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Use gfo light #5

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merged 3 commits into from
Jul 8, 2024
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Use gfo light #5

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2446b3a
Use gfo light
ChristophB Jul 5, 2024
d34ba5e
Update references to gfo-bio and ncit
ChristophB Jul 5, 2024
a753794
Bump up version
ChristophB Jul 5, 2024
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120 changes: 60 additions & 60 deletions cop.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -15,10 +15,10 @@
xmlns:bibo="http://purl.org/ontology/bibo/">

<owl:Ontology rdf:about="https://w3id.org/cop">
<owl:versionIRI rdf:resource="https://w3id.org/cop/release/2024-06-11"/>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2024-06-11</owl:versionInfo>
<dc:modified rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2024-06-11</dc:modified>
<owl:priorVersion rdf:resource="https://w3id.org/cop/release/v0.2.1"/>
<owl:versionIRI rdf:resource="https://w3id.org/cop/release/2024-07-08"/>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2024-07-08</owl:versionInfo>
<dc:modified rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2024-07-08</dc:modified>
<owl:priorVersion rdf:resource="https://w3id.org/cop/release/2026-06-11"/>
<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2020-01-20</dc:created>
<vann:preferredNamespaceURI>https://w3id.org/cop/</vann:preferredNamespaceURI>
<vann:preferredNamespacePrefix>cop</vann:preferredNamespacePrefix>
Expand All @@ -32,9 +32,9 @@
<dc:creator>Konrad Höffner</dc:creator>
<dc:creator>Ralph Schäfermeier</dc:creator>
<terms:license rdf:resource="http://creativecommons.org/licenses/by/4.0/"/>
<terms:references>GFO-Bio: https://www.onto-med.de/ontologies/gfo-bio; https://bioportal.bioontology.org/ontologies/GFO-BIO</terms:references>
<terms:references>General Formal Ontology (GFO): https://onto-med.github.io/GFO; https://www.onto-med.de/ontologies/gfo</terms:references>
<terms:references>National Cancer Institute NCI Thesaurus: https://ncit.nci.nih.gov; https://bioportal.bioontology.org/ontologies/NCIT</terms:references>
<terms:references>GFO-Bio: https://www.onto-med.de/ontologies/gfo-bio; http://onto.eva.mpg.de/ontologies/gfo-bio.owl</terms:references>
<terms:references>General Formal Ontology (GFO) (light version): https://onto-med.github.io/GFO; http://purl.org/ontology/gfo-light</terms:references>
<terms:references>National Cancer Institute NCI Thesaurus: https://ncit.nci.nih.gov; http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl</terms:references>
<foaf:homepage>https://github.com/Onto-Med/COP</foaf:homepage>
<doap:repository rdf:resource="https://github.com/Onto-Med/COP"/>
<bibo:doi rdf:resource="https://zenodo.org/doi/10.5281/zenodo.5205497"/>
Expand Down Expand Up @@ -160,7 +160,7 @@
<!-- https://w3id.org/cop/hasPhenotype -->

<owl:ObjectProperty rdf:about="https://w3id.org/cop/hasPhenotype">
<rdfs:subPropertyOf rdf:resource="https://purl.org/ontology/gfo/hasAttributive"/>
<rdfs:subPropertyOf rdf:resource="https://purl.org/ontology/gfo-light/hasAttributive"/>
<owl:inverseOf rdf:resource="https://w3id.org/cop/phenotypeOf"/>
<rdfs:domain rdf:resource="http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Organism"/>
<rdfs:range rdf:resource="https://w3id.org/cop/Phenotype"/>
Expand Down Expand Up @@ -192,7 +192,7 @@

<owl:ObjectProperty rdf:about="https://w3id.org/cop/hasRepresentationAttribute">
<owl:inverseOf rdf:resource="https://w3id.org/cop/representationAttributeOf"/>
<rdfs:domain rdf:resource="https://purl.org/ontology/gfo/Entity"/>
<rdfs:domain rdf:resource="https://purl.org/ontology/gfo-light/Entity"/>
<rdfs:range rdf:resource="https://w3id.org/cop/RepresentationEntity"/>
</owl:ObjectProperty>

Expand Down Expand Up @@ -220,7 +220,7 @@
<!-- https://w3id.org/cop/phenotypeOf -->

<owl:ObjectProperty rdf:about="https://w3id.org/cop/phenotypeOf">
<rdfs:subPropertyOf rdf:resource="https://purl.org/ontology/gfo/attributiveOf"/>
<rdfs:subPropertyOf rdf:resource="https://purl.org/ontology/gfo-light/attributiveOf"/>
<rdfs:domain rdf:resource="https://w3id.org/cop/Phenotype"/>
<rdfs:range rdf:resource="http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Organism"/>
</owl:ObjectProperty>
Expand All @@ -231,7 +231,7 @@

<owl:ObjectProperty rdf:about="https://w3id.org/cop/realises">
<rdfs:domain rdf:resource="http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C17146"/>
<rdfs:range rdf:resource="https://purl.org/ontology/gfo/Process"/>
<rdfs:range rdf:resource="https://purl.org/ontology/gfo-light/Process"/>
</owl:ObjectProperty>


Expand All @@ -240,7 +240,7 @@

<owl:ObjectProperty rdf:about="https://w3id.org/cop/representationAttributeOf">
<rdfs:domain rdf:resource="https://w3id.org/cop/RepresentationEntity"/>
<rdfs:range rdf:resource="https://purl.org/ontology/gfo/Entity"/>
<rdfs:range rdf:resource="https://purl.org/ontology/gfo-light/Entity"/>
</owl:ObjectProperty>


Expand All @@ -263,38 +263,38 @@



<!-- https://purl.org/ontology/gfo/attributiveOf -->
<!-- https://purl.org/ontology/gfo-light/attributiveOf -->

<owl:ObjectProperty rdf:about="https://purl.org/ontology/gfo/attributiveOf">
<owl:inverseOf rdf:resource="https://purl.org/ontology/gfo/hasAttributive"/>
<rdfs:domain rdf:resource="https://purl.org/ontology/gfo/Attributive"/>
<owl:ObjectProperty rdf:about="https://purl.org/ontology/gfo-light/attributiveOf">
<owl:inverseOf rdf:resource="https://purl.org/ontology/gfo-light/hasAttributive"/>
<rdfs:domain rdf:resource="https://purl.org/ontology/gfo-light/Attributive"/>
</owl:ObjectProperty>



<!-- https://purl.org/ontology/gfo/hasAttributive -->
<!-- https://purl.org/ontology/gfo-light/hasAttributive -->

<owl:ObjectProperty rdf:about="https://purl.org/ontology/gfo/hasAttributive">
<rdfs:range rdf:resource="https://purl.org/ontology/gfo/Attributive"/>
<owl:ObjectProperty rdf:about="https://purl.org/ontology/gfo-light/hasAttributive">
<rdfs:range rdf:resource="https://purl.org/ontology/gfo-light/Attributive"/>
</owl:ObjectProperty>



<!-- https://purl.org/ontology/gfo/instanceOf -->
<!-- https://purl.org/ontology/gfo-light/instanceOf -->

<owl:ObjectProperty rdf:about="https://purl.org/ontology/gfo/instanceOf">
<owl:inverseOf rdf:resource="https://purl.org/ontology/gfo/instantiatedBy"/>
<rdfs:domain rdf:resource="https://purl.org/ontology/gfo/Entity"/>
<rdfs:range rdf:resource="https://purl.org/ontology/gfo/Category"/>
<owl:ObjectProperty rdf:about="https://purl.org/ontology/gfo-light/instanceOf">
<owl:inverseOf rdf:resource="https://purl.org/ontology/gfo-light/instantiatedBy"/>
<rdfs:domain rdf:resource="https://purl.org/ontology/gfo-light/Entity"/>
<rdfs:range rdf:resource="https://purl.org/ontology/gfo-light/Category"/>
</owl:ObjectProperty>



<!-- https://purl.org/ontology/gfo/instantiatedBy -->
<!-- https://purl.org/ontology/gfo-light/instantiatedBy -->

<owl:ObjectProperty rdf:about="https://purl.org/ontology/gfo/instantiatedBy">
<rdfs:domain rdf:resource="https://purl.org/ontology/gfo/Category"/>
<rdfs:range rdf:resource="https://purl.org/ontology/gfo/Entity"/>
<owl:ObjectProperty rdf:about="https://purl.org/ontology/gfo-light/instantiatedBy">
<rdfs:domain rdf:resource="https://purl.org/ontology/gfo-light/Category"/>
<rdfs:range rdf:resource="https://purl.org/ontology/gfo-light/Entity"/>
</owl:ObjectProperty>


Expand Down Expand Up @@ -349,7 +349,7 @@
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="https://w3id.org/cop/realises"/>
<owl:someValuesFrom rdf:resource="https://purl.org/ontology/gfo/Process"/>
<owl:someValuesFrom rdf:resource="https://purl.org/ontology/gfo-light/Process"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment xml:lang="en">A set of coded instructions, which a computer follows in processing data, performing an operation, or solving a logical problem, upon execution of the program.</rdfs:comment>
Expand Down Expand Up @@ -529,7 +529,7 @@
<!-- http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Organism -->

<owl:Class rdf:about="http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Organism">
<rdfs:subClassOf rdf:resource="https://purl.org/ontology/gfo/Individual"/>
<rdfs:subClassOf rdf:resource="https://purl.org/ontology/gfo-light/Individual"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="https://w3id.org/cop/hasPhenotype"/>
Expand Down Expand Up @@ -644,10 +644,10 @@
<!-- https://w3id.org/cop/Phenotype -->

<owl:Class rdf:about="https://w3id.org/cop/Phenotype">
<rdfs:subClassOf rdf:resource="https://purl.org/ontology/gfo/Attributive"/>
<rdfs:subClassOf rdf:resource="https://purl.org/ontology/gfo-light/Attributive"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="https://purl.org/ontology/gfo/instanceOf"/>
<owl:onProperty rdf:resource="https://purl.org/ontology/gfo-light/instanceOf"/>
<owl:someValuesFrom rdf:resource="https://w3id.org/cop/PhenotypeClass"/>
</owl:Restriction>
</rdfs:subClassOf>
Expand Down Expand Up @@ -700,7 +700,7 @@
<!-- https://w3id.org/cop/PhenotypeClass -->

<owl:Class rdf:about="https://w3id.org/cop/PhenotypeClass">
<rdfs:subClassOf rdf:resource="https://purl.org/ontology/gfo/Property"/>
<rdfs:subClassOf rdf:resource="https://purl.org/ontology/gfo-light/Property"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="https://w3id.org/cop/hasRepresentationAttribute"/>
Expand All @@ -709,7 +709,7 @@
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="https://purl.org/ontology/gfo/instantiatedBy"/>
<owl:onProperty rdf:resource="https://purl.org/ontology/gfo-light/instantiatedBy"/>
<owl:allValuesFrom rdf:resource="https://w3id.org/cop/Phenotype"/>
</owl:Restriction>
</rdfs:subClassOf>
Expand Down Expand Up @@ -798,7 +798,7 @@
<!-- https://w3id.org/cop/Phenotyping -->

<owl:Class rdf:about="https://w3id.org/cop/Phenotyping">
<rdfs:subClassOf rdf:resource="https://purl.org/ontology/gfo/Process"/>
<rdfs:subClassOf rdf:resource="https://purl.org/ontology/gfo-light/Process"/>
<rdfs:comment xml:lang="en">Phenotyping is a process of identifying or classifiyng phenotypes. This includes the identifying of individuals with certain phenotypes, determining phenotypes of individuals and deriving further phenotypes.</rdfs:comment>
<rdfs:comment xml:lang="de">Die Phänotypisierung ist ein Prozess der Identifizierung oder Klassifizierung von Phänotypen. Dazu gehören die Identifizierung von Personen mit bestimmten Phänotypen, die Bestimmung von Phänotypen von Personen und die Ableitung weiterer Phänotypen.</rdfs:comment>
<rdfs:label xml:lang="en">Phenotyping</rdfs:label>
Expand Down Expand Up @@ -873,21 +873,21 @@



<!-- https://purl.org/ontology/gfo/Attributive -->
<!-- https://purl.org/ontology/gfo-light/Attributive -->

<owl:Class rdf:about="https://purl.org/ontology/gfo/Attributive">
<rdfs:subClassOf rdf:resource="https://purl.org/ontology/gfo/Individual"/>
<owl:Class rdf:about="https://purl.org/ontology/gfo-light/Attributive">
<rdfs:subClassOf rdf:resource="https://purl.org/ontology/gfo-light/Individual"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="https://purl.org/ontology/gfo/instanceOf"/>
<owl:someValuesFrom rdf:resource="https://purl.org/ontology/gfo/Property"/>
<owl:onProperty rdf:resource="https://purl.org/ontology/gfo-light/instanceOf"/>
<owl:someValuesFrom rdf:resource="https://purl.org/ontology/gfo-light/Property"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="https://purl.org/ontology/gfo/attributiveOf"/>
<owl:onProperty rdf:resource="https://purl.org/ontology/gfo-light/attributiveOf"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
<owl:onClass rdf:resource="https://purl.org/ontology/gfo/Entity"/>
<owl:onClass rdf:resource="https://purl.org/ontology/gfo-light/Entity"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment xml:lang="en">Individuals that are related to other individuals by some kind of dependency relation are called attributives.</rdfs:comment>
Expand All @@ -896,33 +896,33 @@



<!-- https://purl.org/ontology/gfo/Category -->
<!-- https://purl.org/ontology/gfo-light/Category -->

<owl:Class rdf:about="https://purl.org/ontology/gfo/Category">
<rdfs:subClassOf rdf:resource="https://purl.org/ontology/gfo/Entity"/>
<owl:Class rdf:about="https://purl.org/ontology/gfo-light/Category">
<rdfs:subClassOf rdf:resource="https://purl.org/ontology/gfo-light/Entity"/>
<rdfs:comment xml:lang="en">The notion of category covers all abstract entities that can be instantiated by or are predicated of other entities.</rdfs:comment>
<rdfs:label xml:lang="en">Category</rdfs:label>
</owl:Class>



<!-- https://purl.org/ontology/gfo/Entity -->
<!-- https://purl.org/ontology/gfo-light/Entity -->

<owl:Class rdf:about="https://purl.org/ontology/gfo/Entity">
<owl:Class rdf:about="https://purl.org/ontology/gfo-light/Entity">
<rdfs:comment xml:lang="en">Everything which exists is called an entity.</rdfs:comment>
<rdfs:label xml:lang="en">Entity</rdfs:label>
</owl:Class>



<!-- https://purl.org/ontology/gfo/Individual -->
<!-- https://purl.org/ontology/gfo-light/Individual -->

<owl:Class rdf:about="https://purl.org/ontology/gfo/Individual">
<rdfs:subClassOf rdf:resource="https://purl.org/ontology/gfo/Entity"/>
<owl:Class rdf:about="https://purl.org/ontology/gfo-light/Individual">
<rdfs:subClassOf rdf:resource="https://purl.org/ontology/gfo-light/Entity"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="https://purl.org/ontology/gfo/instanceOf"/>
<owl:someValuesFrom rdf:resource="https://purl.org/ontology/gfo/Category"/>
<owl:onProperty rdf:resource="https://purl.org/ontology/gfo-light/instanceOf"/>
<owl:someValuesFrom rdf:resource="https://purl.org/ontology/gfo-light/Category"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment xml:lang="en">Individuals are entities which cannot be further instantiated.</rdfs:comment>
Expand All @@ -931,24 +931,24 @@



<!-- https://purl.org/ontology/gfo/Process -->
<!-- https://purl.org/ontology/gfo-light/Process -->

<owl:Class rdf:about="https://purl.org/ontology/gfo/Process">
<rdfs:subClassOf rdf:resource="https://purl.org/ontology/gfo/Individual"/>
<owl:Class rdf:about="https://purl.org/ontology/gfo-light/Process">
<rdfs:subClassOf rdf:resource="https://purl.org/ontology/gfo-light/Individual"/>
<rdfs:comment xml:lang="en">Processes are concrete individuals that have a temporal extension. Processes are directly in time, they have characteristics which cannot be captured by a collection of time boundaries.</rdfs:comment>
<rdfs:label xml:lang="en">Process</rdfs:label>
</owl:Class>



<!-- https://purl.org/ontology/gfo/Property -->
<!-- https://purl.org/ontology/gfo-light/Property -->

<owl:Class rdf:about="https://purl.org/ontology/gfo/Property">
<rdfs:subClassOf rdf:resource="https://purl.org/ontology/gfo/Category"/>
<owl:Class rdf:about="https://purl.org/ontology/gfo-light/Property">
<rdfs:subClassOf rdf:resource="https://purl.org/ontology/gfo-light/Category"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="https://purl.org/ontology/gfo/instantiatedBy"/>
<owl:allValuesFrom rdf:resource="https://purl.org/ontology/gfo/Attributive"/>
<owl:onProperty rdf:resource="https://purl.org/ontology/gfo-light/instantiatedBy"/>
<owl:allValuesFrom rdf:resource="https://purl.org/ontology/gfo-light/Attributive"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment xml:lang="en">Properties are categories that are instantiated by attributives.</rdfs:comment>
Expand Down