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cob-base.owl
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<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/cob/cob-base.owl#"
xml:base="http://purl.obolibrary.org/obo/cob/cob-base.owl"
xmlns:dc="http://purl.org/dc/elements/1.1/"
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/cob-base.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2024-11-14/cob-base.owl"/>
<dc:type rdf:resource="http://purl.obolibrary.org/obo/IAO_8000001"/>
<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>2024-11-14</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>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>term replaced by</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.org/dc/elements/1.1/type -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/type"/>
<!-- 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_0000051 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000051"/>
<!-- http://purl.obolibrary.org/obo/BFO_0000055 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000055"/>
<!-- http://purl.obolibrary.org/obo/COB_0000016 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/COB_0000016">
<rdfs:label>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>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>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>intended plan process type</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000293 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000293"/>
<!-- http://purl.obolibrary.org/obo/OBI_0000299 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000299"/>
<!-- http://purl.obolibrary.org/obo/OBI_0000312 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000312"/>
<!-- http://purl.obolibrary.org/obo/RO_0000057 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000057"/>
<!-- http://purl.obolibrary.org/obo/RO_0002215 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002215"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Data properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/COB_0000511 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/COB_0000511">
<rdfs:label>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>Number of protons in an atomic nucleus</obo:IAO_0000115>
<rdfs:label>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>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>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"/>
<!-- http://purl.obolibrary.org/obo/BFO_0000040 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000040"/>
<!-- http://purl.obolibrary.org/obo/CHEBI_33252 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_33252"/>
<!-- http://purl.obolibrary.org/obo/CHEBI_36342 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_36342">
<owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/COB_0000011"/>
</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>A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it.</obo:IAO_0000115>
<obo:IAO_0000116>This atom is closely related to ChEBI's atom, but not exactly equivalent to.</obo:IAO_0000116>
<rdfs:label>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>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>This molecular entity is different than ChEBI's 'molecular entity'.</obo:IAO_0000116>
<obo:IAO_0000116>We would like to have cardinality restrictions on the logic, but there are some technical limitations.</obo:IAO_0000116>
<rdfs:label>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_0000022 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000022">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000115>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>'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'.</obo:IAO_0000116>
<obo:IAO_0000116>Includes virus - we will later have a class for cellular organisms.</obo:IAO_0000116>
<rdfs:label>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>A material entity processed by human activity with an intent to produce it.</obo:IAO_0000115>
<obo:IAO_0000116>In the COB 2024 workshop there was much disagreement about this label.</obo:IAO_0000116>
<rdfs:label>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>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>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>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>A complex of two or more molecular entities that are not covalently bound.</obo:IAO_0000115>
<rdfs:label>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>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>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>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>A planned process that intends to output material entities from input material entities</obo:IAO_0000115>
<rdfs:label>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>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>A process during which an organism comes into contact with another entity.</obo:IAO_0000115>
<rdfs:label>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>A processed material entity which is designed to be capable of a process.</obo:IAO_0000115>
<rdfs:label>device</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000260 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000260"/>
</rdf:RDF>
<!-- Generated by the OWL API (version 4.5.29) https://github.com/owlcs/owlapi -->