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Merged
jamesaoverton merged 7 commits into from
Feb 20, 2025
Merged

Patch language tags #295

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febe4e5
Rework product creation steps
jamesaoverton Feb 14, 2025
07012d6
Rework language tags, add crosscheck test
jamesaoverton Feb 14, 2025
c1e78f1
Use spaces instead of tabs
jamesaoverton Feb 14, 2025
8ed61e9
RO import should include BFO ObjectProperties
jamesaoverton Feb 14, 2025
82a2334
Replace tabs with spaces, again
jamesaoverton Feb 18, 2025
82186e0
Remove underscores from OBI definitions
jamesaoverton Feb 18, 2025
29440b8
Improve cob.Makefile and rebuild
jamesaoverton Feb 18, 2025
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110 changes: 60 additions & 50 deletions cob-base.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -10,12 +10,12 @@
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:terms="http://purl.org/dc/terms/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob/cob-base.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2025-01-23/cob-base.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2025-02-18/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>2025-01-23</owl:versionInfo>
<owl:versionInfo>2025-02-18</owl:versionInfo>
</owl:Ontology>


Expand All @@ -33,25 +33,19 @@

<!-- 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>
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115"/>



<!-- 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>
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116"/>



<!-- 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>
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0100001"/>



Expand Down Expand Up @@ -105,31 +99,31 @@
<!-- http://purl.obolibrary.org/obo/COB_0000016 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/COB_0000016">
<rdfs:label>executed by</rdfs:label>
<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>intended to realize</rdfs:label>
<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>has plan</rdfs:label>
<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>intended plan process type</rdfs:label>
<rdfs:label xml:lang="en">intended plan process type</rdfs:label>
</owl:ObjectProperty>


Expand Down Expand Up @@ -178,7 +172,7 @@
<!-- http://purl.obolibrary.org/obo/COB_0000511 -->

<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/COB_0000511">
<rdfs:label>has quantity</rdfs:label>
<rdfs:label xml:lang="en">has quantity</rdfs:label>
</owl:DatatypeProperty>


Expand All @@ -187,8 +181,8 @@

<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>
<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>


Expand All @@ -197,15 +191,15 @@

<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>
<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>has inchi string</rdfs:label>
<rdfs:label xml:lang="en">has inchi string</rdfs:label>
</owl:DatatypeProperty>


Expand Down Expand Up @@ -267,9 +261,9 @@
</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&apos;s atom, but not exactly equivalent to.</obo:IAO_0000116>
<rdfs:label>atom</rdfs:label>
<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&apos;s atom, but not exactly equivalent to.</obo:IAO_0000116>
<rdfs:label xml:lang="en">atom</rdfs:label>
</owl:Class>


Expand All @@ -284,10 +278,10 @@
<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&apos;s &apos;molecular entity&apos;.</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>
<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&apos;s &apos;molecular entity&apos;.</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>


Expand All @@ -311,14 +305,24 @@



<!-- 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/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>&apos;Maximal functionally integrated unit&apos; is intended to express unity, which Barry considers synonymous with BFO &apos;object&apos;.</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>
<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">&apos;Maximal functionally integrated unit&apos; is intended to express unity, which Barry considers synonymous with BFO &apos;object&apos;.</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>


Expand All @@ -333,9 +337,9 @@
<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>
<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>


Expand All @@ -360,7 +364,7 @@
</owl:Restriction>
</rdfs:subClassOf>
<owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/COB_0000083"/>
<rdfs:label>completely executed planned process</rdfs:label>
<rdfs:label xml:lang="en">completely executed planned process</rdfs:label>
</owl:Class>


Expand All @@ -369,8 +373,8 @@

<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>
<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>


Expand Down Expand Up @@ -414,8 +418,8 @@
<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>
<obo:IAO_0000115 xml:lang="en">A complex of two or more molecular entities that are not covalently bound.</obo:IAO_0000115>
<rdfs:label xml:lang="en">complex of molecules</rdfs:label>
</owl:Class>


Expand All @@ -424,8 +428,8 @@

<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>
<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>


Expand All @@ -434,7 +438,7 @@

<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>
<rdfs:label xml:lang="en">failed planned process</rdfs:label>
</owl:Class>


Expand All @@ -457,8 +461,8 @@
</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>
<obo:IAO_0000115 xml:lang="en">A 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>


Expand All @@ -484,7 +488,7 @@
<!-- http://purl.obolibrary.org/obo/COB_0000502 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000502">
<rdfs:label>characteristic</rdfs:label>
<rdfs:label xml:lang="en">characteristic</rdfs:label>
</owl:Class>


Expand All @@ -499,8 +503,8 @@
<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>
<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>


Expand All @@ -515,15 +519,21 @@
<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>
<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/OBI_0000260 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000260"/>



<!-- http://purl.obolibrary.org/obo/UBERON_0000465 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000465"/>
</rdf:RDF>


Expand Down
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