @@ def: "x proper_distributary_of y iff x distributary_of y and x does not flow bac subset: ro-eco xref: RO:0002382 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: distributary_of ! distributary of [Typedef] @@ -3633,7 +3631,7 @@ def: "x proper_tributary_of y iff x tributary_of y and x does not originate from subset: ro-eco xref: RO:0002383 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: tributary_of ! tributary of [Typedef] @@ -3642,7 +3640,7 @@ name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string @@ -3654,7 +3652,7 @@ id: provides_nutrients_for name: provides nutrients for subset: ro-eco xref: RO:0002469 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3663,7 +3661,7 @@ name: realizable has basis in xref: RO:0004017 is_a: causally_related_to ! causally related to inverse_of: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:01Z [Typedef] @@ -3672,10 +3670,10 @@ name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] synonym: "triggered by process" EXACT [RO:cjm] xref: RO:0009501 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "David Osumi-Sutherland" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string @@ -3692,7 +3690,7 @@ xref: RO:0004028 domain: BFO:0000017 range: BFO:0000040 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:45:49Z [Typedef] @@ -3700,7 +3698,7 @@ id: receives_input_from name: receives input from xref: RO:0002485 property_value: IAO:0000116 "See notes for inverse relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to inverse_of: sends_output_to ! sends output to @@ -3740,7 +3738,7 @@ name: regulated by def: "inverse of regulates" [] subset: RO:0002259 xref: RO:0002334 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 range: BFO:0000015 @@ -3755,9 +3753,9 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Hill" xsd:string -property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 +property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string @@ -3774,7 +3772,7 @@ id: regulates_activity_of name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] xref: RO:0011002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3794,7 +3792,7 @@ id: regulates_in_other_organism name: regulates in other organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] xref: RO:0002010 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 range: BFO:0000015 is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -3805,7 +3803,7 @@ name: regulates levels of def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] xref: RO:0002332 property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 @@ -3817,7 +3815,7 @@ id: regulates_quantity_of name: regulates quantity of def: "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." [] xref: RO:0011003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3836,7 +3834,7 @@ id: related_via_localization_to name: related via localization to def: "A relationship that holds via some process of localization" [] xref: RO:0002337 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 range: BFO:0000002 @@ -3857,7 +3855,7 @@ id: represses_expression_of name: represses expression of def: "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." [] xref: RO:0003002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3871,7 +3869,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -3916,7 +3914,7 @@ name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] @@ -3936,7 +3934,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002348 property_value: IAO:0000112 "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3948,7 +3946,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002349 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3962,7 +3960,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3972,7 +3970,7 @@ id: results_in_developmental_induction_of name: results in developmental induction of def: "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." [] xref: RO:0002357 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3982,7 +3980,7 @@ def: "p results in the developmental progression of s iff p is a developmental p xref: RO:0002295 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 range: CARO:0000000 @@ -3994,7 +3992,7 @@ name: results in developmental regression of xref: RO:0002301 property_value: IAO:0000112 "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4004,7 +4002,7 @@ name: results in disappearance of xref: RO:0002300 property_value: IAO:0000112 "foramen ovale closure SubClassOf results in disappearance of foramen ovale" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4020,7 +4018,7 @@ id: results_in_ending_of name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4034,7 +4032,7 @@ xref: RO:0002297 property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4056,7 +4054,7 @@ id: results_in_growth_of name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4071,7 +4069,7 @@ xref: RO:0002299 property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4087,7 +4085,7 @@ xref: RO:0002298 property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4100,7 +4098,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002565 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4126,7 +4124,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002356 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4135,7 +4133,7 @@ id: results_in_structural_organization_of name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4151,7 +4149,7 @@ name: results in transport across def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002342 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: occurs_across ! occurs across is_a: results_in_transport_to_from_or_in ! results in transport to from or in @@ -4160,7 +4158,7 @@ id: results_in_transport_along name: results in transport along def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] xref: RO:0002341 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4168,7 +4166,7 @@ id: results_in_transport_to_from_or_in name: results in transport to from or in xref: RO:0002344 property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4183,7 +4181,7 @@ id: sends_output_to name: sends output to xref: RO:0002486 property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to [Typedef] @@ -4225,7 +4223,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcript" xsd:string property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -4235,7 +4233,7 @@ name: sequentially related to def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string @@ -4248,7 +4246,7 @@ name: skeleton of def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 is_a: part_of @@ -4259,7 +4257,7 @@ name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] xref: RO:0002379 property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: overlaps ! overlaps @@ -4271,7 +4269,7 @@ subset: ro-eco xref: RO:0002163 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 @@ -4285,7 +4283,7 @@ name: stabilizes quantity of def: "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." [] xref: RO:0011015 property_value: IAO:0000112 "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_quantity_of ! directly positively regulates quantity of @@ -4294,14 +4292,14 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates id: starts subset: ro-eco xref: RO:0002223 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: starts_with subset: ro-eco xref: RO:0002224 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -4317,7 +4315,7 @@ name: subcluster of def: "A relation between a group and another group it is part of but does not fully constitute." [] xref: RO:0015003 property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." xsd:string -property_value: IAO:0000117 "Shawn Tan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true is_a: part_of @@ -4326,7 +4324,7 @@ is_a: part_of id: subject_participant_in name: subject participant in xref: RO:0002462 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4345,7 +4343,7 @@ name: surrounded by def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] xref: RO:0002219 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to inverse_of: surrounds ! surrounds @@ -4357,7 +4355,7 @@ def: "inverse of surrounded by" [] subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to @@ -4367,7 +4365,7 @@ name: symbiotically interacts with def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] subset: ro-eco xref: RO:0002440 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true @@ -4380,8 +4378,8 @@ def: "Relation between an anatomical structure (including cells) and a neuron th xref: RO:0002103 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: receives_input_from ! receives input from inverse_of: synapsed_to ! synapsed to @@ -4406,8 +4404,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002108 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" [] @@ -4420,8 +4418,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002109 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4434,8 +4432,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002112 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4448,8 +4446,8 @@ comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part som xref: RO:0002120 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: sends_output_to ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -4473,8 +4471,8 @@ def: "A relation between a motor neuron and a muscle that it synapses to via a t comment: Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) xref: RO:0002107 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_II_bouton ! synapsed_by_via_type_II_bouton @@ -4488,8 +4486,8 @@ comment: Expands to: has_part some ('type Ib terminal button' that has_part some xref: RO:0002105 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Ib_bouton ! synapsed_by_via_type_Ib_bouton @@ -4503,8 +4501,8 @@ comment: Expands to: has_part some ('type Is terminal button' that has_part some xref: RO:0002106 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Is_bouton ! synapsed_by_via_type_Is_bouton @@ -4514,7 +4512,7 @@ expand_expression_to: "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that id: target_participant_in name: target participant in xref: RO:0002463 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4523,7 +4521,7 @@ id: temporally_related_to subset: ro-eco xref: RO:0002222 property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string [Typedef] @@ -4531,7 +4529,7 @@ id: transformation_of name: transformation of def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] xref: RO:0002494 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: develops_from ! develops from @@ -4541,7 +4539,7 @@ name: transitively provides input for def: "transitive form of directly_provides_input_for" [] xref: RO:0002414 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." xsd:string property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string domain: BFO:0000015 @@ -4556,7 +4554,7 @@ def: "A relationship that holds between a disease and organism" [] xref: RO:0002451 property_value: IAO:0000112 "all dengue disease transmitted by some mosquito" xsd:string property_value: IAO:0000116 "Add domain and range constraints" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -4576,7 +4574,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002313 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "regulates localization of" xsd:string is_a: related_via_localization_to ! related via localization to is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4590,7 +4588,7 @@ xref: RO:0002376 property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string @@ -4608,7 +4606,7 @@ name: trophically interacts with def: "An interaction relationship in which the partners are related via a feeding relationship." [] subset: ro-eco xref: RO:0002438 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4618,7 +4616,7 @@ name: ubiquitinates def: "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" [] xref: RO:0002480 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with [Typedef] diff --git a/subsets/ro-mereotopology.owl b/subsets/ro-mereotopology.owl index 3c0480b9..55296922 100644 --- a/subsets/ro-mereotopology.owl +++ b/subsets/ro-mereotopology.owl @@ -409,7 +409,7 @@ - David Osumi-Sutherland + RO:0002002 has_2D_boundary @@ -421,7 +421,7 @@ A relation that holds between two neurons that are electrically coupled via gap junctions. - David Osumi-Sutherland + RO:0002003 electrically_synapsed_to @@ -435,7 +435,7 @@ - David Osumi-Sutherland + RO:0002006 has_synaptic_terminal_of @@ -469,7 +469,7 @@ has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland + RO:0002007 bounding_layer_of @@ -505,9 +505,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. + A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. Note from NCEAS meeting: consider changing primary label - David Osumi-Sutherland + RO:0002008 coincident_with @@ -524,7 +524,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - David Osumi-Sutherland + RO:0002010 regulates_in_other_organism regulates in other organism @@ -553,7 +553,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + dos 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -568,7 +568,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + dos 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -584,7 +584,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + dos 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -599,7 +599,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -613,7 +613,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -630,7 +630,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + dos 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -644,7 +644,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + dos 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -658,7 +658,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + dos 2017-07-20T17:11:08Z RO:0002020 transports @@ -672,7 +672,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + dos 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -686,7 +686,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -697,7 +697,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + GOC:dos @@ -708,7 +708,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + dos 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -718,7 +718,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + GOC:dos @@ -729,7 +729,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + dos 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -739,7 +739,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + GOC:dos @@ -750,7 +750,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + dos 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -761,7 +761,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + GOC:dos @@ -780,7 +780,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + dos 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -797,7 +797,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + GOC:dos @@ -814,7 +814,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + RO:0002090 @@ -831,7 +831,7 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure that its soma is part of. - David Osumi-Sutherland + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -852,9 +852,9 @@ Examples include: the relationship between two channels collected simultaneously relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - David Osumi-Sutherland + fasciculates with - (forall (?x ?y) + (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) @@ -890,9 +890,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure its axon forms (chemical) synapses in. - Chris Mungall - David Osumi-Sutherland - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -924,8 +923,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -945,9 +944,9 @@ Examples include: the relationship between two channels collected simultaneously Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - Alexander Diehl - Chris Mungall - Lindsay Cowell + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) @@ -965,8 +964,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -985,8 +984,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -1005,8 +1004,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) RO:0002107 @@ -1023,8 +1022,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1043,8 +1042,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1064,8 +1063,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - Chris Mungall - David Osumi-Sutherland + + synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( @@ -1085,8 +1084,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1168,8 +1167,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -1196,8 +1195,8 @@ N1 SubclassOf ( Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -1218,7 +1217,7 @@ N1 SubclassOf ( A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - David Osumi-Sutherland + has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) @@ -1267,9 +1266,9 @@ N1 SubclassOf ( The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - David Osumi-Sutherland + has fasciculating component - (forall (?x ?y) + (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) @@ -1309,8 +1308,8 @@ N1 SubclassOf ( - X continuous_with Y if and only if X and Y share a fiat boundary. - David Osumi-Sutherland + X continuous_with Y if and only if X and Y share a fiat boundary. + connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) @@ -1329,8 +1328,8 @@ N1 SubclassOf ( x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom - proper overlaps - (forall (?x ?y) + proper overlaps + (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and @@ -1353,7 +1352,7 @@ N1 SubclassOf ( A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - Chris Mungall + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) @@ -1361,7 +1360,7 @@ N1 SubclassOf ( RO:0002163 spatially_disjoint_from - spatially disjoint from + spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern @@ -1498,7 +1497,7 @@ N1 SubclassOf ( A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - Chris Mungall + RO:0002200 has_phenotype @@ -1513,7 +1512,7 @@ N1 SubclassOf ( inverse of has phenotype - Chris Mungall + RO:0002201 @@ -1533,10 +1532,10 @@ N1 SubclassOf ( x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - Terry Meehan + + + + RO:0002202 develops_from This is the transitive form of the develops from relation @@ -1554,9 +1553,9 @@ N1 SubclassOf ( inverse of develops from - Chris Mungall - David Osumi-Sutherland - Terry Meehan + + + RO:0002203 develops_into @@ -1588,12 +1587,12 @@ N1 SubclassOf ( Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - Chris Mungall - David Osumi-Sutherland - has developmental precursor + + FBbt RO:0002207 + has developmental precursor directly_develops_from TODO - add child relations from DOS directly develops from @@ -1651,9 +1650,9 @@ N1 SubclassOf ( p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - Chris Mungall - David Hill - Tanya Berardini + + + GO Regulation precludes parthood; the regulatory process may not be within the regulated process. @@ -1676,7 +1675,7 @@ N1 SubclassOf ( p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - Chris Mungall + negatively regulates (process to process) @@ -1698,7 +1697,7 @@ N1 SubclassOf ( p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - Chris Mungall + positively regulates (process to process) @@ -1721,7 +1720,7 @@ N1 SubclassOf ( mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - Chris Mungall + has function realized in @@ -1740,7 +1739,7 @@ N1 SubclassOf ( c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - Chris Mungall + has function in RO:0002216 capable_of_part_of @@ -1757,7 +1756,7 @@ N1 SubclassOf ( x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - Chris Mungall + RO:0002219 surrounded_by @@ -1779,7 +1778,7 @@ N1 SubclassOf ( x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - Chris Mungall + RO:0002220 @@ -1803,7 +1802,7 @@ N1 SubclassOf ( inverse of surrounded by - Chris Mungall + RO:0002221 @@ -1816,7 +1815,7 @@ N1 SubclassOf ( - Chris Mungall + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 @@ -1830,7 +1829,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002223 starts @@ -1842,7 +1841,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002224 starts_with @@ -1856,7 +1855,7 @@ N1 SubclassOf ( x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - Chris Mungall + RO:0002225 develops_from_part_of develops from part of @@ -1871,7 +1870,7 @@ N1 SubclassOf ( x develops_in y if x is located in y whilst x is developing - Chris Mungall + EHDAA2 Jonathan Bard, EHDAA2 RO:0002226 @@ -1909,7 +1908,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002229 ends @@ -1921,7 +1920,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002230 ends_with @@ -1937,7 +1936,7 @@ N1 SubclassOf ( x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - Chris Mungall + starts with process that occurs in RO:0002231 @@ -1955,7 +1954,7 @@ N1 SubclassOf ( x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - Chris Mungall + ends with process that occurs in RO:0002232 @@ -1973,7 +1972,7 @@ N1 SubclassOf ( p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + consumes RO:0002233 @@ -1993,7 +1992,7 @@ N1 SubclassOf ( p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - Chris Mungall + produces RO:0002234 @@ -2047,7 +2046,7 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - Bill Duncan (https://orcid.org/0000-0001-9625-1899) + This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. @@ -2196,7 +2195,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y - Chris Mungall + RO:0002254 has_developmental_contribution_from has developmental contribution from @@ -2211,7 +2210,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho inverse of has developmental contribution from - Chris Mungall + RO:0002255 developmentally_contributes_to @@ -2229,9 +2228,9 @@ If you need an axiom that says 'has_participant min 2 object', you sho t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - Chris Mungall - David Osumi-Sutherland - Melissa Haendel + + + induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) @@ -2251,7 +2250,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally induced by - Chris Mungall + RO:0002257 developmentally_induces developmentally induces @@ -2269,7 +2268,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - Chris Mungall + In general you should not use this relation to make assertions - use one of the more specific relations below this one RO:0002258 developmentally_preceded_by @@ -2317,7 +2316,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - Chris Mungall + replaces RO:0002285 developmentally_replaces @@ -2332,7 +2331,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally preceded by - Chris Mungall + RO:0002286 developmentally_succeeded_by developmentally succeeded by @@ -2346,7 +2345,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - Chris Mungall + RO:0002287 part_of_developmental_precursor_of part of developmental precursor of @@ -2363,7 +2362,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - Chris Mungall + RO:0002295 results_in_developmental_progression_of results in developmental progression of @@ -2380,7 +2379,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - Chris Mungall + http://www.geneontology.org/GO.doc.development.shtml RO:0002296 @@ -2401,7 +2400,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002297 @@ -2422,7 +2421,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002298 @@ -2443,7 +2442,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002299 @@ -2461,7 +2460,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho foramen ovale closure SubClassOf results in disappearance of foramen ovale - Chris Mungall + May be merged into parent relation RO:0002300 results_in_disappearance_of @@ -2476,7 +2475,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) - Chris Mungall + May be merged into parent relation RO:0002301 results_in_developmental_regression_of @@ -2491,7 +2490,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of 'is substance that treats' - cjm + RO:0002302 is_treated_by_substance @@ -2511,7 +2510,7 @@ where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. - Pier Buttigieg + adapted for living in RO:0002303 @@ -2529,7 +2528,7 @@ where p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - cjm + RO:0002304 @@ -2547,7 +2546,7 @@ where p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - cjm + RO:0002305 @@ -2562,10 +2561,10 @@ where A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. - Austin Meier - Chris Mungall - Marie Angelique Laporte - cjm + + + + 2017-06-05T17:35:04Z RO:0002309 has_exposure_stimulus @@ -2580,7 +2579,7 @@ where Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. - Chris Mungall + regulates localization of RO:0002313 @@ -2600,7 +2599,7 @@ where an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002315 @@ -2617,7 +2616,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions RO:0002321 @@ -2633,7 +2632,7 @@ where An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. - Chris Mungall + adapted for RO:0002322 @@ -2647,7 +2646,7 @@ where A mereological relationship or a topological relationship - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships RO:0002323 @@ -2661,7 +2660,7 @@ where A relationship that holds between entities participating in some developmental process (GO:0032502) - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development RO:0002324 developmentally_related_to @@ -2678,9 +2677,8 @@ where Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. - Chris Mungall + In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - Gene Ontology Consortium RO:0002325 colocalizes_with @@ -2708,7 +2706,7 @@ then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. - Chris Mungall + In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 @@ -2725,7 +2723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - Chris Mungall + catalyzes executes has @@ -2744,7 +2742,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 functionally_related_to @@ -2758,7 +2756,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati this relation holds between c and p when c is part of some c', and c' is capable of p. - Chris Mungall + false RO:0002329 part_of_structure_that_is_capable_of @@ -2773,7 +2771,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati c involved_in p if and only if c enables some process p', and p' is part of p - Chris Mungall + actively involved in enables part of RO:0002331 @@ -2792,7 +2790,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - Chris Mungall + regulates levels of (process to entity) RO:0002332 @@ -2808,7 +2806,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables - Chris Mungall + RO:0002333 enabled_by @@ -2825,7 +2823,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of regulates - Chris Mungall + regulated by (processual) RO:0002334 @@ -2840,7 +2838,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of negatively regulates - Chris Mungall + RO:0002335 negatively_regulated_by @@ -2854,7 +2852,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of positively regulates - Chris Mungall + RO:0002336 positively_regulated_by @@ -2869,7 +2867,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds via some process of localization - Chris Mungall + Do not use this relation directly. It is a grouping relation. RO:0002337 related_via_localization_to @@ -2883,7 +2881,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - Chris Mungall + RO:0002338 @@ -2899,7 +2897,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - Chris Mungall + RO:0002339 @@ -2915,7 +2913,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. - Chris Mungall + RO:0002340 imports @@ -2929,7 +2927,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - Chris Mungall + RO:0002341 results_in_transport_along results in transport along @@ -2943,7 +2941,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - Chris Mungall + RO:0002342 results_in_transport_across @@ -2958,7 +2956,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'pollen tube growth' results_in growth_of some 'pollen tube' - Chris Mungall + RO:0002343 results_in_growth_of results in growth of @@ -2971,7 +2969,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - Chris Mungall + RO:0002344 results_in_transport_to_from_or_in results in transport to from or in @@ -2983,8 +2981,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. - Chris Mungall + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. + RO:0002345 exports @@ -3000,7 +2998,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - Chris Mungall + RO:0002348 @@ -3017,7 +3015,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - Chris Mungall + RO:0002349 @@ -3034,7 +3032,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has input - Chris Mungall + RO:0002352 @@ -3050,7 +3048,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has output - Chris Mungall + RO:0002353 @@ -3064,7 +3062,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002354 formed_as_result_of formed as result of @@ -3078,7 +3076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. - Chris Mungall + RO:0002355 results_in_structural_organization_of results in structural organization of @@ -3092,7 +3090,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - Chris Mungall + RO:0002356 @@ -3108,7 +3106,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. - Chris Mungall + RO:0002357 results_in_developmental_induction_of results in developmental induction of @@ -3120,7 +3118,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + http://neurolex.org/wiki/Property:DendriteLocation RO:0002360 has_dendrite_location @@ -3136,7 +3134,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - Chris Mungall + attached to (anatomical structure to anatomical structure) RO:0002371 @@ -3153,7 +3151,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002372 has_muscle_origin @@ -3176,7 +3174,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002373 has_muscle_insertion @@ -3200,7 +3198,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) @@ -3222,7 +3220,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - Chris Mungall + drains into drains to tributary channel of @@ -3247,7 +3245,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Deschutes River distributary_of Little Lava Lake x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - Chris Mungall + branch of distributary channel of http://en.wikipedia.org/wiki/Distributary @@ -3273,7 +3271,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. - Chris Mungall + anastomoses with RO:0002378 @@ -3289,7 +3287,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - Chris Mungall + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios RO:0002379 spatially_coextensive_with @@ -3312,7 +3310,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - Chris Mungall + RO:0002380 branching_part_of @@ -3331,7 +3329,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. - Chris Mungall + RO:0002381 main_stem_of @@ -3347,7 +3345,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_distributary_of y iff x distributary_of y and x does not flow back into y - Chris Mungall + RO:0002382 proper_distributary_of @@ -3362,7 +3360,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_tributary_of y iff x tributary_of y and x does not originate from y - Chris Mungall + RO:0002383 proper_tributary_of @@ -3379,7 +3377,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - Chris Mungall + RO:0002384 has_developmental_potential_involving has developmental potential involving @@ -3393,7 +3391,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - Chris Mungall + RO:0002385 has_potential_to_developmentally_contribute_to has potential to developmentally contribute to @@ -3407,7 +3405,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - Chris Mungall + RO:0002386 has_potential_to_developmentally_induce has potential to developmentally induce @@ -3421,7 +3419,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has the potential to develop into y iff x develops into y or if x is capable of developing into y - Chris Mungall + RO:0002387 has_potential_to_develop_into has potential to develop into @@ -3435,7 +3433,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - Chris Mungall + RO:0002388 has_potential_to_directly_develop_into has potential to directly develop into @@ -3450,7 +3448,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' RO:0002400 @@ -3468,7 +3466,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of upstream of - Chris Mungall + RO:0002404 causally_downstream_of causally downstream of @@ -3483,7 +3481,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002405 immediately_causally_downstream_of immediately causally downstream of @@ -3498,7 +3496,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - Chris Mungall + indirectly activates RO:0002407 @@ -3515,7 +3513,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - Chris Mungall + indirectly inhibits RO:0002409 @@ -3544,7 +3542,7 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002410 causally_related_to @@ -3566,7 +3564,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - Chris Mungall + RO:0002411 @@ -3582,7 +3580,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - Chris Mungall + RO:0002412 immediately_causally_upstream_of @@ -3598,7 +3596,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit - Chris Mungall + directly provides input for directly provides input for (process to process) @@ -3618,7 +3616,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different transitive form of directly_provides_input_for - Chris Mungall + This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. transitively provides input for (process to process) RO:0002414 @@ -3636,7 +3634,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall + influences (processual) RO:0002418 affects @@ -3652,7 +3650,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - Chris Mungall + RO:0002427 @@ -3668,7 +3666,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - Chris Mungall + RO:0002428 involved_in_regulation_of involved in regulation of @@ -3681,7 +3679,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - Chris Mungall + RO:0002429 involved_in_positive_regulation_of @@ -3695,7 +3693,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - Chris Mungall + RO:0002430 involved_in_negative_regulation_of @@ -3712,7 +3710,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - Chris Mungall + involved in or reguates RO:0002431 involved_in_or_involved_in_regulation_of @@ -3728,7 +3726,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall + executes activity in RO:0002432 enables activity in @@ -3740,8 +3738,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + GOC:cjm + GOC:dos @@ -3751,7 +3749,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - Chris Mungall + RO:0002433 contributes_to_morphology_of contributes to morphology of @@ -3768,7 +3766,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. - Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. RO:0002434 in pairwise interaction with @@ -3787,7 +3785,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) - Chris Mungall + RO:0002435 genetically_interacts_with genetically interacts with @@ -3803,7 +3801,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - Chris Mungall + binds molecularly binds with RO:0002436 @@ -3824,7 +3822,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - Chris Mungall + interacts with on organism level RO:0002437 @@ -3841,7 +3839,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the partners are related via a feeding relationship. - Chris Mungall + RO:0002438 trophically_interacts_with @@ -3859,9 +3857,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] Baleen whale preys on krill An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - Chris Mungall - Jorrit Poelen - Katja Shulz + + + is subject of predation interaction with preys upon RO:0002439 @@ -3880,7 +3878,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A biotic interaction in which the two organisms live together in more or less intimate association. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism RO:0002440 @@ -3896,7 +3894,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002441 @@ -3911,7 +3909,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002442 @@ -3926,7 +3924,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 This relation groups a pair of inverse relations, parasite of and parasitized by RO:0002443 @@ -3944,7 +3942,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human - Chris Mungall + parasitizes RO:0002444 direct parasite of @@ -3961,7 +3959,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + has parasite parasitised by RO:0002445 @@ -3980,7 +3978,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - Chris Mungall + RO:0002446 semibiotically interacts with @@ -3996,7 +3994,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. RO:0002447 phosphorylates @@ -4015,8 +4013,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - Chris Mungall - Vasundra Touré + + RO:0002448 molecularly controls directly_regulates_activity_of @@ -4033,8 +4031,8 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly inhibits RO:0002449 molecularly decreases activity of @@ -4052,8 +4050,8 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly activates RO:0002450 molecularly increases activity of @@ -4070,7 +4068,7 @@ For example, A and B may be gene products and binding of B by A positively regul all dengue disease transmitted by some mosquito A relationship that holds between a disease and organism Add domain and range constraints - Chris Mungall + RO:0002451 transmitted_by transmitted by @@ -4084,7 +4082,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between a disease or an organism and a phenotype - Chris Mungall + RO:0002452 has_symptom has symptom @@ -4096,7 +4094,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) RO:0002453 @@ -4111,7 +4109,7 @@ For example, A and B may be gene products and binding of B by A positively regul X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y - Chris Mungall + RO:0002454 has_host @@ -4128,7 +4126,7 @@ For example, A and B may be gene products and binding of B by A positively regul Bees pollinate Flowers This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - Chris Mungall + is subject of pollination interaction with RO:0002455 @@ -4143,7 +4141,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + has polinator is target of pollination interaction with RO:0002456 @@ -4160,7 +4158,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4175,7 +4173,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of preys on - Chris Mungall + has predator is target of predation interaction with RO:0002458 @@ -4195,7 +4193,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anopheles is a vector for Plasmodium - Chris Mungall + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism RO:0002459 @@ -4209,7 +4207,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002460 has_vector @@ -4222,7 +4220,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target RO:0002461 partner_in @@ -4235,7 +4233,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002462 subject_participant_in @@ -4248,7 +4246,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002463 target_participant_in @@ -4261,7 +4259,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002469 provides_nutrients_for @@ -4274,7 +4272,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is subject of eating interaction with RO:0002470 @@ -4288,7 +4286,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + eaten by is target of eating interaction with RO:0002471 @@ -4307,7 +4305,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - Chris Mungall + RO:0002473 @@ -4326,7 +4324,7 @@ For example, A and B may be gene products and binding of B by A positively regul ABal nucleus child nucleus of ABa nucleus (in C elegans) c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d - Chris Mungall + This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. RO:0002476 child_nucleus_of @@ -4340,7 +4338,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a hermaphroditic organism - Chris Mungall + RO:0002477 child_nucleus_of_in_hermaphrodite child nucleus of in hermaphrodite @@ -4353,7 +4351,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a male organism - Chris Mungall + RO:0002478 child_nucleus_of_in_male child nucleus of in male @@ -4367,7 +4365,7 @@ For example, A and B may be gene products and binding of B by A positively regul p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall + RO:0002479 has_part_that_occurs_in @@ -4382,7 +4380,7 @@ For example, A and B may be gene products and binding of B by A positively regul An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y Axiomatization to GO to be added later - Chris Mungall + RO:0002480 ubiquitinates ubiquitinates @@ -4396,7 +4394,7 @@ For example, A and B may be gene products and binding of B by A positively regul See notes for inverse relation - Chris Mungall + RO:0002485 receives_input_from receives input from @@ -4409,7 +4407,7 @@ For example, A and B may be gene products and binding of B by A positively regul This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - Chris Mungall + RO:0002486 sends_output_to sends output to @@ -4423,7 +4421,7 @@ For example, A and B may be gene products and binding of B by A positively regul x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - Chris Mungall + RO:0002494 transformation_of transformation of @@ -4437,7 +4435,7 @@ For example, A and B may be gene products and binding of B by A positively regul x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - Chris Mungall + RO:0002495 immediate_transformation_of @@ -4467,7 +4465,7 @@ For example, A and B may be gene products and binding of B by A positively regul p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002501 @@ -4483,7 +4481,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c - Chris Mungall + has intermediate product RO:0002505 @@ -4500,7 +4498,7 @@ For example, A and B may be gene products and binding of B by A positively regul The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002506 @@ -4522,11 +4520,11 @@ For example, A and B may be gene products and binding of B by A positively regul A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future - Chris Mungall + determined by (system to material entity) - Chris Mungall - Pier Buttigieg + + RO:0002507 determined_by @@ -4540,7 +4538,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of determined by - Chris Mungall + determines (material entity to system) RO:0002508 @@ -4559,7 +4557,7 @@ For example, A and B may be gene products and binding of B by A positively regul s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. - Chris Mungall + RO:0002509 determined_by_part_of @@ -4574,7 +4572,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between two entities that have the property of being sequences or having sequences. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. @@ -4594,7 +4592,7 @@ For example, A and B may be gene products and binding of B by A positively regul Two consecutive DNA residues are sequentially adjacent Two exons on a processed transcript that were previously connected by an intron are adjacent x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002515 @@ -4612,7 +4610,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as a start sequence the start codon for that transcript x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence - Chris Mungall + started by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4629,7 +4627,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has start sequence - Chris Mungall + starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4649,7 +4647,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence - Chris Mungall + ended by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4666,7 +4664,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has end sequence - Chris Mungall + ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4684,7 +4682,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. In the SO paper, this was defined as an instance-type relation - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002520 @@ -4701,7 +4699,7 @@ For example, A and B may be gene products and binding of B by A positively regul Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering - Chris Mungall + RO:0002521 is_sequentially_aligned_with @@ -4718,7 +4716,7 @@ For example, A and B may be gene products and binding of B by A positively regul The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y - Chris Mungall + RO:0002522 bounds_sequence_of @@ -4733,7 +4731,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of bounds sequence of - Chris Mungall + RO:0002523 @@ -4751,8 +4749,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x has subsequence y iff all of the sequence parts of x are sequence parts of y - Chris Mungall + x has subsequence y iff all of the sequence parts of y are sequence parts of x + contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4771,7 +4769,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has subsequence - Chris Mungall + contained by RO:0002525 @@ -4788,8 +4786,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. - Chris Mungall + x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. + RO:0002526 overlaps_sequence_of @@ -4803,8 +4801,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. - Chris Mungall + x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + disconnected from RO:0002527 @@ -4820,7 +4818,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of downstream of sequence of - Chris Mungall + RO:0002528 is_upstream_of_sequence_of @@ -4836,7 +4834,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. - Chris Mungall + RO:0002529 is_downstream_of_sequence_of @@ -4852,7 +4850,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y - Chris Mungall + RO:0002530 @@ -4869,7 +4867,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript inverse of immediately downstream of - Chris Mungall + RO:0002531 is_immediately_upstream_of_sequence_of @@ -4889,7 +4887,7 @@ For example, A and B may be gene products and binding of B by A positively regul Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - Chris Mungall + has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). RO:0002551 @@ -4911,7 +4909,7 @@ For example, A and B may be gene products and binding of B by A positively regul p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. - Chris Mungall + RO:0002552 results_in_ending_of results in ending of @@ -4926,7 +4924,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - Chris Mungall + http://eol.org/schema/terms/hyperparasitoidOf https://en.wikipedia.org/wiki/Hyperparasite RO:0002553 @@ -4944,7 +4942,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of hyperparasite of - Chris Mungall + RO:0002554 has epiparasite has hyperparasite @@ -4961,7 +4959,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + http://en.wikipedia.org/wiki/Allelopathy RO:0002555 @@ -4978,7 +4976,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002556 pathogen_of @@ -4991,7 +4989,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002557 has_pathogen @@ -5005,7 +5003,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + causally influenced by (entity-centric) RO:0002559 @@ -5020,7 +5018,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - Chris Mungall + RO:0002565 @@ -5039,8 +5037,8 @@ For example, A and B may be gene products and binding of B by A positively regul The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - Chris Mungall - Vasundra Touré + + causally influences (entity-centric) RO:0002566 @@ -5057,7 +5055,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between elements of a musculoskeletal system or its analogs. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. RO:0002567 biomechanically_related_to @@ -5071,7 +5069,7 @@ For example, A and B may be gene products and binding of B by A positively regul m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - Chris Mungall + Wikipedia:Antagonist_(muscle) RO:0002568 has_muscle_antagonist @@ -5087,7 +5085,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of branching part of - Chris Mungall + RO:0002569 @@ -5104,7 +5102,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - Chris Mungall + UBERON:cjm This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. RO:0002570 @@ -5121,7 +5119,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - Chris Mungall + GOC:cjm RO:0002571 @@ -5137,7 +5135,7 @@ For example, A and B may be gene products and binding of B by A positively regul s is luminal space of x iff s is lumen_of x and s is an immaterial entity - Chris Mungall + RO:0002572 luminal_space_of @@ -5152,7 +5150,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002574 participates_in_a_biotic-biotic_interaction_with @@ -5169,7 +5167,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has skeleton - Chris Mungall + RO:0002576 skeleton_of @@ -5184,7 +5182,7 @@ For example, A and B may be gene products and binding of B by A positively regul p directly regulates q iff p is immediately causally upstream of q and p regulates q. - Chris Mungall + directly regulates (processual) @@ -5205,7 +5203,7 @@ For example, A and B may be gene products and binding of B by A positively regul gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - Chris Mungall + RO:0002584 has_part_structure_that_is_capable_of has part structure that is capable of @@ -5320,7 +5318,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall + RO:0002595 causal_relation_between_material_entity_and_a_process @@ -5723,7 +5721,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. - Vasundra Touré + RO:0003002 represses_expression_of represses expression of @@ -5738,7 +5736,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. - Vasundra Touré + RO:0003003 increases_expression_of increases expression of @@ -5883,7 +5881,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:38:20Z RO:0004000 condition_has_genetic_basis_in @@ -5897,7 +5895,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:20Z RO:0004001 has_material_basis_in_gain_of_function_germline_mutation_in @@ -5913,7 +5911,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:37Z RO:0004002 has_material_basis_in_loss_of_function_germline_mutation_in @@ -5927,7 +5925,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:54Z RO:0004003 has_material_basis_in_germline_mutation_in @@ -5942,7 +5940,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:07Z RO:0004004 has_material_basis_in_somatic_mutation_in @@ -5957,7 +5955,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:26Z RO:0004005 has_major_susceptibility_factor @@ -5971,7 +5969,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:57Z RO:0004006 has_partial_material_basis_in_germline_mutation_in @@ -5985,7 +5983,7 @@ Environmental exposures include those imposed by natural environments, experimen p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - cjm + 2018-12-13T11:26:17Z RO:0004007 @@ -6001,7 +5999,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - cjm + 2018-12-13T11:26:32Z RO:0004008 @@ -6012,8 +6010,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6027,7 +6025,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - cjm + 2018-12-13T11:26:56Z RO:0004009 @@ -6038,8 +6036,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6053,7 +6051,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:53:08Z RO:0004010 is_genetic_basis_for_condition @@ -6067,7 +6065,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:55:51Z RO:0004011 is_causal_gain_of_function_germline_mutation_of_in @@ -6082,7 +6080,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:06Z RO:0004012 is_causal_loss_of_function_germline_mutation_of_in @@ -6098,7 +6096,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:40Z RO:0004013 is_causal_germline_mutation_in @@ -6114,7 +6112,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:57:07Z RO:0004014 is_causal_somatic_mutation_in @@ -6129,7 +6127,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. - cjm + 2017-11-05T02:57:43Z RO:0004015 is_causal_susceptibility_factor_for @@ -6145,7 +6143,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. - cjm + 2017-11-05T02:58:43Z RO:0004016 is_causal_germline_mutation_partially_giving_rise_to @@ -6160,7 +6158,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:01Z RO:0004017 realizable_has_basis_in @@ -6173,7 +6171,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:29Z RO:0004018 is_basis_for_realizable @@ -6188,7 +6186,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:26:47Z RO:0004019 disease_has_basis_in @@ -6204,7 +6202,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) - cjm + 2017-11-05T03:29:32Z RO:0004020 disease_has_basis_in_dysfunction_of @@ -6220,7 +6218,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. disease has basis in disruption of (disease to process) - cjm + 2017-11-05T03:37:52Z RO:0004021 disease_has_basis_in_disruption_of @@ -6244,7 +6242,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. - cjm + 2017-11-05T03:46:07Z RO:0004022 disease_has_basis_in_feature @@ -6260,7 +6258,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. - cjm + 2017-11-05T03:50:54Z RO:0004023 causal_relationship_with_disease_as_subject @@ -6277,7 +6275,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and a process where the disease process disrupts the execution of the process. disease causes disruption of (disease to process) - cjm + 2017-11-05T03:51:09Z RO:0004024 disease_causes_disruption_of @@ -6293,7 +6291,7 @@ Environmental exposures include those imposed by natural environments, experimen disease causes dysfunction of (disease to anatomical entity) - cjm + 2017-11-05T03:58:20Z RO:0004025 disease_causes_dysfunction_of @@ -6319,7 +6317,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. - cjm + 2017-11-05T04:06:02Z RO:0004026 disease_has_location @@ -6343,7 +6341,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity - cjm + 2017-12-26T19:37:31Z RO:0004027 disease_has_inflammation_site @@ -6359,7 +6357,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - cjm + 2017-12-26T19:45:49Z RO:0004028 realized_in_response_to_stimulus @@ -6382,7 +6380,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. - cjm + 2017-12-26T19:50:53Z RO:0004029 disease_has_feature @@ -6397,7 +6395,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. - cjm + 2017-12-26T19:58:44Z RO:0004030 disease_arises_from_alteration_in_structure @@ -6411,7 +6409,7 @@ Environmental exposures include those imposed by natural environments, experimen Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - cjm + 2018-01-25T23:20:13Z RO:0004031 enables_subfunction @@ -6425,7 +6423,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:30Z RO:0004032 @@ -6441,7 +6439,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:51Z RO:0004033 @@ -6458,7 +6456,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - cjm + 2018-01-26T23:53:14Z RO:0004034 @@ -6476,7 +6474,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - cjm + 2018-01-26T23:53:22Z RO:0004035 @@ -6492,7 +6490,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:05Z RO:0004046 causally_upstream_of_or_within,_negative_effect @@ -6506,7 +6504,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:19Z RO:0004047 causally_upstream_of_or_within,_positive_effect @@ -6633,10 +6631,10 @@ Environmental exposures include those imposed by natural environments, experimen An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - Austin Meier - Chris Mungall - David Osumi-Sutherland - Marie Angelique Laporte + + + + RO:0009501 triggered by process realized_in_response_to @@ -6659,7 +6657,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - Vasundra Touré + RO:0011002 regulates_activity_of regulates activity of @@ -6674,7 +6672,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. - Vasundra Touré + RO:0011003 regulates_quantity_of regulates quantity of @@ -6689,7 +6687,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. - Vasundra Touré + RO:0011004 indirectly_regulates_activity_of indirectly regulates activity of @@ -6706,7 +6704,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011007 decreases_by_repression_quantity_of decreases by repression quantity of @@ -6723,7 +6721,7 @@ For example, protein A (transcription factor) indirectly decreases by repression The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011008 increases_by_expression_quantity_of increases by expression quantity of @@ -6738,7 +6736,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly positively regulates the quantity of B. - Vasundra Touré + RO:0011009 directly_positively_regulates_quantity_of directly positively regulates quantity of @@ -6753,7 +6751,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly negatively regulates the quantity of B. - Vasundra Touré + RO:0011010 directly_negatively_regulates_quantity_of directly negatively regulates quantity of @@ -6768,7 +6766,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. - Vasundra Touré + indirectly activates RO:0011013 indirectly_positively_regulates_activity_of @@ -6785,7 +6783,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. - Vasundra Touré + RO:0011014 destabilizes_quantity_of destabilizes quantity of @@ -6801,7 +6799,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. - Vasundra Touré + RO:0011015 stabilizes_quantity_of stabilizes quantity of @@ -6814,7 +6812,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. - Vasundra Touré + indirectly inhibits RO:0011016 indirectly_negatively_regulates_activity_of @@ -6828,7 +6826,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. - Vasundra Touré + RO:0011021 directly_regulates_quantity_of directly regulates quantity of @@ -6841,7 +6839,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011022 indirectly_regulates_quantity_of indirectly regulates quantity of @@ -6854,7 +6852,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011023 indirectly_negatively_regulates_quantity_of indirectly negatively regulates quantity of @@ -6867,7 +6865,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011024 indirectly_positively_regulates_quantity_of indirectly positively regulates quantity of @@ -6880,8 +6878,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is regulated by the small molecule continuant + pg 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -6895,8 +6893,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is activated by the small molecule continuant + pg 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -6910,8 +6908,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant + pg 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -6924,8 +6922,8 @@ For example, protein A (transcription factor) indirectly increases by expression - p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + p acts on population of c iff c' is a collection, has members of type c, and p has participant c + pg 2020-06-08T17:21:33Z RO:0012003 @@ -6941,8 +6939,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process + pg 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -6956,8 +6954,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process + pg 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of @@ -6971,8 +6969,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process + pg 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of @@ -6985,8 +6983,8 @@ For example, protein A (transcription factor) indirectly increases by expression - The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. + pg 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -6999,7 +6997,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + pg 2021-02-26T07:28:29Z RO:0012008 @@ -7016,7 +7014,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + pg 2022-09-26T06:01:01Z RO:0012009 @@ -7032,7 +7030,7 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + pg 2022-09-26T06:06:20Z RO:0012010 @@ -7048,7 +7046,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + pg 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7063,7 +7061,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + pg 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7229,7 +7227,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relation between a group and another group it is part of but does not fully constitute. X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. - Shawn Tan + This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. RO:0015003 subcluster_of @@ -7301,7 +7299,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - http://orcid.org/0000-0002-7463-6306 + 2021-11-05T17:30:44Z RO:0016002 has_disease @@ -7457,7 +7455,7 @@ For example, protein A (transcription factor) indirectly increases by expression This relation groups relations between diseases and any other kind of entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. - cjm + 2018-09-26T00:00:32Z RO:0040035 disease_relationship @@ -7471,7 +7469,7 @@ For example, protein A (transcription factor) indirectly increases by expression p has anatomical participant c iff p has participant c, and c is an anatomical entity - cjm + 2018-09-26T01:08:58Z RO:0040036 results_in_changes_to_anatomical_or_cellular_structure diff --git a/subsets/ro-sequence.obo b/subsets/ro-sequence.obo index 33d92cb8..3df12e6c 100644 --- a/subsets/ro-sequence.obo +++ b/subsets/ro-sequence.obo @@ -13,7 +13,7 @@ id: acquires_nutrients_from name: acquires nutrients from subset: ro-eco xref: RO:0002457 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for @@ -58,7 +58,7 @@ property_value: RO:0004050 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:22Z [Typedef] @@ -71,7 +71,7 @@ property_value: RO:0004049 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:14Z [Typedef] @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z [Typedef] @@ -103,7 +103,7 @@ xref: RO:0004032 property_value: RO:0004049 RO:0002264 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z [Typedef] @@ -120,7 +120,7 @@ property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cy property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 domain: BFO:0000004 range: BFO:0000004 @@ -131,7 +131,7 @@ id: allelopath_of name: allelopath of subset: ro-eco xref: RO:0002555 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string @@ -153,7 +153,7 @@ def: "x anabranch_of y if x is a distributary of y (i.e. it channels a from a la subset: ro-eco xref: RO:0002378 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "anastomoses with" xsd:string is_a: distributary_of ! distributary of disjoint_from: proper_distributary_of ! proper distributary of @@ -165,7 +165,7 @@ name: attached to def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] subset: ro-eco xref: RO:0002371 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: attached_to_part_of ! attached to part of @@ -189,9 +189,8 @@ def: "Relation between a neuron and some structure its axon forms (chemical) syn xref: RO:0002102 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in @@ -202,7 +201,7 @@ id: biomechanically_related_to name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] xref: RO:0002567 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: CARO:0000003 range: CARO:0000003 @@ -214,7 +213,7 @@ name: biotically interacts with def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] subset: ro-eco xref: RO:0002437 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string @@ -231,7 +230,7 @@ def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\ comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco xref: RO:0002007 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 is_a: part_of @@ -242,7 +241,7 @@ def: "x bounds the sequence of y iff the upstream-most part of x is upstream of xref: RO:0002522 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to inverse_of: is_bound_by_sequence_of ! is bound by sequence of @@ -254,7 +253,7 @@ def: "x is a branching part of y if and only if x is part of y and x is connecte subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso FMA:85994 xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with @@ -269,7 +268,7 @@ subset: ro-eco xref: RO:0002215 property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 @@ -302,7 +301,7 @@ id: capable_of_part_of name: capable of part of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ is_a: causal_agent_in_process ! causal agent in process @@ -350,7 +349,7 @@ id: causal_relation_between_entities name: causal relation between entities xref: RO:0002506 property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000002 @@ -363,7 +362,7 @@ name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] xref: RO:0002595 property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 range: BFO:0000015 @@ -374,7 +373,7 @@ id: causal_relation_between_processes name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 @@ -389,7 +388,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: OGMS:0000031 is_a: causally_related_to ! causally related to is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:50:54Z [Typedef] @@ -398,7 +397,7 @@ name: causally downstream of def: "inverse of upstream of" [] xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within is_a: preceded_by inverse_of: causally_upstream_of ! causally upstream of @@ -409,7 +408,7 @@ name: causally downstream of or within def: "inverse of causally upstream of or within" [] subset: RO:0002259 xref: RO:0002427 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -418,7 +417,7 @@ is_a: causal_relation_between_processes ! causal relation between processes id: causally_influenced_by name: causally influenced by xref: RO:0002559 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: causal_relation_between_entities ! causal relation between entities @@ -429,8 +428,8 @@ id: causally_influences name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] xref: RO:0002566 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 @@ -443,7 +442,7 @@ name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] @@ -453,7 +452,7 @@ def: "p is causally upstream of q iff p is causally related to q, the end of p p subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes @@ -465,7 +464,7 @@ def: "p is causally upstream of, negative effect q iff p is casually upstream of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -478,7 +477,7 @@ comment: holds between x and y if and only if x is causally upstream of y and th subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -490,7 +489,7 @@ def: "p is 'causally upstream or within' q iff p is causally related to q, and t synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -502,7 +501,7 @@ name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -511,7 +510,7 @@ name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -537,7 +536,7 @@ name: child nucleus of def: "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" [] xref: RO:0002476 property_value: IAO:0000112 "ABal nucleus child nucleus of ABa nucleus (in C elegans)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." xsd:string domain: GO:0005634 range: GO:0005634 @@ -548,7 +547,7 @@ id: child_nucleus_of_in_hermaphrodite name: child nucleus of in hermaphrodite def: "A child nucleus relationship in which the cells are part of a hermaphroditic organism" [] xref: RO:0002477 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -556,7 +555,7 @@ id: child_nucleus_of_in_male name: child nucleus of in male def: "A child nucleus relationship in which the cells are part of a male organism" [] xref: RO:0002478 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -576,7 +575,7 @@ comment: Example: if we define region of chromosome as any subdivision of a chro subset: ro-eco xref: RO:0002008 property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -585,9 +584,8 @@ name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 -property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -599,7 +597,7 @@ name: commensually interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] subset: ro-eco xref: RO:0002441 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -610,7 +608,7 @@ def: "x composed_primarily_of y if and only if more than half of the mass of x i subset: ro-eco xref: RO:0002473 property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 @@ -639,7 +637,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: BFO:0000017 is_a: causally_related_to ! causally related to inverse_of: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:38:20Z [Typedef] @@ -648,7 +646,7 @@ name: conduit for def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] subset: ro-eco xref: RO:0002570 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 UBERON:cjm xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 @@ -661,7 +659,7 @@ name: confers advantage in subset: ro-eco xref: RO:0002322 property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "adapted for" xsd:string range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -727,7 +725,7 @@ name: continuous with def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 @@ -746,7 +744,7 @@ property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a het property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -771,7 +769,7 @@ id: contributes_to_morphology_of name: contributes to morphology of def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] xref: RO:0002433 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -796,7 +794,7 @@ id: decreases_by_repression_quantity_of name: decreases by repression quantity of def: "The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011007 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_negatively_regulates_quantity_of ! indirectly negatively regulates quantity of @@ -808,8 +806,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in wh xref: RO:0002121 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in @@ -821,7 +819,7 @@ name: destabilizes quantity of def: "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." [] xref: RO:0011014 property_value: IAO:0000112 "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_quantity_of ! directly negatively regulates quantity of @@ -832,11 +830,11 @@ name: determined by def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] subset: ro-eco xref: RO:0002507 -property_value: http://purl.org/dc/terms/creator "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/creator "Pier Buttigieg" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-4366-3088 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "A coral reef environment is determined by a particular coral reef" xsd:string property_value: IAO:0000116 "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602 property_value: IAO:0000589 "determined by (system to material entity)" xsd:string domain: RO:0002577 @@ -852,7 +850,7 @@ name: determined by part of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] subset: ro-eco xref: RO:0002509 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 range: BFO:0000040 is_a: causal_relation_between_entities ! causal relation between entities @@ -865,7 +863,7 @@ def: "inverse of determined by" [] subset: ro-eco subset: RO:0002259 xref: RO:0002508 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "determines (material entity to system)" xsd:string is_a: causally_influences ! causally influences @@ -876,7 +874,7 @@ def: "inverse of has developmental contribution from" [] subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to @@ -886,9 +884,9 @@ name: developmentally induced by def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] xref: RO:0002256 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string property_value: IAO:0000119 GO:0001759 xsd:string @@ -905,7 +903,7 @@ name: developmentally induces def: "Inverse of developmentally induced by" [] xref: RO:0002257 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_induce ! has potential to developmentally induce @@ -917,7 +915,7 @@ comment: This relation groups together various other developmental relations. It xref: RO:0002258 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string domain: BFO:0000002 range: BFO:0000002 @@ -929,7 +927,7 @@ id: developmentally_related_to name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] xref: RO:0002324 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] @@ -939,7 +937,7 @@ def: "x developmentally replaces y if and only if there is some developmental pr xref: RO:0002285 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "replaces" xsd:string is_a: developmentally_preceded_by ! developmentally preceded by @@ -949,7 +947,7 @@ name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] xref: RO:0002286 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -959,10 +957,10 @@ def: "x develops from y if and only if either (a) x directly develops from y or comment: This is the transitive form of the develops from relation xref: RO:0002202 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 domain: BFO:0000004 range: BFO:0000004 is_transitive: true @@ -975,7 +973,7 @@ name: develops from part of def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] xref: RO:0002225 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: develops_from ! develops from [Typedef] @@ -984,7 +982,7 @@ name: develops in def: "x develops_in y if x is located in y whilst x is developing" [] xref: RO:0002226 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string domain: CARO:0000000 @@ -997,9 +995,9 @@ def: "inverse of develops from" [] subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 is_transitive: true is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into @@ -1010,11 +1008,11 @@ id: directly_develops_from name: directly develops from def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] xref: RO:0002207 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "has developmental precursor" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000119 "FBbt" xsd:string property_value: RO:0002575 RO:0002202 is_a: develops_from ! develops from @@ -1060,8 +1058,8 @@ name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] xref: RO:0002449 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1072,7 +1070,7 @@ id: directly_negatively_regulates_quantity_of name: directly negatively regulates quantity of def: "The entity A has an activity that directly negatively regulates the quantity of B." [] xref: RO:0011010 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1107,8 +1105,8 @@ name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] xref: RO:0002450 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1119,7 +1117,7 @@ id: directly_positively_regulates_quantity_of name: directly positively regulates quantity of def: "The entity A has an activity that directly positively regulates the quantity of B." [] xref: RO:0011009 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1142,7 +1140,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002578 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string property_value: RO:0002575 RO:0002211 @@ -1155,8 +1153,8 @@ name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] xref: RO:0002448 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: molecularly_interacts_with ! molecularly interacts with @@ -1167,7 +1165,7 @@ id: directly_regulates_quantity_of name: directly regulates quantity of def: "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B." [] xref: RO:0011021 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -1177,7 +1175,7 @@ def: "A relationship between a disease and an anatomical structure where the mat xref: RO:0004030 range: CARO:0000003 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z [Typedef] @@ -1189,7 +1187,7 @@ property_value: IAO:0000589 "disease causes disruption of (disease to process)" domain: OGMS:0000031 range: BFO:0000015 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:51:09Z [Typedef] @@ -1200,7 +1198,7 @@ property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomica domain: OGMS:0000031 range: CARO:0000006 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z [Typedef] @@ -1210,7 +1208,7 @@ xref: RO:0004019 domain: OGMS:0000031 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject is_a: realizable_has_basis_in ! realizable has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:26:47Z [Typedef] @@ -1221,7 +1219,7 @@ xref: RO:0004021 property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:37:52Z [Typedef] @@ -1232,7 +1230,7 @@ xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string range: CARO:0000006 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z [Typedef] @@ -1243,7 +1241,7 @@ xref: RO:0004022 domain: OGMS:0000031 is_a: disease_has_basis_in ! disease has basis in is_a: has_phenotype ! has phenotype -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:46:07Z [Typedef] @@ -1253,7 +1251,7 @@ def: "A relationship between a disease and some feature of that disease, where t xref: RO:0004029 domain: OGMS:0000031 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:50:53Z [Typedef] @@ -1272,7 +1270,7 @@ xref: RO:0004027 domain: OGMS:0000031 range: BFO:0000004 is_a: disease_has_location ! disease has location -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:37:31Z [Typedef] @@ -1285,7 +1283,7 @@ property_value: IAO:0000232 "This relation is intentionally very general, and co domain: OGMS:0000031 range: BFO:0000004 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T04:06:02Z [Typedef] @@ -1294,7 +1292,7 @@ name: disease relationship def: "This relation groups relations between diseases and any other kind of entity." [] xref: RO:0040035 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z [Typedef] @@ -1306,7 +1304,7 @@ subset: ro-eco xref: RO:0002377 property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string @@ -1316,10 +1314,10 @@ is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: does_not_overlap_sequence_of name: does not overlap sequence of -def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] xref: RO:0002527 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "disconnected from" xsd:string is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -1338,7 +1336,7 @@ id: eats name: eats subset: ro-eco xref: RO:0002470 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -1359,7 +1357,7 @@ def: "A relationship that is mediated in some way by the environment or environm subset: ro-eco xref: RO:0002321 property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string [Typedef] @@ -1377,7 +1375,7 @@ name: electrically_synapsed_to def: "A relation that holds between two neurons that are electrically coupled via gap junctions." [] xref: RO:0002003 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: connected_to ! connected to [Typedef] @@ -1386,7 +1384,7 @@ name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: has_participant @@ -1397,7 +1395,7 @@ def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string property_value: IAO:0000118 "has" xsd:string @@ -1413,7 +1411,7 @@ name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] xref: RO:0004031 is_a: functionally_related_to ! functionally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z [Typedef] @@ -1430,14 +1428,14 @@ inverse_of: has_endoparasite ! has endoparasite id: ends subset: ro-eco xref: RO:0002229 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: ends_with subset: ro-eco xref: RO:0002230 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -1462,7 +1460,7 @@ name: exports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002345 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -1479,7 +1477,7 @@ def: "relationship between a neuron and a neuron projection bundle (e.g.- tract xref: RO:0002101 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 @@ -1492,7 +1490,7 @@ inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron proje id: formed_as_result_of name: formed as result of xref: RO:0002354 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of [Typedef] @@ -1500,7 +1498,7 @@ id: functionally_related_to name: functionally related to def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] xref: RO:0002328 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string [Typedef] @@ -1509,7 +1507,7 @@ name: genetically interacts with xref: RO:0002435 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with @@ -1517,7 +1515,7 @@ is_a: interacts_with ! interacts with [Typedef] id: has_2D_boundary xref: RO:0002002 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1557,7 +1555,7 @@ def: "inverse of branching part of" [] subset: ro-eco subset: RO:0002259 xref: RO:0002569 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: has_part is_a: in_branching_relationship_with ! in branching relationship with @@ -1593,7 +1591,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 "Bill Duncan (https://orcid.org/0000-0001-9625-1899)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant @@ -1622,7 +1620,7 @@ id: has_dendrite_location name: has dendrite location xref: RO:0002360 property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -1632,7 +1630,7 @@ def: "x has developmental contribution from y iff x has some part z such that z xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by @@ -1644,7 +1642,7 @@ name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to @@ -1656,7 +1654,7 @@ def: "p has direct input c iff c is a participant in p, c is present at the star xref: RO:0002400 property_value: IAO:0000112 "'protein catabolic process' SubClassOf has_direct_input some protein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly consumes" xsd:string property_value: IAO:0000232 "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" xsd:string is_a: has_input ! has input @@ -1666,7 +1664,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1711,7 +1709,7 @@ def: "x 'has end location' y if and only if there exists some process z such tha subset: ro-eco xref: RO:0002232 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -1724,7 +1722,7 @@ def: "x has end sequence y if the end of x is identical to the end of y, and x h xref: RO:0002518 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -1776,11 +1774,11 @@ id: has_exposure_stimulus name: has exposure stimulus def: "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002309 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 is_a: related_via_exposure_to ! related via exposure to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:35:04Z [Typedef] @@ -1806,7 +1804,7 @@ def: "The relation between a neuron projection bundle and a neuron projection th xref: RO:0002132 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 @@ -1828,7 +1826,7 @@ subset: ro-eco xref: RO:0002303 property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Pier Buttigieg" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string domain: CARO:0001010 range: ENVO:01000254 @@ -1851,7 +1849,7 @@ name: has host def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] subset: ro-eco xref: RO:0002454 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -1865,7 +1863,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 is_a: has_participant @@ -1886,7 +1884,7 @@ def: "p has intermediate c if and only if p has parts p1, p2 and p1 has output c subset: ro-eco xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string is_a: has_participant @@ -1924,7 +1922,7 @@ name: has major susceptibility factor xref: RO:0004005 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_susceptibility_factor_for ! is causal susceptibility factor for -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:26Z [Typedef] @@ -1935,7 +1933,7 @@ property_value: seeAlso Orphanet:410295 property_value: seeAlso Orphanet:410296 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_gain_of_function_germline_mutation_of_in ! is causal gain of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:20Z [Typedef] @@ -1945,7 +1943,7 @@ xref: RO:0004003 property_value: seeAlso Orphanet:317343 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_in ! is causal germline mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:54Z [Typedef] @@ -1954,7 +1952,7 @@ name: has material basis in loss of function germline mutation in xref: RO:0004002 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_loss_of_function_germline_mutation_of_in ! is causal loss of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:37Z [Typedef] @@ -1964,7 +1962,7 @@ xref: RO:0004004 property_value: seeAlso Orphanet:317344 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z [Typedef] @@ -1980,7 +1978,7 @@ id: has_muscle_antagonist name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string is_a: biomechanically_related_to ! biomechanically related to @@ -1989,7 +1987,7 @@ id: has_muscle_insertion name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} @@ -2001,7 +1999,7 @@ id: has_muscle_origin name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} @@ -2039,7 +2037,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string is_a: has_participant inverse_of: output_of ! output of @@ -2066,7 +2064,7 @@ name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] xref: RO:0002584 property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causal_relation_between_material_entity_and_a_process ! causal relation between material entity and a process is_a: functionally_related_to ! functionally related to @@ -2076,7 +2074,7 @@ name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco xref: RO:0002479 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 range: BFO:0000004 @@ -2086,7 +2084,7 @@ name: has partial material basis in germline mutation in xref: RO:0004006 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_partially_giving_rise_to ! is causal germline mutation partially giving rise to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:57Z [Typedef] @@ -2098,7 +2096,7 @@ id: has_pathogen name: has pathogen subset: ro-eco xref: RO:0002557 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2108,7 +2106,7 @@ def: "A relationship that holds between a biological entity and a phenotype. Her subset: ro-eco xref: RO:0002200 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: UPHENO:0001001 is_a: has_phenotype_or_disease ! has phenotype or disease inverse_of: phenotype_of ! phenotype of @@ -2129,9 +2127,9 @@ def: "Holds between a cell c and a protein complex or protein p if and only if t xref: RO:0002104 property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Alexander Diehl" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 @@ -2157,8 +2155,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in whi xref: RO:0002110 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "synapsed in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2172,7 +2170,7 @@ name: has potential to develop into def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] xref: RO:0002387 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2181,7 +2179,7 @@ name: has potential to developmentally contribute to def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] xref: RO:0002385 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2190,7 +2188,7 @@ name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] xref: RO:0002386 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2199,7 +2197,7 @@ name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] xref: RO:0002388 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_potential_to_develop_into ! has potential to develop into [Typedef] @@ -2223,7 +2221,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -2233,7 +2231,7 @@ def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c o subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -2244,7 +2242,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -2276,7 +2274,7 @@ name: has skeleton def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] xref: RO:0002551 property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 @@ -2321,7 +2319,7 @@ name: has soma location def: "Relation between a neuron and an anatomical structure that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 range: CARO:0000003 @@ -2335,7 +2333,7 @@ def: "x 'has starts location' y if and only if there exists some process z such subset: ro-eco xref: RO:0002231 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -2348,7 +2346,7 @@ def: "x has start sequence y if the start of x is identical to the start of y, a xref: RO:0002516 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2358,10 +2356,10 @@ inverse_of: is_start_sequence_of ! is start sequence of [Typedef] id: has_subsequence name: has subsequence -def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2375,7 +2373,7 @@ id: has_symptom name: has symptom def: "A relation that holds between a disease or an organism and a phenotype" [] xref: RO:0002452 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: OGMS:0000031 is_a: has_phenotype ! has phenotype @@ -2405,7 +2403,7 @@ def: "A general relation between a neuron and some structure in which it either xref: RO:0002130 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has synapse in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2417,7 +2415,7 @@ id: has_synaptic_terminal_of name: has synaptic terminal of xref: RO:0002006 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: overlaps ! overlaps inverse_of: has_synaptic_terminal_in ! has synaptic terminal in @@ -2429,7 +2427,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002339 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2440,7 +2438,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002338 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2448,7 +2446,7 @@ id: has_vector name: has vector subset: ro-eco xref: RO:0002460 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with [Typedef] @@ -2463,7 +2461,7 @@ id: host_of name: host of subset: ro-eco xref: RO:0002453 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2476,7 +2474,7 @@ synonym: "epiparasite of" RELATED [] synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string is_a: has_host ! has host @@ -2492,7 +2490,7 @@ synonym: "has epiparasite" RELATED [] synonym: "has hyperparasite" RELATED [] synonym: "hyperparasitoidized by" RELATED [] xref: RO:0002554 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2500,7 +2498,7 @@ id: immediate_transformation_of name: immediate transformation of def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] xref: RO:0002495 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002494 is_a: directly_develops_from ! directly develops from is_a: transformation_of ! transformation of @@ -2510,7 +2508,7 @@ id: immediately_causally_downstream_of name: immediately causally downstream of xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of is_a: immediately_preceded_by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of @@ -2520,7 +2518,7 @@ id: immediately_causally_upstream_of name: immediately causally upstream of def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: immediately_precedes @@ -2533,7 +2531,7 @@ xref: RO:0002087 id: immediately_precedes subset: ro-eco xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0002575 BFO:0000063 [Typedef] @@ -2542,7 +2540,7 @@ name: imports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002340 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -2551,7 +2549,7 @@ name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] xref: RO:0002375 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 @@ -2577,7 +2575,7 @@ id: increases_by_expression_quantity_of name: increases by expression quantity of def: "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011008 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_positively_regulates_quantity_of ! indirectly positively regulates quantity of @@ -2587,7 +2585,7 @@ id: increases_expression_of name: increases expression of def: "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." [] xref: RO:0003003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -2606,7 +2604,7 @@ id: indirectly_negatively_regulates name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true @@ -2618,7 +2616,7 @@ id: indirectly_negatively_regulates_activity_of name: indirectly negatively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B." [] xref: RO:0011016 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly inhibits" xsd:string is_a: indirectly_regulates_activity_of ! indirectly regulates activity of @@ -2627,7 +2625,7 @@ id: indirectly_negatively_regulates_quantity_of name: indirectly negatively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B." [] xref: RO:0011023 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2635,7 +2633,7 @@ id: indirectly_positively_regulates name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 is_transitive: true @@ -2647,7 +2645,7 @@ id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." [] xref: RO:0011013 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -2658,7 +2656,7 @@ id: indirectly_positively_regulates_quantity_of name: indirectly positively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B." [] xref: RO:0011024 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2676,7 +2674,7 @@ id: indirectly_regulates_activity_of name: indirectly regulates activity of def: "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." [] xref: RO:0011004 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: regulates_activity_of ! regulates activity of @@ -2686,7 +2684,7 @@ id: indirectly_regulates_quantity_of name: indirectly regulates quantity of def: "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B." [] xref: RO:0011022 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -2696,7 +2694,7 @@ def: "inverse of has input" [] subset: ro-eco subset: RO:0002259 xref: RO:0002352 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -2710,7 +2708,7 @@ xref: RO:0002434 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI domain: BFO:0000040 @@ -2723,7 +2721,7 @@ name: interacts with via parasite-host interaction def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] subset: ro-eco xref: RO:0002443 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2751,7 +2749,7 @@ id: involved_in name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] xref: RO:0002331 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in @@ -2763,7 +2761,7 @@ id: involved_in_negative_regulation_of name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] xref: RO:0002430 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2773,7 +2771,7 @@ name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in_process ! causal agent in process @@ -2784,7 +2782,7 @@ id: involved_in_positive_regulation_of name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] xref: RO:0002429 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2793,7 +2791,7 @@ id: involved_in_regulation_of name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] xref: RO:0002428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of @@ -2804,7 +2802,7 @@ def: "c executes activity in d if and only if c enables p and p occurs_in d. As synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -2853,7 +2851,7 @@ id: is_basis_for_realizable name: is basis for realizable xref: RO:0004018 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:29Z [Typedef] @@ -2863,7 +2861,7 @@ def: "inverse of bounds sequence of" [] subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to @@ -2874,7 +2872,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004011 property_value: seeAlso Orphanet:410296 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:55:51Z [Typedef] @@ -2885,7 +2883,7 @@ xref: RO:0004013 property_value: seeAlso Orphanet:317343 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:40Z [Typedef] @@ -2896,7 +2894,7 @@ xref: RO:0004016 property_value: seeAlso Orphanet:317346 is_a: contributes_to_condition ! contributes to condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:58:43Z [Typedef] @@ -2906,7 +2904,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004012 property_value: seeAlso Orphanet:410295 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:06Z [Typedef] @@ -2917,7 +2915,7 @@ xref: RO:0004014 property_value: seeAlso Orphanet:317344 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:07Z [Typedef] @@ -2927,7 +2925,7 @@ def: "Relates a gene to condition, such that a mutation in this gene predisposes xref: RO:0004015 property_value: seeAlso Orphanet:317345 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:43Z [Typedef] @@ -2937,7 +2935,7 @@ def: "x is a consecutive sequence of y iff x has subsequence y, and all the part xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: has_subsequence ! has subsequence @@ -2947,7 +2945,7 @@ name: is downstream of sequence of def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] xref: RO:0002529 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of @@ -2957,7 +2955,7 @@ id: is_eaten_by name: is eaten by subset: ro-eco xref: RO:0002471 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -2969,7 +2967,7 @@ def: "inverse of has end sequence" [] subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2982,7 +2980,7 @@ xref: RO:0004010 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string range: BFO:0000017 is_a: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:53:08Z [Typedef] @@ -2992,7 +2990,7 @@ def: "x is immediately downstream of the sequence of y iff either (1) x and y ha xref: RO:0002530 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002529 is_a: is_downstream_of_sequence_of ! is downstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3004,7 +3002,7 @@ def: "inverse of immediately downstream of" [] xref: RO:0002531 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: is_upstream_of_sequence_of ! is upstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3031,7 +3029,7 @@ def: "x is sequentially aligned with if a significant portion bases of x and y c xref: RO:0002521 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -3071,7 +3069,7 @@ def: "inverse of has start sequence" [] subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3084,7 +3082,7 @@ def: "inverse of has subsequence" [] subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of @@ -3107,7 +3105,7 @@ name: is treated by substance def: "Inverse of 'is substance that treats'" [] subset: RO:0002259 xref: RO:0002302 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 is_a: causally_related_to ! causally related to inverse_of: is_substance_that_treats ! is substance that treats @@ -3117,7 +3115,7 @@ name: is upstream of sequence of def: "inverse of downstream of sequence of" [] xref: RO:0002528 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -3127,7 +3125,7 @@ name: is vector for subset: ro-eco xref: RO:0002459 property_value: IAO:0000112 "Anopheles is a vector for Plasmodium" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: has_vector ! has vector @@ -3179,7 +3177,7 @@ name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco xref: RO:0002571 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:cjm xsd:string range: BFO:0000040 is_a: part_of @@ -3190,7 +3188,7 @@ name: luminal space of def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] subset: ro-eco xref: RO:0002572 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000141 is_a: lumen_of ! lumen of @@ -3202,7 +3200,7 @@ subset: ro-eco xref: RO:0002381 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with is_a: part_of @@ -3212,7 +3210,7 @@ id: mereotopologically_related_to name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] xref: RO:0002323 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string property_value: RO:0001900 RO:0001901 @@ -3230,7 +3228,7 @@ name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 @@ -3243,7 +3241,7 @@ name: mutualistically interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] subset: ro-eco xref: RO:0002442 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -3270,7 +3268,7 @@ name: negatively regulated by def: "inverse of negatively regulates" [] subset: RO:0002259 xref: RO:0002335 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3281,7 +3279,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 @@ -3330,7 +3328,7 @@ def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -3351,10 +3349,10 @@ expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://p [Typedef] id: overlaps_sequence_of name: overlaps sequence of -def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] xref: RO:0002526 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: overlaps ! overlaps is_a: sequentially_related_to ! sequentially related to @@ -3366,7 +3364,7 @@ subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string is_a: has_host ! has host @@ -3379,7 +3377,7 @@ name: parasitized by subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string @@ -3418,7 +3416,7 @@ name: part of developmental precursor of xref: RO:0002287 property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by [Typedef] @@ -3426,7 +3424,7 @@ id: part_of_structure_that_is_capable_of name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] xref: RO:0002329 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean is_a: functionally_related_to ! functionally related to @@ -3455,7 +3453,7 @@ subset: ro-eco synonym: "semibiotically interacts with" RELATED [] xref: RO:0002446 property_value: IAO:0000112 "Porifiera attaches to substrate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: biotically_interacts_with ! biotically interacts with @@ -3464,7 +3462,7 @@ id: participates_in_a_biotic-biotic_interaction_with name: participates in a biotic-biotic interaction with subset: ro-eco xref: RO:0002574 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 domain: CARO:0001010 range: CARO:0001010 @@ -3474,7 +3472,7 @@ is_a: biotically_interacts_with ! biotically interacts with id: partner_in name: partner in xref: RO:0002461 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string is_a: participates_in @@ -3483,7 +3481,7 @@ id: pathogen_of name: pathogen of subset: ro-eco xref: RO:0002556 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_host ! has host inverse_of: has_pathogen ! has pathogen @@ -3495,7 +3493,7 @@ subset: ro-eco subset: RO:0002259 xref: RO:0002201 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_functional: true [Typedef] @@ -3503,7 +3501,7 @@ id: phosphorylates name: phosphorylates xref: RO:0002447 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: molecularly_interacts_with ! molecularly interacts with @@ -3512,7 +3510,7 @@ id: pollinated_by name: pollinated by subset: ro-eco xref: RO:0002456 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string @@ -3525,7 +3523,7 @@ subset: ro-eco xref: RO:0002455 property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with @@ -3537,7 +3535,7 @@ name: positively regulated by def: "inverse of positively regulates" [] subset: RO:0002259 xref: RO:0002336 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3548,7 +3546,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002211 @@ -3583,7 +3581,7 @@ def: "inverse of preys on" [] subset: ro-eco subset: RO:0002259 xref: RO:0002458 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string @@ -3598,9 +3596,9 @@ subset: ro-eco xref: RO:0002439 property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Jorrit Poelen" xsd:string -property_value: IAO:0000117 "Katja Shulz" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7134-3324 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string @@ -3623,7 +3621,7 @@ def: "x proper_distributary_of y iff x distributary_of y and x does not flow bac subset: ro-eco xref: RO:0002382 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: distributary_of ! distributary of [Typedef] @@ -3633,7 +3631,7 @@ def: "x proper_tributary_of y iff x tributary_of y and x does not originate from subset: ro-eco xref: RO:0002383 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: tributary_of ! tributary of [Typedef] @@ -3642,7 +3640,7 @@ name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string @@ -3654,7 +3652,7 @@ id: provides_nutrients_for name: provides nutrients for subset: ro-eco xref: RO:0002469 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3663,7 +3661,7 @@ name: realizable has basis in xref: RO:0004017 is_a: causally_related_to ! causally related to inverse_of: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:01Z [Typedef] @@ -3672,10 +3670,10 @@ name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] synonym: "triggered by process" EXACT [RO:cjm] xref: RO:0009501 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "David Osumi-Sutherland" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string @@ -3692,7 +3690,7 @@ xref: RO:0004028 domain: BFO:0000017 range: BFO:0000040 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:45:49Z [Typedef] @@ -3700,7 +3698,7 @@ id: receives_input_from name: receives input from xref: RO:0002485 property_value: IAO:0000116 "See notes for inverse relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to inverse_of: sends_output_to ! sends output to @@ -3740,7 +3738,7 @@ name: regulated by def: "inverse of regulates" [] subset: RO:0002259 xref: RO:0002334 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 range: BFO:0000015 @@ -3755,9 +3753,9 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Hill" xsd:string -property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 +property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string @@ -3774,7 +3772,7 @@ id: regulates_activity_of name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] xref: RO:0011002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3794,7 +3792,7 @@ id: regulates_in_other_organism name: regulates in other organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] xref: RO:0002010 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 range: BFO:0000015 is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -3805,7 +3803,7 @@ name: regulates levels of def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] xref: RO:0002332 property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 @@ -3817,7 +3815,7 @@ id: regulates_quantity_of name: regulates quantity of def: "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." [] xref: RO:0011003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3836,7 +3834,7 @@ id: related_via_localization_to name: related via localization to def: "A relationship that holds via some process of localization" [] xref: RO:0002337 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 range: BFO:0000002 @@ -3857,7 +3855,7 @@ id: represses_expression_of name: represses expression of def: "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." [] xref: RO:0003002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3871,7 +3869,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -3916,7 +3914,7 @@ name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] @@ -3936,7 +3934,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002348 property_value: IAO:0000112 "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3948,7 +3946,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002349 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3962,7 +3960,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3972,7 +3970,7 @@ id: results_in_developmental_induction_of name: results in developmental induction of def: "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." [] xref: RO:0002357 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3982,7 +3980,7 @@ def: "p results in the developmental progression of s iff p is a developmental p xref: RO:0002295 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 range: CARO:0000000 @@ -3994,7 +3992,7 @@ name: results in developmental regression of xref: RO:0002301 property_value: IAO:0000112 "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4004,7 +4002,7 @@ name: results in disappearance of xref: RO:0002300 property_value: IAO:0000112 "foramen ovale closure SubClassOf results in disappearance of foramen ovale" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4020,7 +4018,7 @@ id: results_in_ending_of name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4034,7 +4032,7 @@ xref: RO:0002297 property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4056,7 +4054,7 @@ id: results_in_growth_of name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4071,7 +4069,7 @@ xref: RO:0002299 property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4087,7 +4085,7 @@ xref: RO:0002298 property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4100,7 +4098,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002565 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4126,7 +4124,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002356 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4135,7 +4133,7 @@ id: results_in_structural_organization_of name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4151,7 +4149,7 @@ name: results in transport across def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002342 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: occurs_across ! occurs across is_a: results_in_transport_to_from_or_in ! results in transport to from or in @@ -4160,7 +4158,7 @@ id: results_in_transport_along name: results in transport along def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] xref: RO:0002341 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4168,7 +4166,7 @@ id: results_in_transport_to_from_or_in name: results in transport to from or in xref: RO:0002344 property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4183,7 +4181,7 @@ id: sends_output_to name: sends output to xref: RO:0002486 property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to [Typedef] @@ -4225,7 +4223,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcript" xsd:string property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -4235,7 +4233,7 @@ name: sequentially related to def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string @@ -4248,7 +4246,7 @@ name: skeleton of def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 is_a: part_of @@ -4259,7 +4257,7 @@ name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] xref: RO:0002379 property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: overlaps ! overlaps @@ -4271,7 +4269,7 @@ subset: ro-eco xref: RO:0002163 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 @@ -4285,7 +4283,7 @@ name: stabilizes quantity of def: "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." [] xref: RO:0011015 property_value: IAO:0000112 "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_quantity_of ! directly positively regulates quantity of @@ -4294,14 +4292,14 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates id: starts subset: ro-eco xref: RO:0002223 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: starts_with subset: ro-eco xref: RO:0002224 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -4317,7 +4315,7 @@ name: subcluster of def: "A relation between a group and another group it is part of but does not fully constitute." [] xref: RO:0015003 property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." xsd:string -property_value: IAO:0000117 "Shawn Tan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true is_a: part_of @@ -4326,7 +4324,7 @@ is_a: part_of id: subject_participant_in name: subject participant in xref: RO:0002462 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4345,7 +4343,7 @@ name: surrounded by def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] xref: RO:0002219 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to inverse_of: surrounds ! surrounds @@ -4357,7 +4355,7 @@ def: "inverse of surrounded by" [] subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to @@ -4367,7 +4365,7 @@ name: symbiotically interacts with def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] subset: ro-eco xref: RO:0002440 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true @@ -4380,8 +4378,8 @@ def: "Relation between an anatomical structure (including cells) and a neuron th xref: RO:0002103 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: receives_input_from ! receives input from inverse_of: synapsed_to ! synapsed to @@ -4406,8 +4404,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002108 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" [] @@ -4420,8 +4418,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002109 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4434,8 +4432,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002112 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4448,8 +4446,8 @@ comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part som xref: RO:0002120 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: sends_output_to ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -4473,8 +4471,8 @@ def: "A relation between a motor neuron and a muscle that it synapses to via a t comment: Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) xref: RO:0002107 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_II_bouton ! synapsed_by_via_type_II_bouton @@ -4488,8 +4486,8 @@ comment: Expands to: has_part some ('type Ib terminal button' that has_part some xref: RO:0002105 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Ib_bouton ! synapsed_by_via_type_Ib_bouton @@ -4503,8 +4501,8 @@ comment: Expands to: has_part some ('type Is terminal button' that has_part some xref: RO:0002106 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Is_bouton ! synapsed_by_via_type_Is_bouton @@ -4514,7 +4512,7 @@ expand_expression_to: "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that id: target_participant_in name: target participant in xref: RO:0002463 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4523,7 +4521,7 @@ id: temporally_related_to subset: ro-eco xref: RO:0002222 property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string [Typedef] @@ -4531,7 +4529,7 @@ id: transformation_of name: transformation of def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] xref: RO:0002494 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: develops_from ! develops from @@ -4541,7 +4539,7 @@ name: transitively provides input for def: "transitive form of directly_provides_input_for" [] xref: RO:0002414 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." xsd:string property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string domain: BFO:0000015 @@ -4556,7 +4554,7 @@ def: "A relationship that holds between a disease and organism" [] xref: RO:0002451 property_value: IAO:0000112 "all dengue disease transmitted by some mosquito" xsd:string property_value: IAO:0000116 "Add domain and range constraints" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -4576,7 +4574,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002313 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "regulates localization of" xsd:string is_a: related_via_localization_to ! related via localization to is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4590,7 +4588,7 @@ xref: RO:0002376 property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string @@ -4608,7 +4606,7 @@ name: trophically interacts with def: "An interaction relationship in which the partners are related via a feeding relationship." [] subset: ro-eco xref: RO:0002438 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4618,7 +4616,7 @@ name: ubiquitinates def: "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" [] xref: RO:0002480 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with [Typedef] diff --git a/subsets/ro-sequence.owl b/subsets/ro-sequence.owl index e0f35ac5..bfa36ffb 100644 --- a/subsets/ro-sequence.owl +++ b/subsets/ro-sequence.owl @@ -409,7 +409,7 @@ - David Osumi-Sutherland + RO:0002002 has_2D_boundary @@ -421,7 +421,7 @@ A relation that holds between two neurons that are electrically coupled via gap junctions. - David Osumi-Sutherland + RO:0002003 electrically_synapsed_to @@ -435,7 +435,7 @@ - David Osumi-Sutherland + RO:0002006 has_synaptic_terminal_of @@ -469,7 +469,7 @@ has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland + RO:0002007 bounding_layer_of @@ -505,9 +505,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. + A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. Note from NCEAS meeting: consider changing primary label - David Osumi-Sutherland + RO:0002008 coincident_with @@ -524,7 +524,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - David Osumi-Sutherland + RO:0002010 regulates_in_other_organism regulates in other organism @@ -553,7 +553,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + dos 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -568,7 +568,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + dos 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -584,7 +584,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + dos 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -599,7 +599,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -613,7 +613,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -630,7 +630,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + dos 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -644,7 +644,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + dos 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -658,7 +658,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + dos 2017-07-20T17:11:08Z RO:0002020 transports @@ -672,7 +672,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + dos 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -686,7 +686,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -697,7 +697,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + GOC:dos @@ -708,7 +708,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + dos 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -718,7 +718,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + GOC:dos @@ -729,7 +729,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + dos 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -739,7 +739,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + GOC:dos @@ -750,7 +750,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + dos 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -761,7 +761,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + GOC:dos @@ -780,7 +780,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + dos 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -797,7 +797,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + GOC:dos @@ -814,7 +814,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + RO:0002090 @@ -831,7 +831,7 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure that its soma is part of. - David Osumi-Sutherland + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -852,9 +852,9 @@ Examples include: the relationship between two channels collected simultaneously relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - David Osumi-Sutherland + fasciculates with - (forall (?x ?y) + (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) @@ -890,9 +890,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure its axon forms (chemical) synapses in. - Chris Mungall - David Osumi-Sutherland - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -924,8 +923,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -945,9 +944,9 @@ Examples include: the relationship between two channels collected simultaneously Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - Alexander Diehl - Chris Mungall - Lindsay Cowell + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) @@ -965,8 +964,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -985,8 +984,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -1005,8 +1004,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) RO:0002107 @@ -1023,8 +1022,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1043,8 +1042,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1064,8 +1063,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - Chris Mungall - David Osumi-Sutherland + + synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( @@ -1085,8 +1084,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1168,8 +1167,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -1196,8 +1195,8 @@ N1 SubclassOf ( Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -1218,7 +1217,7 @@ N1 SubclassOf ( A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - David Osumi-Sutherland + has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) @@ -1267,9 +1266,9 @@ N1 SubclassOf ( The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - David Osumi-Sutherland + has fasciculating component - (forall (?x ?y) + (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) @@ -1309,8 +1308,8 @@ N1 SubclassOf ( - X continuous_with Y if and only if X and Y share a fiat boundary. - David Osumi-Sutherland + X continuous_with Y if and only if X and Y share a fiat boundary. + connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) @@ -1329,8 +1328,8 @@ N1 SubclassOf ( x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom - proper overlaps - (forall (?x ?y) + proper overlaps + (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and @@ -1353,7 +1352,7 @@ N1 SubclassOf ( A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - Chris Mungall + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) @@ -1361,7 +1360,7 @@ N1 SubclassOf ( RO:0002163 spatially_disjoint_from - spatially disjoint from + spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern @@ -1498,7 +1497,7 @@ N1 SubclassOf ( A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - Chris Mungall + RO:0002200 has_phenotype @@ -1513,7 +1512,7 @@ N1 SubclassOf ( inverse of has phenotype - Chris Mungall + RO:0002201 @@ -1533,10 +1532,10 @@ N1 SubclassOf ( x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - Terry Meehan + + + + RO:0002202 develops_from This is the transitive form of the develops from relation @@ -1554,9 +1553,9 @@ N1 SubclassOf ( inverse of develops from - Chris Mungall - David Osumi-Sutherland - Terry Meehan + + + RO:0002203 develops_into @@ -1588,12 +1587,12 @@ N1 SubclassOf ( Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - Chris Mungall - David Osumi-Sutherland - has developmental precursor + + FBbt RO:0002207 + has developmental precursor directly_develops_from TODO - add child relations from DOS directly develops from @@ -1651,9 +1650,9 @@ N1 SubclassOf ( p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - Chris Mungall - David Hill - Tanya Berardini + + + GO Regulation precludes parthood; the regulatory process may not be within the regulated process. @@ -1676,7 +1675,7 @@ N1 SubclassOf ( p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - Chris Mungall + negatively regulates (process to process) @@ -1698,7 +1697,7 @@ N1 SubclassOf ( p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - Chris Mungall + positively regulates (process to process) @@ -1721,7 +1720,7 @@ N1 SubclassOf ( mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - Chris Mungall + has function realized in @@ -1740,7 +1739,7 @@ N1 SubclassOf ( c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - Chris Mungall + has function in RO:0002216 capable_of_part_of @@ -1757,7 +1756,7 @@ N1 SubclassOf ( x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - Chris Mungall + RO:0002219 surrounded_by @@ -1779,7 +1778,7 @@ N1 SubclassOf ( x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - Chris Mungall + RO:0002220 @@ -1803,7 +1802,7 @@ N1 SubclassOf ( inverse of surrounded by - Chris Mungall + RO:0002221 @@ -1816,7 +1815,7 @@ N1 SubclassOf ( - Chris Mungall + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 @@ -1830,7 +1829,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002223 starts @@ -1842,7 +1841,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002224 starts_with @@ -1856,7 +1855,7 @@ N1 SubclassOf ( x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - Chris Mungall + RO:0002225 develops_from_part_of develops from part of @@ -1871,7 +1870,7 @@ N1 SubclassOf ( x develops_in y if x is located in y whilst x is developing - Chris Mungall + EHDAA2 Jonathan Bard, EHDAA2 RO:0002226 @@ -1909,7 +1908,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002229 ends @@ -1921,7 +1920,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002230 ends_with @@ -1937,7 +1936,7 @@ N1 SubclassOf ( x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - Chris Mungall + starts with process that occurs in RO:0002231 @@ -1955,7 +1954,7 @@ N1 SubclassOf ( x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - Chris Mungall + ends with process that occurs in RO:0002232 @@ -1973,7 +1972,7 @@ N1 SubclassOf ( p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + consumes RO:0002233 @@ -1993,7 +1992,7 @@ N1 SubclassOf ( p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - Chris Mungall + produces RO:0002234 @@ -2047,7 +2046,7 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - Bill Duncan (https://orcid.org/0000-0001-9625-1899) + This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. @@ -2196,7 +2195,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y - Chris Mungall + RO:0002254 has_developmental_contribution_from has developmental contribution from @@ -2211,7 +2210,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho inverse of has developmental contribution from - Chris Mungall + RO:0002255 developmentally_contributes_to @@ -2229,9 +2228,9 @@ If you need an axiom that says 'has_participant min 2 object', you sho t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - Chris Mungall - David Osumi-Sutherland - Melissa Haendel + + + induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) @@ -2251,7 +2250,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally induced by - Chris Mungall + RO:0002257 developmentally_induces developmentally induces @@ -2269,7 +2268,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - Chris Mungall + In general you should not use this relation to make assertions - use one of the more specific relations below this one RO:0002258 developmentally_preceded_by @@ -2317,7 +2316,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - Chris Mungall + replaces RO:0002285 developmentally_replaces @@ -2332,7 +2331,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally preceded by - Chris Mungall + RO:0002286 developmentally_succeeded_by developmentally succeeded by @@ -2346,7 +2345,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - Chris Mungall + RO:0002287 part_of_developmental_precursor_of part of developmental precursor of @@ -2363,7 +2362,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - Chris Mungall + RO:0002295 results_in_developmental_progression_of results in developmental progression of @@ -2380,7 +2379,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - Chris Mungall + http://www.geneontology.org/GO.doc.development.shtml RO:0002296 @@ -2401,7 +2400,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002297 @@ -2422,7 +2421,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002298 @@ -2443,7 +2442,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002299 @@ -2461,7 +2460,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho foramen ovale closure SubClassOf results in disappearance of foramen ovale - Chris Mungall + May be merged into parent relation RO:0002300 results_in_disappearance_of @@ -2476,7 +2475,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) - Chris Mungall + May be merged into parent relation RO:0002301 results_in_developmental_regression_of @@ -2491,7 +2490,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of 'is substance that treats' - cjm + RO:0002302 is_treated_by_substance @@ -2511,7 +2510,7 @@ where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. - Pier Buttigieg + adapted for living in RO:0002303 @@ -2529,7 +2528,7 @@ where p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - cjm + RO:0002304 @@ -2547,7 +2546,7 @@ where p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - cjm + RO:0002305 @@ -2562,10 +2561,10 @@ where A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. - Austin Meier - Chris Mungall - Marie Angelique Laporte - cjm + + + + 2017-06-05T17:35:04Z RO:0002309 has_exposure_stimulus @@ -2580,7 +2579,7 @@ where Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. - Chris Mungall + regulates localization of RO:0002313 @@ -2600,7 +2599,7 @@ where an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002315 @@ -2617,7 +2616,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions RO:0002321 @@ -2633,7 +2632,7 @@ where An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. - Chris Mungall + adapted for RO:0002322 @@ -2647,7 +2646,7 @@ where A mereological relationship or a topological relationship - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships RO:0002323 @@ -2661,7 +2660,7 @@ where A relationship that holds between entities participating in some developmental process (GO:0032502) - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development RO:0002324 developmentally_related_to @@ -2678,9 +2677,8 @@ where Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. - Chris Mungall + In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - Gene Ontology Consortium RO:0002325 colocalizes_with @@ -2708,7 +2706,7 @@ then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. - Chris Mungall + In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 @@ -2725,7 +2723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - Chris Mungall + catalyzes executes has @@ -2744,7 +2742,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 functionally_related_to @@ -2758,7 +2756,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati this relation holds between c and p when c is part of some c', and c' is capable of p. - Chris Mungall + false RO:0002329 part_of_structure_that_is_capable_of @@ -2773,7 +2771,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati c involved_in p if and only if c enables some process p', and p' is part of p - Chris Mungall + actively involved in enables part of RO:0002331 @@ -2792,7 +2790,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - Chris Mungall + regulates levels of (process to entity) RO:0002332 @@ -2808,7 +2806,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables - Chris Mungall + RO:0002333 enabled_by @@ -2825,7 +2823,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of regulates - Chris Mungall + regulated by (processual) RO:0002334 @@ -2840,7 +2838,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of negatively regulates - Chris Mungall + RO:0002335 negatively_regulated_by @@ -2854,7 +2852,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of positively regulates - Chris Mungall + RO:0002336 positively_regulated_by @@ -2869,7 +2867,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds via some process of localization - Chris Mungall + Do not use this relation directly. It is a grouping relation. RO:0002337 related_via_localization_to @@ -2883,7 +2881,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - Chris Mungall + RO:0002338 @@ -2899,7 +2897,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - Chris Mungall + RO:0002339 @@ -2915,7 +2913,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. - Chris Mungall + RO:0002340 imports @@ -2929,7 +2927,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - Chris Mungall + RO:0002341 results_in_transport_along results in transport along @@ -2943,7 +2941,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - Chris Mungall + RO:0002342 results_in_transport_across @@ -2958,7 +2956,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'pollen tube growth' results_in growth_of some 'pollen tube' - Chris Mungall + RO:0002343 results_in_growth_of results in growth of @@ -2971,7 +2969,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - Chris Mungall + RO:0002344 results_in_transport_to_from_or_in results in transport to from or in @@ -2983,8 +2981,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. - Chris Mungall + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. + RO:0002345 exports @@ -3000,7 +2998,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - Chris Mungall + RO:0002348 @@ -3017,7 +3015,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - Chris Mungall + RO:0002349 @@ -3034,7 +3032,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has input - Chris Mungall + RO:0002352 @@ -3050,7 +3048,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has output - Chris Mungall + RO:0002353 @@ -3064,7 +3062,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002354 formed_as_result_of formed as result of @@ -3078,7 +3076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. - Chris Mungall + RO:0002355 results_in_structural_organization_of results in structural organization of @@ -3092,7 +3090,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - Chris Mungall + RO:0002356 @@ -3108,7 +3106,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. - Chris Mungall + RO:0002357 results_in_developmental_induction_of results in developmental induction of @@ -3120,7 +3118,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + http://neurolex.org/wiki/Property:DendriteLocation RO:0002360 has_dendrite_location @@ -3136,7 +3134,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - Chris Mungall + attached to (anatomical structure to anatomical structure) RO:0002371 @@ -3153,7 +3151,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002372 has_muscle_origin @@ -3176,7 +3174,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002373 has_muscle_insertion @@ -3200,7 +3198,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) @@ -3222,7 +3220,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - Chris Mungall + drains into drains to tributary channel of @@ -3247,7 +3245,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Deschutes River distributary_of Little Lava Lake x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - Chris Mungall + branch of distributary channel of http://en.wikipedia.org/wiki/Distributary @@ -3273,7 +3271,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. - Chris Mungall + anastomoses with RO:0002378 @@ -3289,7 +3287,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - Chris Mungall + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios RO:0002379 spatially_coextensive_with @@ -3312,7 +3310,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - Chris Mungall + RO:0002380 branching_part_of @@ -3331,7 +3329,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. - Chris Mungall + RO:0002381 main_stem_of @@ -3347,7 +3345,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_distributary_of y iff x distributary_of y and x does not flow back into y - Chris Mungall + RO:0002382 proper_distributary_of @@ -3362,7 +3360,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_tributary_of y iff x tributary_of y and x does not originate from y - Chris Mungall + RO:0002383 proper_tributary_of @@ -3379,7 +3377,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - Chris Mungall + RO:0002384 has_developmental_potential_involving has developmental potential involving @@ -3393,7 +3391,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - Chris Mungall + RO:0002385 has_potential_to_developmentally_contribute_to has potential to developmentally contribute to @@ -3407,7 +3405,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - Chris Mungall + RO:0002386 has_potential_to_developmentally_induce has potential to developmentally induce @@ -3421,7 +3419,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has the potential to develop into y iff x develops into y or if x is capable of developing into y - Chris Mungall + RO:0002387 has_potential_to_develop_into has potential to develop into @@ -3435,7 +3433,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - Chris Mungall + RO:0002388 has_potential_to_directly_develop_into has potential to directly develop into @@ -3450,7 +3448,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' RO:0002400 @@ -3468,7 +3466,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of upstream of - Chris Mungall + RO:0002404 causally_downstream_of causally downstream of @@ -3483,7 +3481,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002405 immediately_causally_downstream_of immediately causally downstream of @@ -3498,7 +3496,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - Chris Mungall + indirectly activates RO:0002407 @@ -3515,7 +3513,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - Chris Mungall + indirectly inhibits RO:0002409 @@ -3544,7 +3542,7 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002410 causally_related_to @@ -3566,7 +3564,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - Chris Mungall + RO:0002411 @@ -3582,7 +3580,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - Chris Mungall + RO:0002412 immediately_causally_upstream_of @@ -3598,7 +3596,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit - Chris Mungall + directly provides input for directly provides input for (process to process) @@ -3618,7 +3616,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different transitive form of directly_provides_input_for - Chris Mungall + This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. transitively provides input for (process to process) RO:0002414 @@ -3636,7 +3634,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall + influences (processual) RO:0002418 affects @@ -3652,7 +3650,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - Chris Mungall + RO:0002427 @@ -3668,7 +3666,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - Chris Mungall + RO:0002428 involved_in_regulation_of involved in regulation of @@ -3681,7 +3679,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - Chris Mungall + RO:0002429 involved_in_positive_regulation_of @@ -3695,7 +3693,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - Chris Mungall + RO:0002430 involved_in_negative_regulation_of @@ -3712,7 +3710,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - Chris Mungall + involved in or reguates RO:0002431 involved_in_or_involved_in_regulation_of @@ -3728,7 +3726,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall + executes activity in RO:0002432 enables activity in @@ -3740,8 +3738,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + GOC:cjm + GOC:dos @@ -3751,7 +3749,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - Chris Mungall + RO:0002433 contributes_to_morphology_of contributes to morphology of @@ -3768,7 +3766,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. - Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. RO:0002434 in pairwise interaction with @@ -3787,7 +3785,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) - Chris Mungall + RO:0002435 genetically_interacts_with genetically interacts with @@ -3803,7 +3801,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - Chris Mungall + binds molecularly binds with RO:0002436 @@ -3824,7 +3822,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - Chris Mungall + interacts with on organism level RO:0002437 @@ -3841,7 +3839,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the partners are related via a feeding relationship. - Chris Mungall + RO:0002438 trophically_interacts_with @@ -3859,9 +3857,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] Baleen whale preys on krill An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - Chris Mungall - Jorrit Poelen - Katja Shulz + + + is subject of predation interaction with preys upon RO:0002439 @@ -3880,7 +3878,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A biotic interaction in which the two organisms live together in more or less intimate association. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism RO:0002440 @@ -3896,7 +3894,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002441 @@ -3911,7 +3909,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002442 @@ -3926,7 +3924,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 This relation groups a pair of inverse relations, parasite of and parasitized by RO:0002443 @@ -3944,7 +3942,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human - Chris Mungall + parasitizes RO:0002444 direct parasite of @@ -3961,7 +3959,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + has parasite parasitised by RO:0002445 @@ -3980,7 +3978,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - Chris Mungall + RO:0002446 semibiotically interacts with @@ -3996,7 +3994,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. RO:0002447 phosphorylates @@ -4015,8 +4013,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - Chris Mungall - Vasundra Touré + + RO:0002448 molecularly controls directly_regulates_activity_of @@ -4033,8 +4031,8 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly inhibits RO:0002449 molecularly decreases activity of @@ -4052,8 +4050,8 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly activates RO:0002450 molecularly increases activity of @@ -4070,7 +4068,7 @@ For example, A and B may be gene products and binding of B by A positively regul all dengue disease transmitted by some mosquito A relationship that holds between a disease and organism Add domain and range constraints - Chris Mungall + RO:0002451 transmitted_by transmitted by @@ -4084,7 +4082,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between a disease or an organism and a phenotype - Chris Mungall + RO:0002452 has_symptom has symptom @@ -4096,7 +4094,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) RO:0002453 @@ -4111,7 +4109,7 @@ For example, A and B may be gene products and binding of B by A positively regul X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y - Chris Mungall + RO:0002454 has_host @@ -4128,7 +4126,7 @@ For example, A and B may be gene products and binding of B by A positively regul Bees pollinate Flowers This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - Chris Mungall + is subject of pollination interaction with RO:0002455 @@ -4143,7 +4141,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + has polinator is target of pollination interaction with RO:0002456 @@ -4160,7 +4158,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4175,7 +4173,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of preys on - Chris Mungall + has predator is target of predation interaction with RO:0002458 @@ -4195,7 +4193,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anopheles is a vector for Plasmodium - Chris Mungall + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism RO:0002459 @@ -4209,7 +4207,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002460 has_vector @@ -4222,7 +4220,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target RO:0002461 partner_in @@ -4235,7 +4233,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002462 subject_participant_in @@ -4248,7 +4246,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002463 target_participant_in @@ -4261,7 +4259,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002469 provides_nutrients_for @@ -4274,7 +4272,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is subject of eating interaction with RO:0002470 @@ -4288,7 +4286,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + eaten by is target of eating interaction with RO:0002471 @@ -4307,7 +4305,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - Chris Mungall + RO:0002473 @@ -4326,7 +4324,7 @@ For example, A and B may be gene products and binding of B by A positively regul ABal nucleus child nucleus of ABa nucleus (in C elegans) c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d - Chris Mungall + This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. RO:0002476 child_nucleus_of @@ -4340,7 +4338,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a hermaphroditic organism - Chris Mungall + RO:0002477 child_nucleus_of_in_hermaphrodite child nucleus of in hermaphrodite @@ -4353,7 +4351,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a male organism - Chris Mungall + RO:0002478 child_nucleus_of_in_male child nucleus of in male @@ -4367,7 +4365,7 @@ For example, A and B may be gene products and binding of B by A positively regul p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall + RO:0002479 has_part_that_occurs_in @@ -4382,7 +4380,7 @@ For example, A and B may be gene products and binding of B by A positively regul An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y Axiomatization to GO to be added later - Chris Mungall + RO:0002480 ubiquitinates ubiquitinates @@ -4396,7 +4394,7 @@ For example, A and B may be gene products and binding of B by A positively regul See notes for inverse relation - Chris Mungall + RO:0002485 receives_input_from receives input from @@ -4409,7 +4407,7 @@ For example, A and B may be gene products and binding of B by A positively regul This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - Chris Mungall + RO:0002486 sends_output_to sends output to @@ -4423,7 +4421,7 @@ For example, A and B may be gene products and binding of B by A positively regul x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - Chris Mungall + RO:0002494 transformation_of transformation of @@ -4437,7 +4435,7 @@ For example, A and B may be gene products and binding of B by A positively regul x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - Chris Mungall + RO:0002495 immediate_transformation_of @@ -4467,7 +4465,7 @@ For example, A and B may be gene products and binding of B by A positively regul p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002501 @@ -4483,7 +4481,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c - Chris Mungall + has intermediate product RO:0002505 @@ -4500,7 +4498,7 @@ For example, A and B may be gene products and binding of B by A positively regul The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002506 @@ -4522,11 +4520,11 @@ For example, A and B may be gene products and binding of B by A positively regul A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future - Chris Mungall + determined by (system to material entity) - Chris Mungall - Pier Buttigieg + + RO:0002507 determined_by @@ -4540,7 +4538,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of determined by - Chris Mungall + determines (material entity to system) RO:0002508 @@ -4559,7 +4557,7 @@ For example, A and B may be gene products and binding of B by A positively regul s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. - Chris Mungall + RO:0002509 determined_by_part_of @@ -4574,7 +4572,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between two entities that have the property of being sequences or having sequences. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. @@ -4594,7 +4592,7 @@ For example, A and B may be gene products and binding of B by A positively regul Two consecutive DNA residues are sequentially adjacent Two exons on a processed transcript that were previously connected by an intron are adjacent x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002515 @@ -4612,7 +4610,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as a start sequence the start codon for that transcript x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence - Chris Mungall + started by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4629,7 +4627,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has start sequence - Chris Mungall + starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4649,7 +4647,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence - Chris Mungall + ended by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4666,7 +4664,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has end sequence - Chris Mungall + ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4684,7 +4682,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. In the SO paper, this was defined as an instance-type relation - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002520 @@ -4701,7 +4699,7 @@ For example, A and B may be gene products and binding of B by A positively regul Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering - Chris Mungall + RO:0002521 is_sequentially_aligned_with @@ -4718,7 +4716,7 @@ For example, A and B may be gene products and binding of B by A positively regul The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y - Chris Mungall + RO:0002522 bounds_sequence_of @@ -4733,7 +4731,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of bounds sequence of - Chris Mungall + RO:0002523 @@ -4751,8 +4749,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x has subsequence y iff all of the sequence parts of x are sequence parts of y - Chris Mungall + x has subsequence y iff all of the sequence parts of y are sequence parts of x + contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4771,7 +4769,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has subsequence - Chris Mungall + contained by RO:0002525 @@ -4788,8 +4786,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. - Chris Mungall + x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. + RO:0002526 overlaps_sequence_of @@ -4803,8 +4801,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. - Chris Mungall + x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + disconnected from RO:0002527 @@ -4820,7 +4818,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of downstream of sequence of - Chris Mungall + RO:0002528 is_upstream_of_sequence_of @@ -4836,7 +4834,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. - Chris Mungall + RO:0002529 is_downstream_of_sequence_of @@ -4852,7 +4850,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y - Chris Mungall + RO:0002530 @@ -4869,7 +4867,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript inverse of immediately downstream of - Chris Mungall + RO:0002531 is_immediately_upstream_of_sequence_of @@ -4889,7 +4887,7 @@ For example, A and B may be gene products and binding of B by A positively regul Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - Chris Mungall + has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). RO:0002551 @@ -4911,7 +4909,7 @@ For example, A and B may be gene products and binding of B by A positively regul p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. - Chris Mungall + RO:0002552 results_in_ending_of results in ending of @@ -4926,7 +4924,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - Chris Mungall + http://eol.org/schema/terms/hyperparasitoidOf https://en.wikipedia.org/wiki/Hyperparasite RO:0002553 @@ -4944,7 +4942,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of hyperparasite of - Chris Mungall + RO:0002554 has epiparasite has hyperparasite @@ -4961,7 +4959,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + http://en.wikipedia.org/wiki/Allelopathy RO:0002555 @@ -4978,7 +4976,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002556 pathogen_of @@ -4991,7 +4989,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002557 has_pathogen @@ -5005,7 +5003,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + causally influenced by (entity-centric) RO:0002559 @@ -5020,7 +5018,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - Chris Mungall + RO:0002565 @@ -5039,8 +5037,8 @@ For example, A and B may be gene products and binding of B by A positively regul The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - Chris Mungall - Vasundra Touré + + causally influences (entity-centric) RO:0002566 @@ -5057,7 +5055,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between elements of a musculoskeletal system or its analogs. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. RO:0002567 biomechanically_related_to @@ -5071,7 +5069,7 @@ For example, A and B may be gene products and binding of B by A positively regul m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - Chris Mungall + Wikipedia:Antagonist_(muscle) RO:0002568 has_muscle_antagonist @@ -5087,7 +5085,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of branching part of - Chris Mungall + RO:0002569 @@ -5104,7 +5102,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - Chris Mungall + UBERON:cjm This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. RO:0002570 @@ -5121,7 +5119,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - Chris Mungall + GOC:cjm RO:0002571 @@ -5137,7 +5135,7 @@ For example, A and B may be gene products and binding of B by A positively regul s is luminal space of x iff s is lumen_of x and s is an immaterial entity - Chris Mungall + RO:0002572 luminal_space_of @@ -5152,7 +5150,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002574 participates_in_a_biotic-biotic_interaction_with @@ -5169,7 +5167,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has skeleton - Chris Mungall + RO:0002576 skeleton_of @@ -5184,7 +5182,7 @@ For example, A and B may be gene products and binding of B by A positively regul p directly regulates q iff p is immediately causally upstream of q and p regulates q. - Chris Mungall + directly regulates (processual) @@ -5205,7 +5203,7 @@ For example, A and B may be gene products and binding of B by A positively regul gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - Chris Mungall + RO:0002584 has_part_structure_that_is_capable_of has part structure that is capable of @@ -5320,7 +5318,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall + RO:0002595 causal_relation_between_material_entity_and_a_process @@ -5723,7 +5721,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. - Vasundra Touré + RO:0003002 represses_expression_of represses expression of @@ -5738,7 +5736,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. - Vasundra Touré + RO:0003003 increases_expression_of increases expression of @@ -5883,7 +5881,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:38:20Z RO:0004000 condition_has_genetic_basis_in @@ -5897,7 +5895,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:20Z RO:0004001 has_material_basis_in_gain_of_function_germline_mutation_in @@ -5913,7 +5911,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:37Z RO:0004002 has_material_basis_in_loss_of_function_germline_mutation_in @@ -5927,7 +5925,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:54Z RO:0004003 has_material_basis_in_germline_mutation_in @@ -5942,7 +5940,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:07Z RO:0004004 has_material_basis_in_somatic_mutation_in @@ -5957,7 +5955,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:26Z RO:0004005 has_major_susceptibility_factor @@ -5971,7 +5969,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:57Z RO:0004006 has_partial_material_basis_in_germline_mutation_in @@ -5985,7 +5983,7 @@ Environmental exposures include those imposed by natural environments, experimen p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - cjm + 2018-12-13T11:26:17Z RO:0004007 @@ -6001,7 +5999,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - cjm + 2018-12-13T11:26:32Z RO:0004008 @@ -6012,8 +6010,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6027,7 +6025,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - cjm + 2018-12-13T11:26:56Z RO:0004009 @@ -6038,8 +6036,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6053,7 +6051,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:53:08Z RO:0004010 is_genetic_basis_for_condition @@ -6067,7 +6065,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:55:51Z RO:0004011 is_causal_gain_of_function_germline_mutation_of_in @@ -6082,7 +6080,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:06Z RO:0004012 is_causal_loss_of_function_germline_mutation_of_in @@ -6098,7 +6096,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:40Z RO:0004013 is_causal_germline_mutation_in @@ -6114,7 +6112,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:57:07Z RO:0004014 is_causal_somatic_mutation_in @@ -6129,7 +6127,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. - cjm + 2017-11-05T02:57:43Z RO:0004015 is_causal_susceptibility_factor_for @@ -6145,7 +6143,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. - cjm + 2017-11-05T02:58:43Z RO:0004016 is_causal_germline_mutation_partially_giving_rise_to @@ -6160,7 +6158,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:01Z RO:0004017 realizable_has_basis_in @@ -6173,7 +6171,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:29Z RO:0004018 is_basis_for_realizable @@ -6188,7 +6186,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:26:47Z RO:0004019 disease_has_basis_in @@ -6204,7 +6202,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) - cjm + 2017-11-05T03:29:32Z RO:0004020 disease_has_basis_in_dysfunction_of @@ -6220,7 +6218,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. disease has basis in disruption of (disease to process) - cjm + 2017-11-05T03:37:52Z RO:0004021 disease_has_basis_in_disruption_of @@ -6244,7 +6242,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. - cjm + 2017-11-05T03:46:07Z RO:0004022 disease_has_basis_in_feature @@ -6260,7 +6258,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. - cjm + 2017-11-05T03:50:54Z RO:0004023 causal_relationship_with_disease_as_subject @@ -6277,7 +6275,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and a process where the disease process disrupts the execution of the process. disease causes disruption of (disease to process) - cjm + 2017-11-05T03:51:09Z RO:0004024 disease_causes_disruption_of @@ -6293,7 +6291,7 @@ Environmental exposures include those imposed by natural environments, experimen disease causes dysfunction of (disease to anatomical entity) - cjm + 2017-11-05T03:58:20Z RO:0004025 disease_causes_dysfunction_of @@ -6319,7 +6317,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. - cjm + 2017-11-05T04:06:02Z RO:0004026 disease_has_location @@ -6343,7 +6341,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity - cjm + 2017-12-26T19:37:31Z RO:0004027 disease_has_inflammation_site @@ -6359,7 +6357,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - cjm + 2017-12-26T19:45:49Z RO:0004028 realized_in_response_to_stimulus @@ -6382,7 +6380,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. - cjm + 2017-12-26T19:50:53Z RO:0004029 disease_has_feature @@ -6397,7 +6395,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. - cjm + 2017-12-26T19:58:44Z RO:0004030 disease_arises_from_alteration_in_structure @@ -6411,7 +6409,7 @@ Environmental exposures include those imposed by natural environments, experimen Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - cjm + 2018-01-25T23:20:13Z RO:0004031 enables_subfunction @@ -6425,7 +6423,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:30Z RO:0004032 @@ -6441,7 +6439,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:51Z RO:0004033 @@ -6458,7 +6456,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - cjm + 2018-01-26T23:53:14Z RO:0004034 @@ -6476,7 +6474,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - cjm + 2018-01-26T23:53:22Z RO:0004035 @@ -6492,7 +6490,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:05Z RO:0004046 causally_upstream_of_or_within,_negative_effect @@ -6506,7 +6504,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:19Z RO:0004047 causally_upstream_of_or_within,_positive_effect @@ -6633,10 +6631,10 @@ Environmental exposures include those imposed by natural environments, experimen An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - Austin Meier - Chris Mungall - David Osumi-Sutherland - Marie Angelique Laporte + + + + RO:0009501 triggered by process realized_in_response_to @@ -6659,7 +6657,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - Vasundra Touré + RO:0011002 regulates_activity_of regulates activity of @@ -6674,7 +6672,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. - Vasundra Touré + RO:0011003 regulates_quantity_of regulates quantity of @@ -6689,7 +6687,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. - Vasundra Touré + RO:0011004 indirectly_regulates_activity_of indirectly regulates activity of @@ -6706,7 +6704,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011007 decreases_by_repression_quantity_of decreases by repression quantity of @@ -6723,7 +6721,7 @@ For example, protein A (transcription factor) indirectly decreases by repression The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011008 increases_by_expression_quantity_of increases by expression quantity of @@ -6738,7 +6736,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly positively regulates the quantity of B. - Vasundra Touré + RO:0011009 directly_positively_regulates_quantity_of directly positively regulates quantity of @@ -6753,7 +6751,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly negatively regulates the quantity of B. - Vasundra Touré + RO:0011010 directly_negatively_regulates_quantity_of directly negatively regulates quantity of @@ -6768,7 +6766,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. - Vasundra Touré + indirectly activates RO:0011013 indirectly_positively_regulates_activity_of @@ -6785,7 +6783,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. - Vasundra Touré + RO:0011014 destabilizes_quantity_of destabilizes quantity of @@ -6801,7 +6799,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. - Vasundra Touré + RO:0011015 stabilizes_quantity_of stabilizes quantity of @@ -6814,7 +6812,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. - Vasundra Touré + indirectly inhibits RO:0011016 indirectly_negatively_regulates_activity_of @@ -6828,7 +6826,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. - Vasundra Touré + RO:0011021 directly_regulates_quantity_of directly regulates quantity of @@ -6841,7 +6839,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011022 indirectly_regulates_quantity_of indirectly regulates quantity of @@ -6854,7 +6852,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011023 indirectly_negatively_regulates_quantity_of indirectly negatively regulates quantity of @@ -6867,7 +6865,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011024 indirectly_positively_regulates_quantity_of indirectly positively regulates quantity of @@ -6880,8 +6878,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is regulated by the small molecule continuant + pg 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -6895,8 +6893,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is activated by the small molecule continuant + pg 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -6910,8 +6908,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant + pg 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -6924,8 +6922,8 @@ For example, protein A (transcription factor) indirectly increases by expression - p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + p acts on population of c iff c' is a collection, has members of type c, and p has participant c + pg 2020-06-08T17:21:33Z RO:0012003 @@ -6941,8 +6939,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process + pg 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -6956,8 +6954,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process + pg 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of @@ -6971,8 +6969,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process + pg 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of @@ -6985,8 +6983,8 @@ For example, protein A (transcription factor) indirectly increases by expression - The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. + pg 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -6999,7 +6997,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + pg 2021-02-26T07:28:29Z RO:0012008 @@ -7016,7 +7014,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + pg 2022-09-26T06:01:01Z RO:0012009 @@ -7032,7 +7030,7 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + pg 2022-09-26T06:06:20Z RO:0012010 @@ -7048,7 +7046,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + pg 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7063,7 +7061,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + pg 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7229,7 +7227,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relation between a group and another group it is part of but does not fully constitute. X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. - Shawn Tan + This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. RO:0015003 subcluster_of @@ -7301,7 +7299,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - http://orcid.org/0000-0002-7463-6306 + 2021-11-05T17:30:44Z RO:0016002 has_disease @@ -7457,7 +7455,7 @@ For example, protein A (transcription factor) indirectly increases by expression This relation groups relations between diseases and any other kind of entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. - cjm + 2018-09-26T00:00:32Z RO:0040035 disease_relationship @@ -7471,7 +7469,7 @@ For example, protein A (transcription factor) indirectly increases by expression p has anatomical participant c iff p has participant c, and c is an anatomical entity - cjm + 2018-09-26T01:08:58Z RO:0040036 results_in_changes_to_anatomical_or_cellular_structure diff --git a/subsets/ro-time-interval.obo b/subsets/ro-time-interval.obo index 32edb9a6..7aeb28f2 100644 --- a/subsets/ro-time-interval.obo +++ b/subsets/ro-time-interval.obo @@ -13,7 +13,7 @@ id: acquires_nutrients_from name: acquires nutrients from subset: ro-eco xref: RO:0002457 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for @@ -58,7 +58,7 @@ property_value: RO:0004050 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:22Z [Typedef] @@ -71,7 +71,7 @@ property_value: RO:0004049 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:14Z [Typedef] @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z [Typedef] @@ -103,7 +103,7 @@ xref: RO:0004032 property_value: RO:0004049 RO:0002264 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect is_a: acts_upstream_of_or_within ! acts upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z [Typedef] @@ -120,7 +120,7 @@ property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cy property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 domain: BFO:0000004 range: BFO:0000004 @@ -131,7 +131,7 @@ id: allelopath_of name: allelopath of subset: ro-eco xref: RO:0002555 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string @@ -153,7 +153,7 @@ def: "x anabranch_of y if x is a distributary of y (i.e. it channels a from a la subset: ro-eco xref: RO:0002378 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "anastomoses with" xsd:string is_a: distributary_of ! distributary of disjoint_from: proper_distributary_of ! proper distributary of @@ -165,7 +165,7 @@ name: attached to def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] subset: ro-eco xref: RO:0002371 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: attached_to_part_of ! attached to part of @@ -189,9 +189,8 @@ def: "Relation between a neuron and some structure its axon forms (chemical) syn xref: RO:0002102 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in @@ -202,7 +201,7 @@ id: biomechanically_related_to name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] xref: RO:0002567 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: CARO:0000003 range: CARO:0000003 @@ -214,7 +213,7 @@ name: biotically interacts with def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] subset: ro-eco xref: RO:0002437 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string @@ -231,7 +230,7 @@ def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\ comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco xref: RO:0002007 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 is_a: part_of @@ -242,7 +241,7 @@ def: "x bounds the sequence of y iff the upstream-most part of x is upstream of xref: RO:0002522 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to inverse_of: is_bound_by_sequence_of ! is bound by sequence of @@ -254,7 +253,7 @@ def: "x is a branching part of y if and only if x is part of y and x is connecte subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso FMA:85994 xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with @@ -269,7 +268,7 @@ subset: ro-eco xref: RO:0002215 property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 @@ -302,7 +301,7 @@ id: capable_of_part_of name: capable of part of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ is_a: causal_agent_in_process ! causal agent in process @@ -350,7 +349,7 @@ id: causal_relation_between_entities name: causal relation between entities xref: RO:0002506 property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000002 @@ -363,7 +362,7 @@ name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] xref: RO:0002595 property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 range: BFO:0000015 @@ -374,7 +373,7 @@ id: causal_relation_between_processes name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] xref: RO:0002501 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 @@ -389,7 +388,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: OGMS:0000031 is_a: causally_related_to ! causally related to is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:50:54Z [Typedef] @@ -398,7 +397,7 @@ name: causally downstream of def: "inverse of upstream of" [] xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within is_a: preceded_by inverse_of: causally_upstream_of ! causally upstream of @@ -409,7 +408,7 @@ name: causally downstream of or within def: "inverse of causally upstream of or within" [] subset: RO:0002259 xref: RO:0002427 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -418,7 +417,7 @@ is_a: causal_relation_between_processes ! causal relation between processes id: causally_influenced_by name: causally influenced by xref: RO:0002559 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: causal_relation_between_entities ! causal relation between entities @@ -429,8 +428,8 @@ id: causally_influences name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] xref: RO:0002566 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 @@ -443,7 +442,7 @@ name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] xref: RO:0002410 property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] @@ -453,7 +452,7 @@ def: "p is causally upstream of q iff p is causally related to q, the end of p p subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes @@ -465,7 +464,7 @@ def: "p is causally upstream of, negative effect q iff p is casually upstream of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -478,7 +477,7 @@ comment: holds between x and y if and only if x is causally upstream of y and th subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -490,7 +489,7 @@ def: "p is 'causally upstream or within' q iff p is causally related to q, and t synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true is_a: causal_relation_between_processes ! causal relation between processes @@ -502,7 +501,7 @@ name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -511,7 +510,7 @@ name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -537,7 +536,7 @@ name: child nucleus of def: "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" [] xref: RO:0002476 property_value: IAO:0000112 "ABal nucleus child nucleus of ABa nucleus (in C elegans)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." xsd:string domain: GO:0005634 range: GO:0005634 @@ -548,7 +547,7 @@ id: child_nucleus_of_in_hermaphrodite name: child nucleus of in hermaphrodite def: "A child nucleus relationship in which the cells are part of a hermaphroditic organism" [] xref: RO:0002477 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -556,7 +555,7 @@ id: child_nucleus_of_in_male name: child nucleus of in male def: "A child nucleus relationship in which the cells are part of a male organism" [] xref: RO:0002478 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: child_nucleus_of ! child nucleus of [Typedef] @@ -576,7 +575,7 @@ comment: Example: if we define region of chromosome as any subdivision of a chro subset: ro-eco xref: RO:0002008 property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -585,9 +584,8 @@ name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 -property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -599,7 +597,7 @@ name: commensually interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] subset: ro-eco xref: RO:0002441 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -610,7 +608,7 @@ def: "x composed_primarily_of y if and only if more than half of the mass of x i subset: ro-eco xref: RO:0002473 property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 @@ -639,7 +637,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a domain: BFO:0000017 is_a: causally_related_to ! causally related to inverse_of: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:38:20Z [Typedef] @@ -648,7 +646,7 @@ name: conduit for def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] subset: ro-eco xref: RO:0002570 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 UBERON:cjm xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 @@ -661,7 +659,7 @@ name: confers advantage in subset: ro-eco xref: RO:0002322 property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "adapted for" xsd:string range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -727,7 +725,7 @@ name: continuous with def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 @@ -746,7 +744,7 @@ property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a het property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -771,7 +769,7 @@ id: contributes_to_morphology_of name: contributes to morphology of def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] xref: RO:0002433 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -796,7 +794,7 @@ id: decreases_by_repression_quantity_of name: decreases by repression quantity of def: "The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011007 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_negatively_regulates_quantity_of ! indirectly negatively regulates quantity of @@ -808,8 +806,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in wh xref: RO:0002121 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in @@ -821,7 +819,7 @@ name: destabilizes quantity of def: "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." [] xref: RO:0011014 property_value: IAO:0000112 "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_quantity_of ! directly negatively regulates quantity of @@ -832,11 +830,11 @@ name: determined by def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] subset: ro-eco xref: RO:0002507 -property_value: http://purl.org/dc/terms/creator "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/creator "Pier Buttigieg" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-4366-3088 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "A coral reef environment is determined by a particular coral reef" xsd:string property_value: IAO:0000116 "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602 property_value: IAO:0000589 "determined by (system to material entity)" xsd:string domain: RO:0002577 @@ -852,7 +850,7 @@ name: determined by part of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] subset: ro-eco xref: RO:0002509 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 range: BFO:0000040 is_a: causal_relation_between_entities ! causal relation between entities @@ -865,7 +863,7 @@ def: "inverse of determined by" [] subset: ro-eco subset: RO:0002259 xref: RO:0002508 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "determines (material entity to system)" xsd:string is_a: causally_influences ! causally influences @@ -876,7 +874,7 @@ def: "inverse of has developmental contribution from" [] subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to @@ -886,9 +884,9 @@ name: developmentally induced by def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] xref: RO:0002256 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string property_value: IAO:0000119 GO:0001759 xsd:string @@ -905,7 +903,7 @@ name: developmentally induces def: "Inverse of developmentally induced by" [] xref: RO:0002257 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_developmentally_induce ! has potential to developmentally induce @@ -917,7 +915,7 @@ comment: This relation groups together various other developmental relations. It xref: RO:0002258 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string domain: BFO:0000002 range: BFO:0000002 @@ -929,7 +927,7 @@ id: developmentally_related_to name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] xref: RO:0002324 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] @@ -939,7 +937,7 @@ def: "x developmentally replaces y if and only if there is some developmental pr xref: RO:0002285 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "replaces" xsd:string is_a: developmentally_preceded_by ! developmentally preceded by @@ -949,7 +947,7 @@ name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] xref: RO:0002286 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -959,10 +957,10 @@ def: "x develops from y if and only if either (a) x directly develops from y or comment: This is the transitive form of the develops from relation xref: RO:0002202 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 domain: BFO:0000004 range: BFO:0000004 is_transitive: true @@ -975,7 +973,7 @@ name: develops from part of def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] xref: RO:0002225 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: develops_from ! develops from [Typedef] @@ -984,7 +982,7 @@ name: develops in def: "x develops_in y if x is located in y whilst x is developing" [] xref: RO:0002226 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string domain: CARO:0000000 @@ -997,9 +995,9 @@ def: "inverse of develops from" [] subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 is_transitive: true is_a: developmentally_succeeded_by ! developmentally succeeded by is_a: has_potential_to_develop_into ! has potential to develop into @@ -1010,11 +1008,11 @@ id: directly_develops_from name: directly develops from def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] xref: RO:0002207 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "has developmental precursor" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000119 "FBbt" xsd:string property_value: RO:0002575 RO:0002202 is_a: develops_from ! develops from @@ -1060,8 +1058,8 @@ name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] xref: RO:0002449 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1072,7 +1070,7 @@ id: directly_negatively_regulates_quantity_of name: directly negatively regulates quantity of def: "The entity A has an activity that directly negatively regulates the quantity of B." [] xref: RO:0011010 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1107,8 +1105,8 @@ name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] xref: RO:0002450 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -1119,7 +1117,7 @@ id: directly_positively_regulates_quantity_of name: directly positively regulates quantity of def: "The entity A has an activity that directly positively regulates the quantity of B." [] xref: RO:0011009 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_regulates_quantity_of ! directly regulates quantity of @@ -1142,7 +1140,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002578 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string property_value: RO:0002575 RO:0002211 @@ -1155,8 +1153,8 @@ name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] xref: RO:0002448 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: molecularly_interacts_with ! molecularly interacts with @@ -1167,7 +1165,7 @@ id: directly_regulates_quantity_of name: directly regulates quantity of def: "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B." [] xref: RO:0011021 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -1177,7 +1175,7 @@ def: "A relationship between a disease and an anatomical structure where the mat xref: RO:0004030 range: CARO:0000003 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z [Typedef] @@ -1189,7 +1187,7 @@ property_value: IAO:0000589 "disease causes disruption of (disease to process)" domain: OGMS:0000031 range: BFO:0000015 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:51:09Z [Typedef] @@ -1200,7 +1198,7 @@ property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomica domain: OGMS:0000031 range: CARO:0000006 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z [Typedef] @@ -1210,7 +1208,7 @@ xref: RO:0004019 domain: OGMS:0000031 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject is_a: realizable_has_basis_in ! realizable has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:26:47Z [Typedef] @@ -1221,7 +1219,7 @@ xref: RO:0004021 property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:37:52Z [Typedef] @@ -1232,7 +1230,7 @@ xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string range: CARO:0000006 is_a: disease_has_basis_in ! disease has basis in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z [Typedef] @@ -1243,7 +1241,7 @@ xref: RO:0004022 domain: OGMS:0000031 is_a: disease_has_basis_in ! disease has basis in is_a: has_phenotype ! has phenotype -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:46:07Z [Typedef] @@ -1253,7 +1251,7 @@ def: "A relationship between a disease and some feature of that disease, where t xref: RO:0004029 domain: OGMS:0000031 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:50:53Z [Typedef] @@ -1272,7 +1270,7 @@ xref: RO:0004027 domain: OGMS:0000031 range: BFO:0000004 is_a: disease_has_location ! disease has location -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:37:31Z [Typedef] @@ -1285,7 +1283,7 @@ property_value: IAO:0000232 "This relation is intentionally very general, and co domain: OGMS:0000031 range: BFO:0000004 is_a: disease_relationship ! disease relationship -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T04:06:02Z [Typedef] @@ -1294,7 +1292,7 @@ name: disease relationship def: "This relation groups relations between diseases and any other kind of entity." [] xref: RO:0040035 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z [Typedef] @@ -1306,7 +1304,7 @@ subset: ro-eco xref: RO:0002377 property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string @@ -1316,10 +1314,10 @@ is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: does_not_overlap_sequence_of name: does not overlap sequence of -def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] xref: RO:0002527 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "disconnected from" xsd:string is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -1338,7 +1336,7 @@ id: eats name: eats subset: ro-eco xref: RO:0002470 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -1359,7 +1357,7 @@ def: "A relationship that is mediated in some way by the environment or environm subset: ro-eco xref: RO:0002321 property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string [Typedef] @@ -1377,7 +1375,7 @@ name: electrically_synapsed_to def: "A relation that holds between two neurons that are electrically coupled via gap junctions." [] xref: RO:0002003 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: connected_to ! connected to [Typedef] @@ -1386,7 +1384,7 @@ name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: has_participant @@ -1397,7 +1395,7 @@ def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string property_value: IAO:0000118 "has" xsd:string @@ -1413,7 +1411,7 @@ name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] xref: RO:0004031 is_a: functionally_related_to ! functionally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z [Typedef] @@ -1430,14 +1428,14 @@ inverse_of: has_endoparasite ! has endoparasite id: ends subset: ro-eco xref: RO:0002229 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: ends_with subset: ro-eco xref: RO:0002230 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -1462,7 +1460,7 @@ name: exports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002345 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -1479,7 +1477,7 @@ def: "relationship between a neuron and a neuron projection bundle (e.g.- tract xref: RO:0002101 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 @@ -1492,7 +1490,7 @@ inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron proje id: formed_as_result_of name: formed as result of xref: RO:0002354 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of [Typedef] @@ -1500,7 +1498,7 @@ id: functionally_related_to name: functionally related to def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] xref: RO:0002328 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string [Typedef] @@ -1509,7 +1507,7 @@ name: genetically interacts with xref: RO:0002435 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with @@ -1517,7 +1515,7 @@ is_a: interacts_with ! interacts with [Typedef] id: has_2D_boundary xref: RO:0002002 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1557,7 +1555,7 @@ def: "inverse of branching part of" [] subset: ro-eco subset: RO:0002259 xref: RO:0002569 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: has_part is_a: in_branching_relationship_with ! in branching relationship with @@ -1593,7 +1591,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 "Bill Duncan (https://orcid.org/0000-0001-9625-1899)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant @@ -1622,7 +1620,7 @@ id: has_dendrite_location name: has dendrite location xref: RO:0002360 property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] @@ -1632,7 +1630,7 @@ def: "x has developmental contribution from y iff x has some part z such that z xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by @@ -1644,7 +1642,7 @@ name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to @@ -1656,7 +1654,7 @@ def: "p has direct input c iff c is a participant in p, c is present at the star xref: RO:0002400 property_value: IAO:0000112 "'protein catabolic process' SubClassOf has_direct_input some protein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly consumes" xsd:string property_value: IAO:0000232 "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" xsd:string is_a: has_input ! has input @@ -1666,7 +1664,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1711,7 +1709,7 @@ def: "x 'has end location' y if and only if there exists some process z such tha subset: ro-eco xref: RO:0002232 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -1724,7 +1722,7 @@ def: "x has end sequence y if the end of x is identical to the end of y, and x h xref: RO:0002518 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -1776,11 +1774,11 @@ id: has_exposure_stimulus name: has exposure stimulus def: "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002309 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 is_a: related_via_exposure_to ! related via exposure to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:35:04Z [Typedef] @@ -1806,7 +1804,7 @@ def: "The relation between a neuron projection bundle and a neuron projection th xref: RO:0002132 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 @@ -1828,7 +1826,7 @@ subset: ro-eco xref: RO:0002303 property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Pier Buttigieg" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string domain: CARO:0001010 range: ENVO:01000254 @@ -1851,7 +1849,7 @@ name: has host def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] subset: ro-eco xref: RO:0002454 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -1865,7 +1863,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 is_a: has_participant @@ -1886,7 +1884,7 @@ def: "p has intermediate c if and only if p has parts p1, p2 and p1 has output c subset: ro-eco xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string is_a: has_participant @@ -1924,7 +1922,7 @@ name: has major susceptibility factor xref: RO:0004005 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_susceptibility_factor_for ! is causal susceptibility factor for -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:26Z [Typedef] @@ -1935,7 +1933,7 @@ property_value: seeAlso Orphanet:410295 property_value: seeAlso Orphanet:410296 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_gain_of_function_germline_mutation_of_in ! is causal gain of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:20Z [Typedef] @@ -1945,7 +1943,7 @@ xref: RO:0004003 property_value: seeAlso Orphanet:317343 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_in ! is causal germline mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:54Z [Typedef] @@ -1954,7 +1952,7 @@ name: has material basis in loss of function germline mutation in xref: RO:0004002 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_loss_of_function_germline_mutation_of_in ! is causal loss of function germline mutation of in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:37Z [Typedef] @@ -1964,7 +1962,7 @@ xref: RO:0004004 property_value: seeAlso Orphanet:317344 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z [Typedef] @@ -1980,7 +1978,7 @@ id: has_muscle_antagonist name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string is_a: biomechanically_related_to ! biomechanically related to @@ -1989,7 +1987,7 @@ id: has_muscle_insertion name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} @@ -2001,7 +1999,7 @@ id: has_muscle_origin name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} @@ -2039,7 +2037,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string is_a: has_participant inverse_of: output_of ! output of @@ -2066,7 +2064,7 @@ name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] xref: RO:0002584 property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causal_relation_between_material_entity_and_a_process ! causal relation between material entity and a process is_a: functionally_related_to ! functionally related to @@ -2076,7 +2074,7 @@ name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco xref: RO:0002479 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 range: BFO:0000004 @@ -2086,7 +2084,7 @@ name: has partial material basis in germline mutation in xref: RO:0004006 is_a: condition_has_genetic_basis_in ! condition has genetic basis in inverse_of: is_causal_germline_mutation_partially_giving_rise_to ! is causal germline mutation partially giving rise to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:57Z [Typedef] @@ -2098,7 +2096,7 @@ id: has_pathogen name: has pathogen subset: ro-eco xref: RO:0002557 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2108,7 +2106,7 @@ def: "A relationship that holds between a biological entity and a phenotype. Her subset: ro-eco xref: RO:0002200 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: UPHENO:0001001 is_a: has_phenotype_or_disease ! has phenotype or disease inverse_of: phenotype_of ! phenotype of @@ -2129,9 +2127,9 @@ def: "Holds between a cell c and a protein complex or protein p if and only if t xref: RO:0002104 property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Alexander Diehl" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 @@ -2157,8 +2155,8 @@ def: "Relation between a neuron and some structure (e.g.- a brain region) in whi xref: RO:0002110 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "synapsed in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2172,7 +2170,7 @@ name: has potential to develop into def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] xref: RO:0002387 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2181,7 +2179,7 @@ name: has potential to developmentally contribute to def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] xref: RO:0002385 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2190,7 +2188,7 @@ name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] xref: RO:0002386 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_developmental_potential_involving ! has developmental potential involving [Typedef] @@ -2199,7 +2197,7 @@ name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] xref: RO:0002388 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_potential_to_develop_into ! has potential to develop into [Typedef] @@ -2223,7 +2221,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -2233,7 +2231,7 @@ def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c o subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -2244,7 +2242,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output is_a: has_primary_input_or_output ! has primary input or output -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -2276,7 +2274,7 @@ name: has skeleton def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] xref: RO:0002551 property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 @@ -2321,7 +2319,7 @@ name: has soma location def: "Relation between a neuron and an anatomical structure that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 range: CARO:0000003 @@ -2335,7 +2333,7 @@ def: "x 'has starts location' y if and only if there exists some process z such subset: ro-eco xref: RO:0002231 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 range: BFO:0000004 @@ -2348,7 +2346,7 @@ def: "x has start sequence y if the start of x is identical to the start of y, a xref: RO:0002516 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2358,10 +2356,10 @@ inverse_of: is_start_sequence_of ! is start sequence of [Typedef] id: has_subsequence name: has subsequence -def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2375,7 +2373,7 @@ id: has_symptom name: has symptom def: "A relation that holds between a disease or an organism and a phenotype" [] xref: RO:0002452 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: OGMS:0000031 is_a: has_phenotype ! has phenotype @@ -2405,7 +2403,7 @@ def: "A general relation between a neuron and some structure in which it either xref: RO:0002130 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has synapse in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 @@ -2417,7 +2415,7 @@ id: has_synaptic_terminal_of name: has synaptic terminal of xref: RO:0002006 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: overlaps ! overlaps inverse_of: has_synaptic_terminal_in ! has synaptic terminal in @@ -2429,7 +2427,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002339 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2440,7 +2438,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002338 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in [Typedef] @@ -2448,7 +2446,7 @@ id: has_vector name: has vector subset: ro-eco xref: RO:0002460 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with [Typedef] @@ -2463,7 +2461,7 @@ id: host_of name: host of subset: ro-eco xref: RO:0002453 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2476,7 +2474,7 @@ synonym: "epiparasite of" RELATED [] synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string is_a: has_host ! has host @@ -2492,7 +2490,7 @@ synonym: "has epiparasite" RELATED [] synonym: "has hyperparasite" RELATED [] synonym: "hyperparasitoidized by" RELATED [] xref: RO:0002554 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: host_of ! host of [Typedef] @@ -2500,7 +2498,7 @@ id: immediate_transformation_of name: immediate transformation of def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] xref: RO:0002495 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002494 is_a: directly_develops_from ! directly develops from is_a: transformation_of ! transformation of @@ -2510,7 +2508,7 @@ id: immediately_causally_downstream_of name: immediately causally downstream of xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of is_a: immediately_preceded_by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of @@ -2520,7 +2518,7 @@ id: immediately_causally_upstream_of name: immediately causally upstream of def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: immediately_precedes @@ -2533,7 +2531,7 @@ xref: RO:0002087 id: immediately_precedes subset: ro-eco xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0002575 BFO:0000063 [Typedef] @@ -2542,7 +2540,7 @@ name: imports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002340 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: transports ! transports [Typedef] @@ -2551,7 +2549,7 @@ name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] xref: RO:0002375 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 @@ -2577,7 +2575,7 @@ id: increases_by_expression_quantity_of name: increases by expression quantity of def: "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." [] xref: RO:0011008 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: indirectly_positively_regulates_quantity_of ! indirectly positively regulates quantity of @@ -2587,7 +2585,7 @@ id: increases_expression_of name: increases expression of def: "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." [] xref: RO:0003003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -2606,7 +2604,7 @@ id: indirectly_negatively_regulates name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] xref: RO:0002409 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 is_transitive: true @@ -2618,7 +2616,7 @@ id: indirectly_negatively_regulates_activity_of name: indirectly negatively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B." [] xref: RO:0011016 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly inhibits" xsd:string is_a: indirectly_regulates_activity_of ! indirectly regulates activity of @@ -2627,7 +2625,7 @@ id: indirectly_negatively_regulates_quantity_of name: indirectly negatively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B." [] xref: RO:0011023 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2635,7 +2633,7 @@ id: indirectly_positively_regulates name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] xref: RO:0002407 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 is_transitive: true @@ -2647,7 +2645,7 @@ id: indirectly_positively_regulates_activity_of name: indirectly positively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." [] xref: RO:0011013 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly activates" xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -2658,7 +2656,7 @@ id: indirectly_positively_regulates_quantity_of name: indirectly positively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B." [] xref: RO:0011024 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: indirectly_regulates_quantity_of ! indirectly regulates quantity of [Typedef] @@ -2676,7 +2674,7 @@ id: indirectly_regulates_activity_of name: indirectly regulates activity of def: "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." [] xref: RO:0011004 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: regulates_activity_of ! regulates activity of @@ -2686,7 +2684,7 @@ id: indirectly_regulates_quantity_of name: indirectly regulates quantity of def: "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B." [] xref: RO:0011022 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of [Typedef] @@ -2696,7 +2694,7 @@ def: "inverse of has input" [] subset: ro-eco subset: RO:0002259 xref: RO:0002352 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -2710,7 +2708,7 @@ xref: RO:0002434 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI domain: BFO:0000040 @@ -2723,7 +2721,7 @@ name: interacts with via parasite-host interaction def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] subset: ro-eco xref: RO:0002443 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2751,7 +2749,7 @@ id: involved_in name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] xref: RO:0002331 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in @@ -2763,7 +2761,7 @@ id: involved_in_negative_regulation_of name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] xref: RO:0002430 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2773,7 +2771,7 @@ name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within is_a: causal_agent_in_process ! causal agent in process @@ -2784,7 +2782,7 @@ id: involved_in_positive_regulation_of name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] xref: RO:0002429 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002428 is_a: involved_in_regulation_of ! involved in regulation of @@ -2793,7 +2791,7 @@ id: involved_in_regulation_of name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] xref: RO:0002428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: acts_upstream_of ! acts upstream of is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of @@ -2804,7 +2802,7 @@ def: "c executes activity in d if and only if c enables p and p occurs_in d. As synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -2853,7 +2851,7 @@ id: is_basis_for_realizable name: is basis for realizable xref: RO:0004018 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:29Z [Typedef] @@ -2863,7 +2861,7 @@ def: "inverse of bounds sequence of" [] subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: sequentially_related_to ! sequentially related to @@ -2874,7 +2872,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004011 property_value: seeAlso Orphanet:410296 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:55:51Z [Typedef] @@ -2885,7 +2883,7 @@ xref: RO:0004013 property_value: seeAlso Orphanet:317343 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:40Z [Typedef] @@ -2896,7 +2894,7 @@ xref: RO:0004016 property_value: seeAlso Orphanet:317346 is_a: contributes_to_condition ! contributes to condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:58:43Z [Typedef] @@ -2906,7 +2904,7 @@ def: "Relates a gene to condition, such that a mutation in this gene in a germ c xref: RO:0004012 property_value: seeAlso Orphanet:410295 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:06Z [Typedef] @@ -2917,7 +2915,7 @@ xref: RO:0004014 property_value: seeAlso Orphanet:317344 is_a: causes_condition ! causes condition is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:07Z [Typedef] @@ -2927,7 +2925,7 @@ def: "Relates a gene to condition, such that a mutation in this gene predisposes xref: RO:0004015 property_value: seeAlso Orphanet:317345 is_a: is_genetic_basis_for_condition ! is genetic basis for condition -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:43Z [Typedef] @@ -2937,7 +2935,7 @@ def: "x is a consecutive sequence of y iff x has subsequence y, and all the part xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: has_subsequence ! has subsequence @@ -2947,7 +2945,7 @@ name: is downstream of sequence of def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] xref: RO:0002529 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of @@ -2957,7 +2955,7 @@ id: is_eaten_by name: is eaten by subset: ro-eco xref: RO:0002471 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with @@ -2969,7 +2967,7 @@ def: "inverse of has end sequence" [] subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -2982,7 +2980,7 @@ xref: RO:0004010 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string range: BFO:0000017 is_a: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:53:08Z [Typedef] @@ -2992,7 +2990,7 @@ def: "x is immediately downstream of the sequence of y iff either (1) x and y ha xref: RO:0002530 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002529 is_a: is_downstream_of_sequence_of ! is downstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3004,7 +3002,7 @@ def: "inverse of immediately downstream of" [] xref: RO:0002531 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: is_upstream_of_sequence_of ! is upstream of sequence of is_a: sequentially_adjacent_to ! sequentially adjacent to @@ -3031,7 +3029,7 @@ def: "x is sequentially aligned with if a significant portion bases of x and y c xref: RO:0002521 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: sequentially_related_to ! sequentially related to @@ -3071,7 +3069,7 @@ def: "inverse of has start sequence" [] subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_transitive: true @@ -3084,7 +3082,7 @@ def: "inverse of has subsequence" [] subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of @@ -3107,7 +3105,7 @@ name: is treated by substance def: "Inverse of 'is substance that treats'" [] subset: RO:0002259 xref: RO:0002302 -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 is_a: causally_related_to ! causally related to inverse_of: is_substance_that_treats ! is substance that treats @@ -3117,7 +3115,7 @@ name: is upstream of sequence of def: "inverse of downstream of sequence of" [] xref: RO:0002528 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -3127,7 +3125,7 @@ name: is vector for subset: ro-eco xref: RO:0002459 property_value: IAO:0000112 "Anopheles is a vector for Plasmodium" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: has_vector ! has vector @@ -3179,7 +3177,7 @@ name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco xref: RO:0002571 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:cjm xsd:string range: BFO:0000040 is_a: part_of @@ -3190,7 +3188,7 @@ name: luminal space of def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] subset: ro-eco xref: RO:0002572 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000141 is_a: lumen_of ! lumen of @@ -3202,7 +3200,7 @@ subset: ro-eco xref: RO:0002381 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with is_a: part_of @@ -3212,7 +3210,7 @@ id: mereotopologically_related_to name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] xref: RO:0002323 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string property_value: RO:0001900 RO:0001901 @@ -3230,7 +3228,7 @@ name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 @@ -3243,7 +3241,7 @@ name: mutualistically interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] subset: ro-eco xref: RO:0002442 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -3270,7 +3268,7 @@ name: negatively regulated by def: "inverse of negatively regulates" [] subset: RO:0002259 xref: RO:0002335 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3281,7 +3279,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 @@ -3330,7 +3328,7 @@ def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in @@ -3351,10 +3349,10 @@ expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://p [Typedef] id: overlaps_sequence_of name: overlaps sequence of -def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] xref: RO:0002526 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: overlaps ! overlaps is_a: sequentially_related_to ! sequentially related to @@ -3366,7 +3364,7 @@ subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string is_a: has_host ! has host @@ -3379,7 +3377,7 @@ name: parasitized by subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string @@ -3418,7 +3416,7 @@ name: part of developmental precursor of xref: RO:0002287 property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: developmentally_succeeded_by ! developmentally succeeded by [Typedef] @@ -3426,7 +3424,7 @@ id: part_of_structure_that_is_capable_of name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] xref: RO:0002329 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean is_a: functionally_related_to ! functionally related to @@ -3455,7 +3453,7 @@ subset: ro-eco synonym: "semibiotically interacts with" RELATED [] xref: RO:0002446 property_value: IAO:0000112 "Porifiera attaches to substrate" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: biotically_interacts_with ! biotically interacts with @@ -3464,7 +3462,7 @@ id: participates_in_a_biotic-biotic_interaction_with name: participates in a biotic-biotic interaction with subset: ro-eco xref: RO:0002574 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 domain: CARO:0001010 range: CARO:0001010 @@ -3474,7 +3472,7 @@ is_a: biotically_interacts_with ! biotically interacts with id: partner_in name: partner in xref: RO:0002461 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string is_a: participates_in @@ -3483,7 +3481,7 @@ id: pathogen_of name: pathogen of subset: ro-eco xref: RO:0002556 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_host ! has host inverse_of: has_pathogen ! has pathogen @@ -3495,7 +3493,7 @@ subset: ro-eco subset: RO:0002259 xref: RO:0002201 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_functional: true [Typedef] @@ -3503,7 +3501,7 @@ id: phosphorylates name: phosphorylates xref: RO:0002447 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: molecularly_interacts_with ! molecularly interacts with @@ -3512,7 +3510,7 @@ id: pollinated_by name: pollinated by subset: ro-eco xref: RO:0002456 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string @@ -3525,7 +3523,7 @@ subset: ro-eco xref: RO:0002455 property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with @@ -3537,7 +3535,7 @@ name: positively regulated by def: "inverse of positively regulates" [] subset: RO:0002259 xref: RO:0002336 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -3548,7 +3546,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002211 @@ -3583,7 +3581,7 @@ def: "inverse of preys on" [] subset: ro-eco subset: RO:0002259 xref: RO:0002458 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string @@ -3598,9 +3596,9 @@ subset: ro-eco xref: RO:0002439 property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Jorrit Poelen" xsd:string -property_value: IAO:0000117 "Katja Shulz" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7134-3324 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string @@ -3623,7 +3621,7 @@ def: "x proper_distributary_of y iff x distributary_of y and x does not flow bac subset: ro-eco xref: RO:0002382 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: distributary_of ! distributary of [Typedef] @@ -3633,7 +3631,7 @@ def: "x proper_tributary_of y iff x tributary_of y and x does not originate from subset: ro-eco xref: RO:0002383 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: tributary_of ! tributary of [Typedef] @@ -3642,7 +3640,7 @@ name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string @@ -3654,7 +3652,7 @@ id: provides_nutrients_for name: provides nutrients for subset: ro-eco xref: RO:0002469 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3663,7 +3661,7 @@ name: realizable has basis in xref: RO:0004017 is_a: causally_related_to ! causally related to inverse_of: is_basis_for_realizable ! is basis for realizable -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:01Z [Typedef] @@ -3672,10 +3670,10 @@ name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] synonym: "triggered by process" EXACT [RO:cjm] xref: RO:0009501 -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "David Osumi-Sutherland" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string @@ -3692,7 +3690,7 @@ xref: RO:0004028 domain: BFO:0000017 range: BFO:0000040 is_a: causally_related_to ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:45:49Z [Typedef] @@ -3700,7 +3698,7 @@ id: receives_input_from name: receives input from xref: RO:0002485 property_value: IAO:0000116 "See notes for inverse relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to inverse_of: sends_output_to ! sends output to @@ -3740,7 +3738,7 @@ name: regulated by def: "inverse of regulates" [] subset: RO:0002259 xref: RO:0002334 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 range: BFO:0000015 @@ -3755,9 +3753,9 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Hill" xsd:string -property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 +property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string @@ -3774,7 +3772,7 @@ id: regulates_activity_of name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] xref: RO:0011002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3794,7 +3792,7 @@ id: regulates_in_other_organism name: regulates in other organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] xref: RO:0002010 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 range: BFO:0000015 is_a: causally_upstream_of_or_within ! causally upstream of or within @@ -3805,7 +3803,7 @@ name: regulates levels of def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] xref: RO:0002332 property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 @@ -3817,7 +3815,7 @@ id: regulates_quantity_of name: regulates quantity of def: "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." [] xref: RO:0011003 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: causally_influences ! causally influences @@ -3836,7 +3834,7 @@ id: related_via_localization_to name: related via localization to def: "A relationship that holds via some process of localization" [] xref: RO:0002337 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 range: BFO:0000002 @@ -3857,7 +3855,7 @@ id: represses_expression_of name: represses expression of def: "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." [] xref: RO:0003002 -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3871,7 +3869,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -3916,7 +3914,7 @@ name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 is_a: has_participant -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] @@ -3936,7 +3934,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002348 property_value: IAO:0000112 "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3948,7 +3946,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002349 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3962,7 +3960,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3972,7 +3970,7 @@ id: results_in_developmental_induction_of name: results in developmental induction of def: "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." [] xref: RO:0002357 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3982,7 +3980,7 @@ def: "p results in the developmental progression of s iff p is a developmental p xref: RO:0002295 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 range: CARO:0000000 @@ -3994,7 +3992,7 @@ name: results in developmental regression of xref: RO:0002301 property_value: IAO:0000112 "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4004,7 +4002,7 @@ name: results in disappearance of xref: RO:0002300 property_value: IAO:0000112 "foramen ovale closure SubClassOf results in disappearance of foramen ovale" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: results_in_ending_of ! results in ending of @@ -4020,7 +4018,7 @@ id: results_in_ending_of name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4034,7 +4032,7 @@ xref: RO:0002297 property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4056,7 +4054,7 @@ id: results_in_growth_of name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4071,7 +4069,7 @@ xref: RO:0002299 property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4087,7 +4085,7 @@ xref: RO:0002298 property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4100,7 +4098,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002565 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4126,7 +4124,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002356 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4135,7 +4133,7 @@ id: results_in_structural_organization_of name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4151,7 +4149,7 @@ name: results in transport across def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002342 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: occurs_across ! occurs across is_a: results_in_transport_to_from_or_in ! results in transport to from or in @@ -4160,7 +4158,7 @@ id: results_in_transport_along name: results in transport along def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] xref: RO:0002341 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4168,7 +4166,7 @@ id: results_in_transport_to_from_or_in name: results in transport to from or in xref: RO:0002344 property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to [Typedef] @@ -4183,7 +4181,7 @@ id: sends_output_to name: sends output to xref: RO:0002486 property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to [Typedef] @@ -4225,7 +4223,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcript" xsd:string property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of @@ -4235,7 +4233,7 @@ name: sequentially related to def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string @@ -4248,7 +4246,7 @@ name: skeleton of def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 is_a: part_of @@ -4259,7 +4257,7 @@ name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] xref: RO:0002379 property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: overlaps ! overlaps @@ -4271,7 +4269,7 @@ subset: ro-eco xref: RO:0002163 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 @@ -4285,7 +4283,7 @@ name: stabilizes quantity of def: "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." [] xref: RO:0011015 property_value: IAO:0000112 "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 range: BFO:0000040 is_a: directly_positively_regulates_quantity_of ! directly positively regulates quantity of @@ -4294,14 +4292,14 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates id: starts subset: ro-eco xref: RO:0002223 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of [Typedef] id: starts_with subset: ro-eco xref: RO:0002224 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: has_part [Typedef] @@ -4317,7 +4315,7 @@ name: subcluster of def: "A relation between a group and another group it is part of but does not fully constitute." [] xref: RO:0015003 property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." xsd:string -property_value: IAO:0000117 "Shawn Tan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true is_a: part_of @@ -4326,7 +4324,7 @@ is_a: part_of id: subject_participant_in name: subject participant in xref: RO:0002462 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4345,7 +4343,7 @@ name: surrounded by def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] xref: RO:0002219 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to inverse_of: surrounds ! surrounds @@ -4357,7 +4355,7 @@ def: "inverse of surrounded by" [] subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent to @@ -4367,7 +4365,7 @@ name: symbiotically interacts with def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] subset: ro-eco xref: RO:0002440 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true @@ -4380,8 +4378,8 @@ def: "Relation between an anatomical structure (including cells) and a neuron th xref: RO:0002103 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: receives_input_from ! receives input from inverse_of: synapsed_to ! synapsed to @@ -4406,8 +4404,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002108 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" [] @@ -4420,8 +4418,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002109 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4434,8 +4432,8 @@ comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('s xref: RO:0002112 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_by ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] @@ -4448,8 +4446,8 @@ comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part som xref: RO:0002120 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: sends_output_to ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -4473,8 +4471,8 @@ def: "A relation between a motor neuron and a muscle that it synapses to via a t comment: Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) xref: RO:0002107 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_II_bouton ! synapsed_by_via_type_II_bouton @@ -4488,8 +4486,8 @@ comment: Expands to: has_part some ('type Ib terminal button' that has_part some xref: RO:0002105 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Ib_bouton ! synapsed_by_via_type_Ib_bouton @@ -4503,8 +4501,8 @@ comment: Expands to: has_part some ('type Is terminal button' that has_part some xref: RO:0002106 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Marta Costa" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: synapsed_to ! synapsed to inverse_of: synapsed_by_via_type_Is_bouton ! synapsed_by_via_type_Is_bouton @@ -4514,7 +4512,7 @@ expand_expression_to: "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that id: target_participant_in name: target participant in xref: RO:0002463 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: partner_in ! partner in @@ -4523,7 +4521,7 @@ id: temporally_related_to subset: ro-eco xref: RO:0002222 property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string [Typedef] @@ -4531,7 +4529,7 @@ id: transformation_of name: transformation of def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] xref: RO:0002494 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: develops_from ! develops from @@ -4541,7 +4539,7 @@ name: transitively provides input for def: "transitive form of directly_provides_input_for" [] xref: RO:0002414 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." xsd:string property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string domain: BFO:0000015 @@ -4556,7 +4554,7 @@ def: "A relationship that holds between a disease and organism" [] xref: RO:0002451 property_value: IAO:0000112 "all dengue disease transmitted by some mosquito" xsd:string property_value: IAO:0000116 "Add domain and range constraints" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -4576,7 +4574,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002313 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "regulates localization of" xsd:string is_a: related_via_localization_to ! related via localization to is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure @@ -4590,7 +4588,7 @@ xref: RO:0002376 property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string @@ -4608,7 +4606,7 @@ name: trophically interacts with def: "An interaction relationship in which the partners are related via a feeding relationship." [] subset: ro-eco xref: RO:0002438 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4618,7 +4616,7 @@ name: ubiquitinates def: "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" [] xref: RO:0002480 property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with [Typedef] diff --git a/subsets/ro-time-interval.owl b/subsets/ro-time-interval.owl index 06c5dfb4..85959a1e 100644 --- a/subsets/ro-time-interval.owl +++ b/subsets/ro-time-interval.owl @@ -409,7 +409,7 @@ - David Osumi-Sutherland + RO:0002002 has_2D_boundary @@ -421,7 +421,7 @@ A relation that holds between two neurons that are electrically coupled via gap junctions. - David Osumi-Sutherland + RO:0002003 electrically_synapsed_to @@ -435,7 +435,7 @@ - David Osumi-Sutherland + RO:0002006 has_synaptic_terminal_of @@ -469,7 +469,7 @@ has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland + RO:0002007 bounding_layer_of @@ -505,9 +505,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. + A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. Note from NCEAS meeting: consider changing primary label - David Osumi-Sutherland + RO:0002008 coincident_with @@ -524,7 +524,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - David Osumi-Sutherland + RO:0002010 regulates_in_other_organism regulates in other organism @@ -553,7 +553,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + dos 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -568,7 +568,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + dos 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -584,7 +584,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + dos 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -599,7 +599,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -613,7 +613,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -630,7 +630,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + dos 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -644,7 +644,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + dos 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -658,7 +658,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + dos 2017-07-20T17:11:08Z RO:0002020 transports @@ -672,7 +672,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + dos 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -686,7 +686,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + dos 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -697,7 +697,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + GOC:dos @@ -708,7 +708,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + dos 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -718,7 +718,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + GOC:dos @@ -729,7 +729,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + dos 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -739,7 +739,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + GOC:dos @@ -750,7 +750,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + dos 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -761,7 +761,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + GOC:dos @@ -780,7 +780,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + dos 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -797,7 +797,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + GOC:dos @@ -814,7 +814,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + RO:0002090 @@ -831,7 +831,7 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure that its soma is part of. - David Osumi-Sutherland + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -852,9 +852,9 @@ Examples include: the relationship between two channels collected simultaneously relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - David Osumi-Sutherland + fasciculates with - (forall (?x ?y) + (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) @@ -890,9 +890,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure its axon forms (chemical) synapses in. - Chris Mungall - David Osumi-Sutherland - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -924,8 +923,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -945,9 +944,9 @@ Examples include: the relationship between two channels collected simultaneously Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - Alexander Diehl - Chris Mungall - Lindsay Cowell + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) @@ -965,8 +964,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -985,8 +984,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) @@ -1005,8 +1004,8 @@ Examples include: the relationship between two channels collected simultaneously A relation between a motor neuron and a muscle that it synapses to via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) RO:0002107 @@ -1023,8 +1022,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type II bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1043,8 +1042,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1064,8 +1063,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - Chris Mungall - David Osumi-Sutherland + + synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( @@ -1085,8 +1084,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. - David Osumi-Sutherland - Marta Costa + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) @@ -1168,8 +1167,8 @@ Examples include: the relationship between two channels collected simultaneously Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) @@ -1196,8 +1195,8 @@ N1 SubclassOf ( Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. - Chris Mungall - David Osumi-Sutherland + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( @@ -1218,7 +1217,7 @@ N1 SubclassOf ( A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - David Osumi-Sutherland + has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) @@ -1267,9 +1266,9 @@ N1 SubclassOf ( The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - David Osumi-Sutherland + has fasciculating component - (forall (?x ?y) + (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) @@ -1309,8 +1308,8 @@ N1 SubclassOf ( - X continuous_with Y if and only if X and Y share a fiat boundary. - David Osumi-Sutherland + X continuous_with Y if and only if X and Y share a fiat boundary. + connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) @@ -1329,8 +1328,8 @@ N1 SubclassOf ( x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom - proper overlaps - (forall (?x ?y) + proper overlaps + (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and @@ -1353,7 +1352,7 @@ N1 SubclassOf ( A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - Chris Mungall + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) @@ -1361,7 +1360,7 @@ N1 SubclassOf ( RO:0002163 spatially_disjoint_from - spatially disjoint from + spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern @@ -1498,7 +1497,7 @@ N1 SubclassOf ( A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - Chris Mungall + RO:0002200 has_phenotype @@ -1513,7 +1512,7 @@ N1 SubclassOf ( inverse of has phenotype - Chris Mungall + RO:0002201 @@ -1533,10 +1532,10 @@ N1 SubclassOf ( x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - Terry Meehan + + + + RO:0002202 develops_from This is the transitive form of the develops from relation @@ -1554,9 +1553,9 @@ N1 SubclassOf ( inverse of develops from - Chris Mungall - David Osumi-Sutherland - Terry Meehan + + + RO:0002203 develops_into @@ -1588,12 +1587,12 @@ N1 SubclassOf ( Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - Chris Mungall - David Osumi-Sutherland - has developmental precursor + + FBbt RO:0002207 + has developmental precursor directly_develops_from TODO - add child relations from DOS directly develops from @@ -1651,9 +1650,9 @@ N1 SubclassOf ( p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - Chris Mungall - David Hill - Tanya Berardini + + + GO Regulation precludes parthood; the regulatory process may not be within the regulated process. @@ -1676,7 +1675,7 @@ N1 SubclassOf ( p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - Chris Mungall + negatively regulates (process to process) @@ -1698,7 +1697,7 @@ N1 SubclassOf ( p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - Chris Mungall + positively regulates (process to process) @@ -1721,7 +1720,7 @@ N1 SubclassOf ( mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - Chris Mungall + has function realized in @@ -1740,7 +1739,7 @@ N1 SubclassOf ( c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - Chris Mungall + has function in RO:0002216 capable_of_part_of @@ -1757,7 +1756,7 @@ N1 SubclassOf ( x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - Chris Mungall + RO:0002219 surrounded_by @@ -1779,7 +1778,7 @@ N1 SubclassOf ( x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - Chris Mungall + RO:0002220 @@ -1803,7 +1802,7 @@ N1 SubclassOf ( inverse of surrounded by - Chris Mungall + RO:0002221 @@ -1816,7 +1815,7 @@ N1 SubclassOf ( - Chris Mungall + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 @@ -1830,7 +1829,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002223 starts @@ -1842,7 +1841,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002224 starts_with @@ -1856,7 +1855,7 @@ N1 SubclassOf ( x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - Chris Mungall + RO:0002225 develops_from_part_of develops from part of @@ -1871,7 +1870,7 @@ N1 SubclassOf ( x develops_in y if x is located in y whilst x is developing - Chris Mungall + EHDAA2 Jonathan Bard, EHDAA2 RO:0002226 @@ -1909,7 +1908,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002229 ends @@ -1921,7 +1920,7 @@ N1 SubclassOf ( - Chris Mungall + RO:0002230 ends_with @@ -1937,7 +1936,7 @@ N1 SubclassOf ( x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - Chris Mungall + starts with process that occurs in RO:0002231 @@ -1955,7 +1954,7 @@ N1 SubclassOf ( x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - Chris Mungall + ends with process that occurs in RO:0002232 @@ -1973,7 +1972,7 @@ N1 SubclassOf ( p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + consumes RO:0002233 @@ -1993,7 +1992,7 @@ N1 SubclassOf ( p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - Chris Mungall + produces RO:0002234 @@ -2047,7 +2046,7 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - Bill Duncan (https://orcid.org/0000-0001-9625-1899) + This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. @@ -2196,7 +2195,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y - Chris Mungall + RO:0002254 has_developmental_contribution_from has developmental contribution from @@ -2211,7 +2210,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho inverse of has developmental contribution from - Chris Mungall + RO:0002255 developmentally_contributes_to @@ -2229,9 +2228,9 @@ If you need an axiom that says 'has_participant min 2 object', you sho t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - Chris Mungall - David Osumi-Sutherland - Melissa Haendel + + + induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) @@ -2251,7 +2250,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally induced by - Chris Mungall + RO:0002257 developmentally_induces developmentally induces @@ -2269,7 +2268,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - Chris Mungall + In general you should not use this relation to make assertions - use one of the more specific relations below this one RO:0002258 developmentally_preceded_by @@ -2317,7 +2316,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - Chris Mungall + replaces RO:0002285 developmentally_replaces @@ -2332,7 +2331,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of developmentally preceded by - Chris Mungall + RO:0002286 developmentally_succeeded_by developmentally succeeded by @@ -2346,7 +2345,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - Chris Mungall + RO:0002287 part_of_developmental_precursor_of part of developmental precursor of @@ -2363,7 +2362,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - Chris Mungall + RO:0002295 results_in_developmental_progression_of results in developmental progression of @@ -2380,7 +2379,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - Chris Mungall + http://www.geneontology.org/GO.doc.development.shtml RO:0002296 @@ -2401,7 +2400,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002297 @@ -2422,7 +2421,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002298 @@ -2443,7 +2442,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002299 @@ -2461,7 +2460,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho foramen ovale closure SubClassOf results in disappearance of foramen ovale - Chris Mungall + May be merged into parent relation RO:0002300 results_in_disappearance_of @@ -2476,7 +2475,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) - Chris Mungall + May be merged into parent relation RO:0002301 results_in_developmental_regression_of @@ -2491,7 +2490,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho Inverse of 'is substance that treats' - cjm + RO:0002302 is_treated_by_substance @@ -2511,7 +2510,7 @@ where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. - Pier Buttigieg + adapted for living in RO:0002303 @@ -2529,7 +2528,7 @@ where p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - cjm + RO:0002304 @@ -2547,7 +2546,7 @@ where p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - cjm + RO:0002305 @@ -2562,10 +2561,10 @@ where A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. - Austin Meier - Chris Mungall - Marie Angelique Laporte - cjm + + + + 2017-06-05T17:35:04Z RO:0002309 has_exposure_stimulus @@ -2580,7 +2579,7 @@ where Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. - Chris Mungall + regulates localization of RO:0002313 @@ -2600,7 +2599,7 @@ where an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - Chris Mungall + GOC:mtg_berkeley_2013 RO:0002315 @@ -2617,7 +2616,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions RO:0002321 @@ -2633,7 +2632,7 @@ where An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. - Chris Mungall + adapted for RO:0002322 @@ -2647,7 +2646,7 @@ where A mereological relationship or a topological relationship - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships RO:0002323 @@ -2661,7 +2660,7 @@ where A relationship that holds between entities participating in some developmental process (GO:0032502) - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development RO:0002324 developmentally_related_to @@ -2678,9 +2677,8 @@ where Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. - Chris Mungall + In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - Gene Ontology Consortium RO:0002325 colocalizes_with @@ -2708,7 +2706,7 @@ then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. - Chris Mungall + In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 @@ -2725,7 +2723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - Chris Mungall + catalyzes executes has @@ -2744,7 +2742,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 functionally_related_to @@ -2758,7 +2756,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati this relation holds between c and p when c is part of some c', and c' is capable of p. - Chris Mungall + false RO:0002329 part_of_structure_that_is_capable_of @@ -2773,7 +2771,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati c involved_in p if and only if c enables some process p', and p' is part of p - Chris Mungall + actively involved in enables part of RO:0002331 @@ -2792,7 +2790,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - Chris Mungall + regulates levels of (process to entity) RO:0002332 @@ -2808,7 +2806,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables - Chris Mungall + RO:0002333 enabled_by @@ -2825,7 +2823,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of regulates - Chris Mungall + regulated by (processual) RO:0002334 @@ -2840,7 +2838,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of negatively regulates - Chris Mungall + RO:0002335 negatively_regulated_by @@ -2854,7 +2852,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of positively regulates - Chris Mungall + RO:0002336 positively_regulated_by @@ -2869,7 +2867,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds via some process of localization - Chris Mungall + Do not use this relation directly. It is a grouping relation. RO:0002337 related_via_localization_to @@ -2883,7 +2881,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - Chris Mungall + RO:0002338 @@ -2899,7 +2897,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - Chris Mungall + RO:0002339 @@ -2915,7 +2913,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. - Chris Mungall + RO:0002340 imports @@ -2929,7 +2927,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - Chris Mungall + RO:0002341 results_in_transport_along results in transport along @@ -2943,7 +2941,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - Chris Mungall + RO:0002342 results_in_transport_across @@ -2958,7 +2956,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'pollen tube growth' results_in growth_of some 'pollen tube' - Chris Mungall + RO:0002343 results_in_growth_of results in growth of @@ -2971,7 +2969,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - Chris Mungall + RO:0002344 results_in_transport_to_from_or_in results in transport to from or in @@ -2983,8 +2981,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. - Chris Mungall + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. + RO:0002345 exports @@ -3000,7 +2998,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - Chris Mungall + RO:0002348 @@ -3017,7 +3015,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - Chris Mungall + RO:0002349 @@ -3034,7 +3032,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has input - Chris Mungall + RO:0002352 @@ -3050,7 +3048,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has output - Chris Mungall + RO:0002353 @@ -3064,7 +3062,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002354 formed_as_result_of formed as result of @@ -3078,7 +3076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. - Chris Mungall + RO:0002355 results_in_structural_organization_of results in structural organization of @@ -3092,7 +3090,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - Chris Mungall + RO:0002356 @@ -3108,7 +3106,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. - Chris Mungall + RO:0002357 results_in_developmental_induction_of results in developmental induction of @@ -3120,7 +3118,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + http://neurolex.org/wiki/Property:DendriteLocation RO:0002360 has_dendrite_location @@ -3136,7 +3134,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - Chris Mungall + attached to (anatomical structure to anatomical structure) RO:0002371 @@ -3153,7 +3151,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002372 has_muscle_origin @@ -3176,7 +3174,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - Chris Mungall + Wikipedia:Insertion_(anatomy) RO:0002373 has_muscle_insertion @@ -3200,7 +3198,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) @@ -3222,7 +3220,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - Chris Mungall + drains into drains to tributary channel of @@ -3247,7 +3245,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Deschutes River distributary_of Little Lava Lake x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - Chris Mungall + branch of distributary channel of http://en.wikipedia.org/wiki/Distributary @@ -3273,7 +3271,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. - Chris Mungall + anastomoses with RO:0002378 @@ -3289,7 +3287,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - Chris Mungall + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios RO:0002379 spatially_coextensive_with @@ -3312,7 +3310,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - Chris Mungall + RO:0002380 branching_part_of @@ -3331,7 +3329,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. - Chris Mungall + RO:0002381 main_stem_of @@ -3347,7 +3345,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_distributary_of y iff x distributary_of y and x does not flow back into y - Chris Mungall + RO:0002382 proper_distributary_of @@ -3362,7 +3360,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x proper_tributary_of y iff x tributary_of y and x does not originate from y - Chris Mungall + RO:0002383 proper_tributary_of @@ -3379,7 +3377,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - Chris Mungall + RO:0002384 has_developmental_potential_involving has developmental potential involving @@ -3393,7 +3391,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - Chris Mungall + RO:0002385 has_potential_to_developmentally_contribute_to has potential to developmentally contribute to @@ -3407,7 +3405,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - Chris Mungall + RO:0002386 has_potential_to_developmentally_induce has potential to developmentally induce @@ -3421,7 +3419,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has the potential to develop into y iff x develops into y or if x is capable of developing into y - Chris Mungall + RO:0002387 has_potential_to_develop_into has potential to develop into @@ -3435,7 +3433,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - Chris Mungall + RO:0002388 has_potential_to_directly_develop_into has potential to directly develop into @@ -3450,7 +3448,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' RO:0002400 @@ -3468,7 +3466,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of upstream of - Chris Mungall + RO:0002404 causally_downstream_of causally downstream of @@ -3483,7 +3481,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + RO:0002405 immediately_causally_downstream_of immediately causally downstream of @@ -3498,7 +3496,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - Chris Mungall + indirectly activates RO:0002407 @@ -3515,7 +3513,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - Chris Mungall + indirectly inhibits RO:0002409 @@ -3544,7 +3542,7 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002410 causally_related_to @@ -3566,7 +3564,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - Chris Mungall + RO:0002411 @@ -3582,7 +3580,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - Chris Mungall + RO:0002412 immediately_causally_upstream_of @@ -3598,7 +3596,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit - Chris Mungall + directly provides input for directly provides input for (process to process) @@ -3618,7 +3616,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different transitive form of directly_provides_input_for - Chris Mungall + This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. transitively provides input for (process to process) RO:0002414 @@ -3636,7 +3634,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall + influences (processual) RO:0002418 affects @@ -3652,7 +3650,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - Chris Mungall + RO:0002427 @@ -3668,7 +3666,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - Chris Mungall + RO:0002428 involved_in_regulation_of involved in regulation of @@ -3681,7 +3679,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - Chris Mungall + RO:0002429 involved_in_positive_regulation_of @@ -3695,7 +3693,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - Chris Mungall + RO:0002430 involved_in_negative_regulation_of @@ -3712,7 +3710,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - Chris Mungall + involved in or reguates RO:0002431 involved_in_or_involved_in_regulation_of @@ -3728,7 +3726,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall + executes activity in RO:0002432 enables activity in @@ -3740,8 +3738,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + GOC:cjm + GOC:dos @@ -3751,7 +3749,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - Chris Mungall + RO:0002433 contributes_to_morphology_of contributes to morphology of @@ -3768,7 +3766,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. - Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. RO:0002434 in pairwise interaction with @@ -3787,7 +3785,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) - Chris Mungall + RO:0002435 genetically_interacts_with genetically interacts with @@ -3803,7 +3801,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - Chris Mungall + binds molecularly binds with RO:0002436 @@ -3824,7 +3822,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - Chris Mungall + interacts with on organism level RO:0002437 @@ -3841,7 +3839,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the partners are related via a feeding relationship. - Chris Mungall + RO:0002438 trophically_interacts_with @@ -3859,9 +3857,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] Baleen whale preys on krill An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - Chris Mungall - Jorrit Poelen - Katja Shulz + + + is subject of predation interaction with preys upon RO:0002439 @@ -3880,7 +3878,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A biotic interaction in which the two organisms live together in more or less intimate association. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism RO:0002440 @@ -3896,7 +3894,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002441 @@ -3911,7 +3909,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002442 @@ -3926,7 +3924,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 This relation groups a pair of inverse relations, parasite of and parasitized by RO:0002443 @@ -3944,7 +3942,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human - Chris Mungall + parasitizes RO:0002444 direct parasite of @@ -3961,7 +3959,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall + has parasite parasitised by RO:0002445 @@ -3980,7 +3978,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - Chris Mungall + RO:0002446 semibiotically interacts with @@ -3996,7 +3994,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. RO:0002447 phosphorylates @@ -4015,8 +4013,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - Chris Mungall - Vasundra Touré + + RO:0002448 molecularly controls directly_regulates_activity_of @@ -4033,8 +4031,8 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly inhibits RO:0002449 molecularly decreases activity of @@ -4052,8 +4050,8 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré + + directly activates RO:0002450 molecularly increases activity of @@ -4070,7 +4068,7 @@ For example, A and B may be gene products and binding of B by A positively regul all dengue disease transmitted by some mosquito A relationship that holds between a disease and organism Add domain and range constraints - Chris Mungall + RO:0002451 transmitted_by transmitted by @@ -4084,7 +4082,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between a disease or an organism and a phenotype - Chris Mungall + RO:0002452 has_symptom has symptom @@ -4096,7 +4094,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) RO:0002453 @@ -4111,7 +4109,7 @@ For example, A and B may be gene products and binding of B by A positively regul X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y - Chris Mungall + RO:0002454 has_host @@ -4128,7 +4126,7 @@ For example, A and B may be gene products and binding of B by A positively regul Bees pollinate Flowers This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - Chris Mungall + is subject of pollination interaction with RO:0002455 @@ -4143,7 +4141,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + has polinator is target of pollination interaction with RO:0002456 @@ -4160,7 +4158,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4175,7 +4173,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of preys on - Chris Mungall + has predator is target of predation interaction with RO:0002458 @@ -4195,7 +4193,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anopheles is a vector for Plasmodium - Chris Mungall + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism RO:0002459 @@ -4209,7 +4207,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002460 has_vector @@ -4222,7 +4220,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target RO:0002461 partner_in @@ -4235,7 +4233,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002462 subject_participant_in @@ -4248,7 +4246,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002463 target_participant_in @@ -4261,7 +4259,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002469 provides_nutrients_for @@ -4274,7 +4272,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + is subject of eating interaction with RO:0002470 @@ -4288,7 +4286,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + eaten by is target of eating interaction with RO:0002471 @@ -4307,7 +4305,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - Chris Mungall + RO:0002473 @@ -4326,7 +4324,7 @@ For example, A and B may be gene products and binding of B by A positively regul ABal nucleus child nucleus of ABa nucleus (in C elegans) c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d - Chris Mungall + This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. RO:0002476 child_nucleus_of @@ -4340,7 +4338,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a hermaphroditic organism - Chris Mungall + RO:0002477 child_nucleus_of_in_hermaphrodite child nucleus of in hermaphrodite @@ -4353,7 +4351,7 @@ For example, A and B may be gene products and binding of B by A positively regul A child nucleus relationship in which the cells are part of a male organism - Chris Mungall + RO:0002478 child_nucleus_of_in_male child nucleus of in male @@ -4367,7 +4365,7 @@ For example, A and B may be gene products and binding of B by A positively regul p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall + RO:0002479 has_part_that_occurs_in @@ -4382,7 +4380,7 @@ For example, A and B may be gene products and binding of B by A positively regul An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y Axiomatization to GO to be added later - Chris Mungall + RO:0002480 ubiquitinates ubiquitinates @@ -4396,7 +4394,7 @@ For example, A and B may be gene products and binding of B by A positively regul See notes for inverse relation - Chris Mungall + RO:0002485 receives_input_from receives input from @@ -4409,7 +4407,7 @@ For example, A and B may be gene products and binding of B by A positively regul This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - Chris Mungall + RO:0002486 sends_output_to sends output to @@ -4423,7 +4421,7 @@ For example, A and B may be gene products and binding of B by A positively regul x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - Chris Mungall + RO:0002494 transformation_of transformation of @@ -4437,7 +4435,7 @@ For example, A and B may be gene products and binding of B by A positively regul x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - Chris Mungall + RO:0002495 immediate_transformation_of @@ -4467,7 +4465,7 @@ For example, A and B may be gene products and binding of B by A positively regul p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002501 @@ -4483,7 +4481,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c - Chris Mungall + has intermediate product RO:0002505 @@ -4500,7 +4498,7 @@ For example, A and B may be gene products and binding of B by A positively regul The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002506 @@ -4522,11 +4520,11 @@ For example, A and B may be gene products and binding of B by A positively regul A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future - Chris Mungall + determined by (system to material entity) - Chris Mungall - Pier Buttigieg + + RO:0002507 determined_by @@ -4540,7 +4538,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of determined by - Chris Mungall + determines (material entity to system) RO:0002508 @@ -4559,7 +4557,7 @@ For example, A and B may be gene products and binding of B by A positively regul s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. - Chris Mungall + RO:0002509 determined_by_part_of @@ -4574,7 +4572,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between two entities that have the property of being sequences or having sequences. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. @@ -4594,7 +4592,7 @@ For example, A and B may be gene products and binding of B by A positively regul Two consecutive DNA residues are sequentially adjacent Two exons on a processed transcript that were previously connected by an intron are adjacent x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002515 @@ -4612,7 +4610,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as a start sequence the start codon for that transcript x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence - Chris Mungall + started by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4629,7 +4627,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has start sequence - Chris Mungall + starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4649,7 +4647,7 @@ For example, A and B may be gene products and binding of B by A positively regul Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence - Chris Mungall + ended by http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4666,7 +4664,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has end sequence - Chris Mungall + ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4684,7 +4682,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. In the SO paper, this was defined as an instance-type relation - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002520 @@ -4701,7 +4699,7 @@ For example, A and B may be gene products and binding of B by A positively regul Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering - Chris Mungall + RO:0002521 is_sequentially_aligned_with @@ -4718,7 +4716,7 @@ For example, A and B may be gene products and binding of B by A positively regul The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y - Chris Mungall + RO:0002522 bounds_sequence_of @@ -4733,7 +4731,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of bounds sequence of - Chris Mungall + RO:0002523 @@ -4751,8 +4749,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x has subsequence y iff all of the sequence parts of x are sequence parts of y - Chris Mungall + x has subsequence y iff all of the sequence parts of y are sequence parts of x + contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -4771,7 +4769,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has subsequence - Chris Mungall + contained by RO:0002525 @@ -4788,8 +4786,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. - Chris Mungall + x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. + RO:0002526 overlaps_sequence_of @@ -4803,8 +4801,8 @@ For example, A and B may be gene products and binding of B by A positively regul - x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. - Chris Mungall + x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + disconnected from RO:0002527 @@ -4820,7 +4818,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of downstream of sequence of - Chris Mungall + RO:0002528 is_upstream_of_sequence_of @@ -4836,7 +4834,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. - Chris Mungall + RO:0002529 is_downstream_of_sequence_of @@ -4852,7 +4850,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y - Chris Mungall + RO:0002530 @@ -4869,7 +4867,7 @@ For example, A and B may be gene products and binding of B by A positively regul A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript inverse of immediately downstream of - Chris Mungall + RO:0002531 is_immediately_upstream_of_sequence_of @@ -4889,7 +4887,7 @@ For example, A and B may be gene products and binding of B by A positively regul Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - Chris Mungall + has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). RO:0002551 @@ -4911,7 +4909,7 @@ For example, A and B may be gene products and binding of B by A positively regul p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. - Chris Mungall + RO:0002552 results_in_ending_of results in ending of @@ -4926,7 +4924,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - Chris Mungall + http://eol.org/schema/terms/hyperparasitoidOf https://en.wikipedia.org/wiki/Hyperparasite RO:0002553 @@ -4944,7 +4942,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of hyperparasite of - Chris Mungall + RO:0002554 has epiparasite has hyperparasite @@ -4961,7 +4959,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + http://en.wikipedia.org/wiki/Allelopathy RO:0002555 @@ -4978,7 +4976,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002556 pathogen_of @@ -4991,7 +4989,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002557 has_pathogen @@ -5005,7 +5003,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + causally influenced by (entity-centric) RO:0002559 @@ -5020,7 +5018,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - Chris Mungall + RO:0002565 @@ -5039,8 +5037,8 @@ For example, A and B may be gene products and binding of B by A positively regul The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - Chris Mungall - Vasundra Touré + + causally influences (entity-centric) RO:0002566 @@ -5057,7 +5055,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between elements of a musculoskeletal system or its analogs. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. RO:0002567 biomechanically_related_to @@ -5071,7 +5069,7 @@ For example, A and B may be gene products and binding of B by A positively regul m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - Chris Mungall + Wikipedia:Antagonist_(muscle) RO:0002568 has_muscle_antagonist @@ -5087,7 +5085,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of branching part of - Chris Mungall + RO:0002569 @@ -5104,7 +5102,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - Chris Mungall + UBERON:cjm This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. RO:0002570 @@ -5121,7 +5119,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - Chris Mungall + GOC:cjm RO:0002571 @@ -5137,7 +5135,7 @@ For example, A and B may be gene products and binding of B by A positively regul s is luminal space of x iff s is lumen_of x and s is an immaterial entity - Chris Mungall + RO:0002572 luminal_space_of @@ -5152,7 +5150,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + RO:0002574 participates_in_a_biotic-biotic_interaction_with @@ -5169,7 +5167,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has skeleton - Chris Mungall + RO:0002576 skeleton_of @@ -5184,7 +5182,7 @@ For example, A and B may be gene products and binding of B by A positively regul p directly regulates q iff p is immediately causally upstream of q and p regulates q. - Chris Mungall + directly regulates (processual) @@ -5205,7 +5203,7 @@ For example, A and B may be gene products and binding of B by A positively regul gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - Chris Mungall + RO:0002584 has_part_structure_that_is_capable_of has part structure that is capable of @@ -5320,7 +5318,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall + RO:0002595 causal_relation_between_material_entity_and_a_process @@ -5723,7 +5721,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. - Vasundra Touré + RO:0003002 represses_expression_of represses expression of @@ -5738,7 +5736,7 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. - Vasundra Touré + RO:0003003 increases_expression_of increases expression of @@ -5883,7 +5881,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:38:20Z RO:0004000 condition_has_genetic_basis_in @@ -5897,7 +5895,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:20Z RO:0004001 has_material_basis_in_gain_of_function_germline_mutation_in @@ -5913,7 +5911,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:37Z RO:0004002 has_material_basis_in_loss_of_function_germline_mutation_in @@ -5927,7 +5925,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:45:54Z RO:0004003 has_material_basis_in_germline_mutation_in @@ -5942,7 +5940,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:07Z RO:0004004 has_material_basis_in_somatic_mutation_in @@ -5957,7 +5955,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:26Z RO:0004005 has_major_susceptibility_factor @@ -5971,7 +5969,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T02:46:57Z RO:0004006 has_partial_material_basis_in_germline_mutation_in @@ -5985,7 +5983,7 @@ Environmental exposures include those imposed by natural environments, experimen p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - cjm + 2018-12-13T11:26:17Z RO:0004007 @@ -6001,7 +5999,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - cjm + 2018-12-13T11:26:32Z RO:0004008 @@ -6012,8 +6010,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6027,7 +6025,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - cjm + 2018-12-13T11:26:56Z RO:0004009 @@ -6038,8 +6036,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -6053,7 +6051,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm + 2017-11-05T02:53:08Z RO:0004010 is_genetic_basis_for_condition @@ -6067,7 +6065,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:55:51Z RO:0004011 is_causal_gain_of_function_germline_mutation_of_in @@ -6082,7 +6080,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:06Z RO:0004012 is_causal_loss_of_function_germline_mutation_of_in @@ -6098,7 +6096,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:56:40Z RO:0004013 is_causal_germline_mutation_in @@ -6114,7 +6112,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. - cjm + 2017-11-05T02:57:07Z RO:0004014 is_causal_somatic_mutation_in @@ -6129,7 +6127,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. - cjm + 2017-11-05T02:57:43Z RO:0004015 is_causal_susceptibility_factor_for @@ -6145,7 +6143,7 @@ Environmental exposures include those imposed by natural environments, experimen Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. - cjm + 2017-11-05T02:58:43Z RO:0004016 is_causal_germline_mutation_partially_giving_rise_to @@ -6160,7 +6158,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:01Z RO:0004017 realizable_has_basis_in @@ -6173,7 +6171,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:20:29Z RO:0004018 is_basis_for_realizable @@ -6188,7 +6186,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2017-11-05T03:26:47Z RO:0004019 disease_has_basis_in @@ -6204,7 +6202,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) - cjm + 2017-11-05T03:29:32Z RO:0004020 disease_has_basis_in_dysfunction_of @@ -6220,7 +6218,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. disease has basis in disruption of (disease to process) - cjm + 2017-11-05T03:37:52Z RO:0004021 disease_has_basis_in_disruption_of @@ -6244,7 +6242,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. - cjm + 2017-11-05T03:46:07Z RO:0004022 disease_has_basis_in_feature @@ -6260,7 +6258,7 @@ Environmental exposures include those imposed by natural environments, experimen Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. - cjm + 2017-11-05T03:50:54Z RO:0004023 causal_relationship_with_disease_as_subject @@ -6277,7 +6275,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and a process where the disease process disrupts the execution of the process. disease causes disruption of (disease to process) - cjm + 2017-11-05T03:51:09Z RO:0004024 disease_causes_disruption_of @@ -6293,7 +6291,7 @@ Environmental exposures include those imposed by natural environments, experimen disease causes dysfunction of (disease to anatomical entity) - cjm + 2017-11-05T03:58:20Z RO:0004025 disease_causes_dysfunction_of @@ -6319,7 +6317,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. - cjm + 2017-11-05T04:06:02Z RO:0004026 disease_has_location @@ -6343,7 +6341,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity - cjm + 2017-12-26T19:37:31Z RO:0004027 disease_has_inflammation_site @@ -6359,7 +6357,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - cjm + 2017-12-26T19:45:49Z RO:0004028 realized_in_response_to_stimulus @@ -6382,7 +6380,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. - cjm + 2017-12-26T19:50:53Z RO:0004029 disease_has_feature @@ -6397,7 +6395,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. - cjm + 2017-12-26T19:58:44Z RO:0004030 disease_arises_from_alteration_in_structure @@ -6411,7 +6409,7 @@ Environmental exposures include those imposed by natural environments, experimen Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - cjm + 2018-01-25T23:20:13Z RO:0004031 enables_subfunction @@ -6425,7 +6423,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:30Z RO:0004032 @@ -6441,7 +6439,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-01-26T23:49:51Z RO:0004033 @@ -6458,7 +6456,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - cjm + 2018-01-26T23:53:14Z RO:0004034 @@ -6476,7 +6474,7 @@ Environmental exposures include those imposed by natural environments, experimen c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - cjm + 2018-01-26T23:53:22Z RO:0004035 @@ -6492,7 +6490,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:05Z RO:0004046 causally_upstream_of_or_within,_negative_effect @@ -6506,7 +6504,7 @@ Environmental exposures include those imposed by natural environments, experimen - cjm + 2018-03-13T23:55:19Z RO:0004047 causally_upstream_of_or_within,_positive_effect @@ -6633,10 +6631,10 @@ Environmental exposures include those imposed by natural environments, experimen An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - Austin Meier - Chris Mungall - David Osumi-Sutherland - Marie Angelique Laporte + + + + RO:0009501 triggered by process realized_in_response_to @@ -6659,7 +6657,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - Vasundra Touré + RO:0011002 regulates_activity_of regulates activity of @@ -6674,7 +6672,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. - Vasundra Touré + RO:0011003 regulates_quantity_of regulates quantity of @@ -6689,7 +6687,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. - Vasundra Touré + RO:0011004 indirectly_regulates_activity_of indirectly regulates activity of @@ -6706,7 +6704,7 @@ Environmental exposures include those imposed by natural environments, experimen The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011007 decreases_by_repression_quantity_of decreases by repression quantity of @@ -6723,7 +6721,7 @@ For example, protein A (transcription factor) indirectly decreases by repression The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. - Vasundra Touré + RO:0011008 increases_by_expression_quantity_of increases by expression quantity of @@ -6738,7 +6736,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly positively regulates the quantity of B. - Vasundra Touré + RO:0011009 directly_positively_regulates_quantity_of directly positively regulates quantity of @@ -6753,7 +6751,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A has an activity that directly negatively regulates the quantity of B. - Vasundra Touré + RO:0011010 directly_negatively_regulates_quantity_of directly negatively regulates quantity of @@ -6768,7 +6766,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. - Vasundra Touré + indirectly activates RO:0011013 indirectly_positively_regulates_activity_of @@ -6785,7 +6783,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. - Vasundra Touré + RO:0011014 destabilizes_quantity_of destabilizes quantity of @@ -6801,7 +6799,7 @@ For example, protein A (transcription factor) indirectly increases by expression AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. - Vasundra Touré + RO:0011015 stabilizes_quantity_of stabilizes quantity of @@ -6814,7 +6812,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. - Vasundra Touré + indirectly inhibits RO:0011016 indirectly_negatively_regulates_activity_of @@ -6828,7 +6826,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. - Vasundra Touré + RO:0011021 directly_regulates_quantity_of directly regulates quantity of @@ -6841,7 +6839,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011022 indirectly_regulates_quantity_of indirectly regulates quantity of @@ -6854,7 +6852,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011023 indirectly_negatively_regulates_quantity_of indirectly negatively regulates quantity of @@ -6867,7 +6865,7 @@ For example, protein A (transcription factor) indirectly increases by expression The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. - Vasundra Touré + RO:0011024 indirectly_positively_regulates_quantity_of indirectly positively regulates quantity of @@ -6880,8 +6878,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is regulated by the small molecule continuant + pg 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -6895,8 +6893,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is activated by the small molecule continuant + pg 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -6910,8 +6908,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant + pg 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -6924,8 +6922,8 @@ For example, protein A (transcription factor) indirectly increases by expression - p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + p acts on population of c iff c' is a collection, has members of type c, and p has participant c + pg 2020-06-08T17:21:33Z RO:0012003 @@ -6941,8 +6939,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process + pg 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -6956,8 +6954,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process + pg 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of @@ -6971,8 +6969,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process + pg 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of @@ -6985,8 +6983,8 @@ For example, protein A (transcription factor) indirectly increases by expression - The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. + pg 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -6999,7 +6997,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + pg 2021-02-26T07:28:29Z RO:0012008 @@ -7016,7 +7014,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + pg 2022-09-26T06:01:01Z RO:0012009 @@ -7032,7 +7030,7 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + pg 2022-09-26T06:06:20Z RO:0012010 @@ -7048,7 +7046,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + pg 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7063,7 +7061,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + pg 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7229,7 +7227,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relation between a group and another group it is part of but does not fully constitute. X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. - Shawn Tan + This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. RO:0015003 subcluster_of @@ -7301,7 +7299,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - http://orcid.org/0000-0002-7463-6306 + 2021-11-05T17:30:44Z RO:0016002 has_disease @@ -7457,7 +7455,7 @@ For example, protein A (transcription factor) indirectly increases by expression This relation groups relations between diseases and any other kind of entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. - cjm + 2018-09-26T00:00:32Z RO:0040035 disease_relationship @@ -7471,7 +7469,7 @@ For example, protein A (transcription factor) indirectly increases by expression p has anatomical participant c iff p has participant c, and c is an anatomical entity - cjm + 2018-09-26T01:08:58Z RO:0040036 results_in_changes_to_anatomical_or_cellular_structure