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cob.owl
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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/2025-01-23/cob.owl"/>
<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>2025-01-23</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/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>a core relation that holds between a part and its whole</obo:IAO_0000115>
<rdfs:label>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>a core relation that holds between a whole and its part</obo:IAO_0000115>
<rdfs:label>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>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>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>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/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>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_0000082"/>
<obo:IAO_0000115>The inverse property of is_specified_input_of</obo:IAO_0000115>
<rdfs:label>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_0000082"/>
<obo:IAO_0000115>A relation between a 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>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_0000082"/>
<obo:IAO_0000115>The inverse property of is_specified_output_of</obo:IAO_0000115>
<rdfs:label>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_0000082"/>
<obo:IAO_0000115>A relation between a 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>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>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>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>Inverse of characteristic_of</obo:IAO_0000115>
<rdfs:label>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>a relation between a continuant and a process, in which the continuant is somehow involved in the process</obo:IAO_0000115>
<rdfs:label>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>a relation between a process and a continuant, in which the continuant is somehow involved in the process</obo:IAO_0000115>
<rdfs:label>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>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>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>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>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>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>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>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>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>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>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>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>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>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>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>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>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>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">
<rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<rdfs:label>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>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>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>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>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>function</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000040 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000040">
<rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<obo:IAO_0000116>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>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:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<rdfs:label>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>Some people may be uncomfortable calling every proton an atomic nucleus</obo:IAO_0000116>
<obo:IAO_0000116>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/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>CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.</obo:IAO_0000116>
<obo:IAO_0000116>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/COB_0000005 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000005">
<rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<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:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<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">
<rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<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>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>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>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:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<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">
<rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<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:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<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">
<rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<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:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<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:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<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:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<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/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>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>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>environmental process</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>This is the same as GO molecular function</obo:IAO_0000116>
<rdfs:label>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>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>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>
<!-- http://purl.obolibrary.org/obo/GO_0110165 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0110165">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0005575"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
<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 part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.</obo:IAO_0000115>
<obo:IAO_0000116>Components are larger than individual macromolecular entities. It is tricky to define distinction between 'cell component' and 'macromolecular entity', e.g. ribosome. We would like to exclude most protein complexes.</obo:IAO_0000116>
<obo:IAO_0000116>Overlaps with some cellular components from GO</obo:IAO_0000116>
<rdfs:label>cellular anatomical entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000005 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000005">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000033"/>
<obo:IAO_0000115>A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.</obo:IAO_0000115>
<rdfs:label>objective specification</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000007 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000007">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000033"/>
<obo:IAO_0000115>A directive information entity that describes an action the bearer will take.</obo:IAO_0000115>
<rdfs:label>action specification</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000027 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000027">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000115>An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.</obo:IAO_0000115>
<rdfs:label>data item</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000030 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000030">
<rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<obo:IAO_0000115>A generically dependent continuant that is about some thing.</obo:IAO_0000115>
<obo:IAO_0000116>Pier: 'data, information or knowledge'. OR 'representation'</obo:IAO_0000116>
<rdfs:label>information content entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000033 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000033">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000115>An information content entity whose concretizations indicate to their bearer how to realize them in a process.</obo:IAO_0000115>
<rdfs:label>directive information entity</rdfs:label>
</owl:Class>