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core.owl edit: add process to domain to range of concretizes (#738)
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* add process (BFO_0000015) to domain of concretizes

* update definition of concretizes to include process

* add process (BFO_0000015) to range of is concretized as

* update definition of is concretized as to include process

* change dc:license annotation to dcterms:license

* update core.owl

* revert core.owl

* delete duplicate xmlns:terms="http://purl.org/dc/terms/"

---------

Co-authored-by: Anita Caron <anitac@ebi.ac.uk>
Co-authored-by: shawntanzk <tzks@novonordisk.com>
Co-authored-by: Chris Mungall <cjm@berkeleybop.org>
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@wdduncan @shawntanzknn @cmungall
4 people authored Aug 13, 2024
1 parent 658becc commit f1d66ab
Showing 1 changed file with 112 additions and 13 deletions.
125 changes: 112 additions & 13 deletions src/ontology/components/core.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,12 @@



<!-- http://purl.obolibrary.org/obo/IAO_0000115 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115"/>



<!-- http://purl.obolibrary.org/obo/IAO_0000116 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116"/>
Expand Down Expand Up @@ -78,9 +84,9 @@



<!-- http://purl.org/dc/terms/license -->
<!-- http://purl.org/dc/elements/1.1/license -->

<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/license"/>
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/license"/>



Expand All @@ -90,6 +96,12 @@



<!-- http://purl.org/dc/terms/license -->

<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/license"/>



<!-- http://xmlns.com/foaf/0.1/homepage -->

<owl:AnnotationProperty rdf:about="http://xmlns.com/foaf/0.1/homepage"/>
Expand Down Expand Up @@ -301,10 +313,17 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000058">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000059"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<rdfs:range>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000015"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000020"/>
</owl:unionOf>
</owl:Class>
</rdfs:range>
<obo:IAO_0000112 xml:lang="en">A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.</obo:IAO_0000115>
<obo:IAO_0000115 xml:lang="en">A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes.</obo:IAO_0000115>
<rdfs:label xml:lang="en">is concretized as</rdfs:label>
</owl:ObjectProperty>

Expand All @@ -313,11 +332,18 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
<!-- http://purl.obolibrary.org/obo/RO_0000059 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000059">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000015"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000020"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<obo:IAO_0000112 xml:lang="en">A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.</obo:IAO_0000115>
<obo:IAO_0000115 xml:lang="en">A relationship between a specifically dependent continuant or process and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant.</obo:IAO_0000115>
<rdfs:label xml:lang="en">concretizes</rdfs:label>
</owl:ObjectProperty>

Expand Down Expand Up @@ -524,13 +550,13 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
</owl:ObjectProperty>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0001025"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#range"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#domain"/>
<owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<obo:IAO_0000116>This is redundant with the more specific &apos;independent and not spatial region&apos; constraint. We leave in the redundant axiom for use with reasoners that do not use negation.</obo:IAO_0000116>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0001025"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#domain"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#range"/>
<owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<obo:IAO_0000116>This is redundant with the more specific &apos;independent and not spatial region&apos; constraint. We leave in the redundant axiom for use with reasoners that do not use negation.</obo:IAO_0000116>
</owl:Axiom>
Expand Down Expand Up @@ -633,27 +659,99 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.

<!-- http://purl.obolibrary.org/obo/BFO_0000002 -->

<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000002">
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000002">
<owl:disjointWith>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
</owl:Restriction>
</owl:disjointWith>
</rdf:Description>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/BFO_0000003 -->

<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000003">
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000003">
<owl:disjointWith>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
</owl:Restriction>
</owl:disjointWith>
</rdf:Description>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/BFO_0000004 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000004"/>



<!-- http://purl.obolibrary.org/obo/BFO_0000006 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000006"/>



<!-- http://purl.obolibrary.org/obo/BFO_0000015 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000015"/>



<!-- http://purl.obolibrary.org/obo/BFO_0000016 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000016"/>



<!-- http://purl.obolibrary.org/obo/BFO_0000017 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000017"/>



<!-- http://purl.obolibrary.org/obo/BFO_0000019 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000019"/>



<!-- http://purl.obolibrary.org/obo/BFO_0000020 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000020"/>



<!-- http://purl.obolibrary.org/obo/BFO_0000023 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000023"/>



<!-- http://purl.obolibrary.org/obo/BFO_0000031 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000031"/>



<!-- http://purl.obolibrary.org/obo/BFO_0000034 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000034"/>



<!-- http://purl.obolibrary.org/obo/BFO_0000040 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000040"/>



<!-- http://purl.obolibrary.org/obo/BFO_0000141 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000141"/>



Expand Down Expand Up @@ -847,4 +945,5 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.



<!-- Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.25.2023-02-15T19:15:49Z) https://github.com/owlcs/owlapi -->

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