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cob-root.owl
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1407 lines (907 loc) · 63.5 KB
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<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/cob.owl#"
xml:base="http://purl.obolibrary.org/obo/cob.owl"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
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"/>
<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"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0001-9189-9661"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0001-9625-1899"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0001-9990-8331"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0002-1604-3078"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0002-2999-0103"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0002-7356-1779"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0002-8457-6693"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0002-8688-6599"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0002-8844-9165"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0003-1640-9989"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0003-4423-4370"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0003-4871-5569"/>
<terms:contributor rdf:resource="https://orcid.org/0009-0009-4008-3801"/>
<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:Ontology>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/IAO_0000115 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
<rdfs:label>definition</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000116 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116">
<rdfs:label xml:lang="en">editor note</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0100001 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0100001">
<rdfs:label xml:lang="en">term replaced by</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.org/dc/terms/contributor -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/contributor"/>
<!-- http://purl.org/dc/terms/description -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/description"/>
<!-- http://purl.org/dc/terms/license -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/license"/>
<!-- http://purl.org/dc/terms/title -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/title"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Object Properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/BFO_0000050 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000050">
<obo:IAO_0000115 xml:lang="en">a core relation that holds between a part and its whole</obo:IAO_0000115>
<rdfs:label xml:lang="en">part of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000051 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000051">
<obo:IAO_0000115 xml:lang="en">a core relation that holds between a whole and its part</obo:IAO_0000115>
<rdfs:label xml:lang="en">has part</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000055 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000055">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<obo:IAO_0000115 xml:lang="en">Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process</obo:IAO_0000115>
<rdfs:label xml:lang="en">realizes</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/COB_0000016 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/COB_0000016">
<rdfs:label xml:lang="en">executed by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/COB_0000081 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/COB_0000081">
<rdfs:label xml:lang="en">intended to realize</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/COB_0000084 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/COB_0000084">
<rdfs:label xml:lang="en">has plan</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/COB_0000085 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/COB_0000085">
<rdfs:label xml:lang="en">intended plan process type</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000136 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000136">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:label xml:lang="en">is about</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000293 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000293">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
<obo:IAO_0000115>The inverse property of is specified input of</obo:IAO_0000115>
<rdfs:label xml:lang="en">has specified input</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000295 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000295">
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
<obo:IAO_0000115>A relation between a completely executed planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.</obo:IAO_0000115>
<rdfs:label xml:lang="en">is specified input of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000299 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000299">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
<obo:IAO_0000115>The inverse property of is specified output of</obo:IAO_0000115>
<rdfs:label xml:lang="en">has specified output</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000312 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000312">
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
<obo:IAO_0000115 xml:lang="en">A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.</obo:IAO_0000115>
<rdfs:label xml:lang="en">is specified output of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000052 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000052">
<obo:IAO_0000115 xml:lang="en">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.</obo:IAO_0000115>
<rdfs:label xml:lang="en">characteristic of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000053 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000053">
<obo:IAO_0000115 xml:lang="en">Inverse of characteristic_of</obo:IAO_0000115>
<rdfs:label xml:lang="en">has characteristic</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000056 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000056">
<obo:IAO_0000115 xml:lang="en">a relation between a continuant and a process, in which the continuant is somehow involved in the process</obo:IAO_0000115>
<rdfs:label xml:lang="en">participates in</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000057 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000057">
<obo:IAO_0000115 xml:lang="en">a relation between a process and a continuant, in which the continuant is somehow involved in the process</obo:IAO_0000115>
<rdfs:label xml:lang="en">has participant</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000058 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000058">
<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>
<rdfs:label xml:lang="en">is concretized as</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000059 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000059">
<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>
<rdfs:label xml:lang="en">concretizes</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0001000 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0001000">
<obo:IAO_0000115 xml:lang="en">a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity</obo:IAO_0000115>
<rdfs:label xml:lang="en">derives from</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0001015 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0001015">
<obo:IAO_0000115 xml:lang="en">a relation between two independent continuants, the location and the target, in which the target is entirely within the location</obo:IAO_0000115>
<rdfs:label xml:lang="en">location of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0001025 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0001025">
<obo:IAO_0000115 xml:lang="en">a relation between two independent continuants, the target and the location, in which the target is entirely within the location</obo:IAO_0000115>
<rdfs:label xml:lang="en">located in</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002215 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002215">
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<obo:IAO_0000115>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.</obo:IAO_0000115>
<rdfs:label xml:lang="en">capable of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002219 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002219">
<obo:IAO_0000115>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</obo:IAO_0000115>
<rdfs:label xml:lang="en">surrounded by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002221 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002221">
<obo:IAO_0000115>inverse of surrounded by</obo:IAO_0000115>
<rdfs:label xml:lang="en">surrounds</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002233 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002233">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<obo:IAO_0000115>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.</obo:IAO_0000115>
<rdfs:label xml:lang="en">has input</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002234 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002234">
<obo:IAO_0000115>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.</obo:IAO_0000115>
<rdfs:label xml:lang="en">has output</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002333 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002333">
<obo:IAO_0000115>inverse of enables</obo:IAO_0000115>
<rdfs:label xml:lang="en">enabled by</rdfs:label>
</owl:ObjectProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Data properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/COB_0000511 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/COB_0000511">
<rdfs:label xml:lang="en">has quantity</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/COB_0000800 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/COB_0000800">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/COB_0000011"/>
<obo:IAO_0000115 xml:lang="en">Number of protons in an atomic nucleus</obo:IAO_0000115>
<rdfs:label xml:lang="en">has atomic number</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/COB_0000801 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/COB_0000801">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<rdfs:label xml:lang="en">has number of atomic nuclei</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/COB_0000803 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/COB_0000803">
<rdfs:label xml:lang="en">has inchi string</rdfs:label>
</owl:DatatypeProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/BFO_0000015 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000015">
<rdfs:label xml:lang="en">process</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000016 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000016">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<rdfs:label xml:lang="en">disposition</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000017 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000017">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000502"/>
<rdfs:label xml:lang="en">realizable entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000023 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000023">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<rdfs:label xml:lang="en">role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000029 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000029">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000141"/>
<rdfs:label xml:lang="en">site</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000034 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000034">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
<rdfs:label xml:lang="en">function</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000040 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000040">
<obo:IAO_0000116 xml:lang="en">Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.</obo:IAO_0000116>
<rdfs:label xml:lang="en">material entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000141 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000141">
<rdfs:label xml:lang="en">immaterial entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_10545 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_10545">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_36342"/>
<obo:IAO_0000115>Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV.</obo:IAO_0000115>
<rdfs:label>electron</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_24636 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_24636">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_36342"/>
<obo:IAO_0000115>Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u.</obo:IAO_0000115>
<rdfs:label>proton</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_30222 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_30222">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_36342"/>
<obo:IAO_0000115>Nuclear particle of zero charge, spin 1/2 and rest mass of 1.008664904(14) u.</obo:IAO_0000115>
<rdfs:label>neutron</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_33252 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_33252">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_36342"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_24636"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A nucleus is the positively charged central portion of an atom, excluding the orbital electrons.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Some people may be uncomfortable calling every proton an atomic nucleus</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">This is equivalent to CHEBI:33252</obo:IAO_0000116>
<rdfs:label>atomic nucleus</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_36342 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_36342">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/COB_0000011"/>
<obo:IAO_0000115>A particle smaller than an atom.</obo:IAO_0000115>
<rdfs:label>subatomic particle</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CLO_0000001 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CLO_0000001">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CL_0000010"/>
<obo:IAO_0000115 xml:lang="en">A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture</obo:IAO_0000115>
<rdfs:label xml:lang="en">cell line cell</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CL_0000000 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_0000000">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
<obo:IAO_0000115>A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism.</obo:IAO_0000116>
<rdfs:label>cell</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CL_0000010 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_0000010">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CL_0000578"/>
<obo:IAO_0000115 xml:lang="en">A cell in vitro that is or has been maintained or propagated as part of a cell culture.</obo:IAO_0000115>
<rdfs:label xml:lang="en">cultured cell</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CL_0000578 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_0000578">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CL_0001034"/>
<obo:IAO_0000115 xml:lang="en">A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.</obo:IAO_0000115>
<rdfs:label xml:lang="en">experimentally modified cell in vitro</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CL_0001034 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_0001034">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CL_0000000"/>
<obo:IAO_0000115>A cell that is maintained or propagated in a controlled artificial environment for use in an investigation.</obo:IAO_0000115>
<rdfs:label>cell in vitro</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0000005 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000005">
<rdfs:label>obsolete elementary charge</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0000011 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000011">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33252"/>
</owl:Restriction>
</rdfs:subClassOf>
<owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/COB_0000013"/>
<obo:IAO_0000115 xml:lang="en">A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">This atom is closely related to ChEBI's atom, but not exactly equivalent to.</obo:IAO_0000116>
<rdfs:label xml:lang="en">atom</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0000013 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000013">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/COB_0000011"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115 xml:lang="en">A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">This molecular entity is different than ChEBI's 'molecular entity'.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">We would like to have cardinality restrictions on the logic, but there are some technical limitations.</obo:IAO_0000116>
<rdfs:label xml:lang="en">molecule</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0000014 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000014">
<rdfs:label>obsolete macromolecular entity</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0000020 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000020">
<obo:IAO_0100001 rdf:resource="http://purl.obolibrary.org/obo/GO_0110165"/>
<rdfs:label>obsolete subcellular structure</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0000021 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000021">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
<obo:IAO_0000115 xml:lang="en">A part of a multicellular organism that is a collection of cell components that are not all contained in one cell.</obo:IAO_0000115>
<rdfs:label xml:lang="en">gross anatomical part</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0000022 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000022">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
<obo:IAO_0000115 xml:lang="en">A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Includes virus - we will later have a class for cellular organisms.</obo:IAO_0000116>
<rdfs:label xml:lang="en">organism</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0000026 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000026">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/COB_0000110"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115 xml:lang="en">A material entity processed by human activity with an intent to produce it.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">In the COB 2024 workshop there was much disagreement about this label.</obo:IAO_0000116>
<rdfs:label xml:lang="en">processed material entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0000032 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000032">
<rdfs:label>obsolete geographical location</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0000035 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000035">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000082"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000260"/>
</owl:Restriction>
</rdfs:subClassOf>
<owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/COB_0000083"/>
<rdfs:label xml:lang="en">completely executed planned process</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0000049 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000049">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000013"/>
<obo:IAO_0000115 xml:lang="en">A molecule that consists of nucleotides (unmodified nucleotide residues and/or modified nucleotide residues) linked by phosphodiester bonds or derivatives of such bonds.</obo:IAO_0000115>
<rdfs:label xml:lang="en">nucleic acid chain</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0000056 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000056">
<obo:IAO_0100001 rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000466"/>
<rdfs:label>obsolete immaterial anatomical entity</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0000073 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000073">
<rdfs:label>obsolete gene product</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0000077 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000077">
<obo:IAO_0100001 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000007"/>
<rdfs:label>obsolete action specification</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0000080 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000080">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/COB_0000013"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115 xml:lang="en">A complex of two or more molecules that are not covalently bound.</obo:IAO_0000115>
<rdfs:label xml:lang="en">complex of molecules</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0000082 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000082">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<obo:IAO_0000115 xml:lang="en">A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification.</obo:IAO_0000115>
<rdfs:label xml:lang="en">planned process</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0000083 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000083">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000082"/>
<rdfs:label xml:lang="en">failed planned process</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0000110 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000110">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000115 xml:lang="en">A completely executed planned process that intends to output material entities from input material entities</obo:IAO_0000115>
<rdfs:label xml:lang="en">material processing</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0000116 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000116">
<rdfs:label>obsolete cellular membrane</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0000122 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000122">
<rdfs:label>obsolete physical information carrier</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0000502 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000502">
<rdfs:label xml:lang="en">characteristic</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0001000 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0001000">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115 xml:lang="en">A process during which an organism comes into contact with another entity.</obo:IAO_0000115>
<rdfs:label xml:lang="en">exposure of organism</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/COB_0001300 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0001300">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000026"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002215"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115 xml:lang="en">A processed material entity which is designed to be capable of a process.</obo:IAO_0000115>
<rdfs:label xml:lang="en">device</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/DRON_00000005 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/DRON_00000005">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000026"/>
<obo:IAO_0000115 xml:lang="en">a material entity (1) containing at least one scattered molecular aggregate as part that is the bearer of an active ingredient role and (2) that is itself the bearer of a clinical drug role</obo:IAO_0000115>
<rdfs:label xml:lang="en">drug product</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ENVO_01000813 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/ENVO_01000813">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000115>A material part of an astronomical body.</obo:IAO_0000115>
<rdfs:label xml:lang="en">geophysical entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ENVO_01001110 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/ENVO_01001110">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000115>An environmental system which includes both living and non-living components.</obo:IAO_0000115>
<rdfs:label xml:lang="en">ecosystem</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ENVO_02500000 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/ENVO_02500000">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<obo:IAO_0000115>A process in which includes the components of an environmental system as participants.</obo:IAO_0000115>
<rdfs:label xml:lang="en">environmental system process</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/FOODON_00002403 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/FOODON_00002403">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000115 xml:lang="en">Any substance that can be consumed by an organism to satisfy nutritional or other health needs, or to provide a social or organoleptic food experience</obo:IAO_0000115>
<rdfs:label xml:lang="en">food material</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GO_0003674 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0003674">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<obo:IAO_0000115>A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">This is the same as GO molecular function</obo:IAO_0000116>
<rdfs:label xml:lang="en">gene product or complex activity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GO_0005575 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0005575">
<owl:equivalentClass>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GO_0032991"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GO_0044423"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GO_0110165"/>
</owl:unionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000115>A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).</obo:IAO_0000115>
<rdfs:label>cellular_component</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GO_0008150 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0008150">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0003674"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.</obo:IAO_0000115>
<rdfs:label xml:lang="en">biological process</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GO_0032991 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0032991">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000080"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0005575"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PR_000000001"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">This is not covalently bonded, which conflicts with changes to the parent definition.</obo:IAO_0000116>
<rdfs:label>protein-containing complex</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GO_0044423 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0044423">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0005575"/>
<obo:IAO_0000115>Any constituent part of a virion, a complete fully infectious extracellular virus particle.</obo:IAO_0000115>
<rdfs:label>virion component</rdfs:label>
</owl:Class>