RO release (#677)

oborel · Feb 19, 2023 · 74a7e92 · 74a7e92
1 parent 703e733
commit 74a7e92
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Showing 41 changed files with 14,659 additions and 14,646 deletions.
diff --git 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
@@ -148,5 +148,5 @@
 
 
 
-<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->
 
diff --git a/ro-base.json b/ro-base.json
diff --git a/ro-base.obo b/ro-base.obo
diff --git a/ro-base.owl b/ro-base.owl
diff --git a/ro.json b/ro.json
diff --git a/ro.obo b/ro.obo
diff --git a/ro.owl b/ro.owl
diff --git a/src/ontology/generated-axioms.owl b/src/ontology/generated-axioms.owl
@@ -148,5 +148,5 @@
 
 
 
-<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->
 
diff --git a/src/ontology/subsets/ro-causal.obo b/src/ontology/subsets/ro-causal.obo
diff --git a/src/ontology/subsets/ro-causal.owl b/src/ontology/subsets/ro-causal.owl
diff --git 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
diff --git a/src/ontology/subsets/ro-developmental.obo b/src/ontology/subsets/ro-developmental.obo
diff --git a/src/ontology/subsets/ro-developmental.owl b/src/ontology/subsets/ro-developmental.owl
diff --git a/src/ontology/subsets/ro-eco.obo b/src/ontology/subsets/ro-eco.obo
diff --git a/src/ontology/subsets/ro-eco.owl b/src/ontology/subsets/ro-eco.owl
diff --git a/src/ontology/subsets/ro-interaction.obo b/src/ontology/subsets/ro-interaction.obo
diff --git a/src/ontology/subsets/ro-interaction.owl b/src/ontology/subsets/ro-interaction.owl
diff --git a/src/ontology/subsets/ro-mereotopology.obo b/src/ontology/subsets/ro-mereotopology.obo
diff --git a/src/ontology/subsets/ro-mereotopology.owl b/src/ontology/subsets/ro-mereotopology.owl
diff --git a/src/ontology/subsets/ro-sequence.obo b/src/ontology/subsets/ro-sequence.obo
diff --git a/src/ontology/subsets/ro-sequence.owl b/src/ontology/subsets/ro-sequence.owl
diff --git a/src/ontology/subsets/ro-time-interval.obo b/src/ontology/subsets/ro-time-interval.obo
diff --git a/src/ontology/subsets/ro-time-interval.owl b/src/ontology/subsets/ro-time-interval.owl
diff --git a/subsets/ro-causal.obo b/subsets/ro-causal.obo
diff --git a/subsets/ro-causal.owl b/subsets/ro-causal.owl
diff --git 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
Original file line number	Diff line number	Diff line change
Expand Up		@@ -148,5 +148,5 @@



		<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
		<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->