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Add NCBITaxon:virus as a subclass of organism #313

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4 changes: 2 additions & 2 deletions cob-base.owl
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Expand Up @@ -10,7 +10,7 @@
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:terms="http://purl.org/dc/terms/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob/cob-base.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2025-12-12/cob-base.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2025-12-15/cob-base.owl"/>
<dc:type rdf:resource="http://purl.obolibrary.org/obo/IAO_8000001"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0001-5139-5557"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0001-5809-9523"/>
Expand All @@ -32,7 +32,7 @@
<terms:description xml:lang="en">COB brings together key terms from a wide range of OBO projects to improve interoperability.</terms:description>
<terms:license rdf:resource="https://creativecommons.org/publicdomain/zero/1.0/"/>
<terms:title xml:lang="en">Core Ontology for Biology and Biomedicine</terms:title>
<owl:versionInfo>2025-12-12</owl:versionInfo>
<owl:versionInfo>2025-12-15</owl:versionInfo>
</owl:Ontology>


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13 changes: 11 additions & 2 deletions cob-root.owl
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Expand Up @@ -9,7 +9,7 @@
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:terms="http://purl.org/dc/terms/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2025-12-12/cob-root.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2025-12-15/cob-root.owl"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0001-5139-5557"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0001-5809-9523"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0001-8910-9851"/>
Expand All @@ -30,7 +30,7 @@
<terms:description xml:lang="en">COB brings together key terms from a wide range of OBO projects to improve interoperability.</terms:description>
<terms:license rdf:resource="https://creativecommons.org/publicdomain/zero/1.0/"/>
<terms:title xml:lang="en">Core Ontology for Biology and Biomedicine</terms:title>
<owl:versionInfo>2025-12-12</owl:versionInfo>
<owl:versionInfo>2025-12-15</owl:versionInfo>
</owl:Ontology>


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<!-- http://purl.obolibrary.org/obo/NCBITaxon_10239 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10239">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
<rdfs:label xml:lang="en">virus</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/NCBITaxon_131567 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_131567">
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13 changes: 11 additions & 2 deletions cob.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:terms="http://purl.org/dc/terms/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2025-12-12/cob.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2025-12-15/cob.owl"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0001-5139-5557"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0001-5809-9523"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0001-8910-9851"/>
Expand All @@ -30,7 +30,7 @@
<terms:description xml:lang="en">COB brings together key terms from a wide range of OBO projects to improve interoperability.</terms:description>
<terms:license rdf:resource="https://creativecommons.org/publicdomain/zero/1.0/"/>
<terms:title xml:lang="en">Core Ontology for Biology and Biomedicine</terms:title>
<owl:versionInfo>2025-12-12</owl:versionInfo>
<owl:versionInfo>2025-12-15</owl:versionInfo>
</owl:Ontology>


Expand Down Expand Up @@ -1038,6 +1038,15 @@



<!-- http://purl.obolibrary.org/obo/NCBITaxon_10239 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10239">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
<rdfs:label xml:lang="en">virus</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/NCBITaxon_131567 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_131567">
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1 change: 1 addition & 0 deletions cob.tsv
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Expand Up @@ -53,6 +53,7 @@ IAO:0000033 directive information entity An information content entity whose con
IAO:0000104 plan specification A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. IAO:0000033 directive information entity
IAO:0000109 measurement datum A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. IAO:0000027 data item
MOP:0000543 physico-chemical process A process in which at least one of the participants is a molecule. BFO:0000015 process
NCBITaxon:10239 virus COB:0000022 organism
NCBITaxon:131567 cellular organism COB:0000022 organism
OBI:0000066 investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). COB:0000035 completely executed planned process
OBI:0000070 assay A planned process that has the objective to produce information about a material entity (the evaluant) by examining it. COB:0000035 completely executed planned process (OBI:0000293 some BFO:0000040) and (OBI:0000299 some IAO:0000027) (has specified input some material entity) and (has specified output some data item)
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1 change: 1 addition & 0 deletions src/ontology/cob-edit.tsv
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Expand Up @@ -57,6 +57,7 @@ UBERON:0000465 material anatomical entity owl:Class Anatomical entity that has m
PO:0025131 plant anatomical entity owl:Class An anatomical entity that is or was part of a plant. ROOT GROUP: CHILD material anatomical entity
COB:0000022 organism owl:Class A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome Includes virus - we will later have a class for cellular organisms.|'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'. BASE material entity
NCBITaxon:131567 cellular organism owl:Class FULL unmodified & in scope organism
NCBITaxon:10239 virus owl:Class FULL in scope & only label modified organism
PCO:0000000 collection of organisms owl:Class A material entity that consists of two or more organisms, viruses, or viroids. FULL unmodified & in scope material entity 'has material part' some organism
ENVO:01000813 geophysical entity owl:Class A material part of an astronomical body. FULL in scope & only label modified material entity ENVO calls this 'astronomical body part'
ENVO:01001110 ecosystem owl:Class An environmental system which includes both living and non-living components. FULL unmodified & in scope material entity
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