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Remove COB_based_on due to lack of proper OBO ID #281

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merged 4 commits into from
Sep 16, 2024
Merged

Remove COB_based_on due to lack of proper OBO ID #281

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507796a
Remove COB_based_on
sebastianduesing Aug 29, 2024
26a5f2d
Add based-on pairs to cob-to-external
sebastianduesing Sep 6, 2024
c1ae393
Revert "Add based-on pairs to cob-to-external"
sebastianduesing Sep 6, 2024
c2116d8
Actually add based-on pairs to cob-to-external
sebastianduesing Sep 6, 2024
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11 changes: 0 additions & 11 deletions src/ontology/cob-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -30,12 +30,6 @@



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

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



<!-- http://purl.obolibrary.org/obo/IAO_0000115 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
Expand Down Expand Up @@ -329,7 +323,6 @@
<!-- http://purl.obolibrary.org/obo/COB_0000513 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/COB_0000513">
<obo:COB_based_on>http://purl.obolibrary.org/obo/IAO_0000136</obo:COB_based_on>
<rdfs:label>is about</rdfs:label>
</owl:ObjectProperty>

Expand Down Expand Up @@ -1065,7 +1058,6 @@

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000088">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000026"/>
<obo:COB_based_on rdf:resource="http://purl.obolibrary.org/obo/DRON_00000005"/>
<obo:IAO_0000115>A processed material entity created to be administered to an individual with the intent to improve health.</obo:IAO_0000115>
<rdfs:label>drug product</rdfs:label>
</owl:Class>
Expand Down Expand Up @@ -1247,7 +1239,6 @@

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000119">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000114"/>
<obo:COB_based_on>OBI:0000067</obo:COB_based_on>
<rdfs:label>evaluant role</rdfs:label>
</owl:Class>

Expand All @@ -1263,7 +1254,6 @@
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000502"/>
<obo:COB_based_on>http://purl.obolibrary.org/obo/IAO_0000015</obo:COB_based_on>
<rdfs:comment>Pier &apos;representational entity&apos;</rdfs:comment>
<rdfs:comment>This captures: pattern of writing in a book; neural state in the brain, electronic charges in computer memory etc</rdfs:comment>
<rdfs:label>information representation</rdfs:label>
Expand All @@ -1275,7 +1265,6 @@

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000121">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000102"/>
<obo:COB_based_on>http://purl.obolibrary.org/obo/IAO_0000109</obo:COB_based_on>
<rdfs:label>measurement datum</rdfs:label>
</owl:Class>

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200 changes: 1 addition & 199 deletions src/ontology/components/cob-annotations.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -11,207 +11,9 @@
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob/components/cob-annotations.owl">
<owl:versionInfo>2024-08-20</owl:versionInfo>
</owl:Ontology>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->




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

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/COB_based_on">
<rdfs:label>based on</rdfs:label>
</owl:AnnotationProperty>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotations
//
///////////////////////////////////////////////////////////////////////////////////////
-->

<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000003">
<obo:COB_based_on>http://purl.obolibrary.org/obo/PATO_0000125</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000004">
<obo:COB_based_on>http://purl.obolibrary.org/obo/PATO_0002193</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000006">
<obo:COB_based_on>http://purl.obolibrary.org/obo/BFO_0000040</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000007">
<obo:COB_based_on>http://purl.obolibrary.org/obo/CHEBI_36342</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000008">
<obo:COB_based_on>http://purl.obolibrary.org/obo/CHEBI_24636</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000009">
<obo:COB_based_on>http://purl.obolibrary.org/obo/CHEBI_30222</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000010">
<obo:COB_based_on>http://purl.obolibrary.org/obo/CHEBI_10545</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000012">
<obo:COB_based_on>http://purl.obolibrary.org/obo/CHEBI_33252</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000015">
<obo:COB_based_on>http://purl.obolibrary.org/obo/CHEBI_16541</obo:COB_based_on>
<obo:COB_based_on>http://purl.obolibrary.org/obo/PR_000000001</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000017">
<obo:COB_based_on>http://purl.obolibrary.org/obo/CL_0000000</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000018">
<obo:COB_based_on>http://purl.obolibrary.org/obo/CL_0000003</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000019">
<obo:COB_based_on>http://purl.obolibrary.org/obo/CL_0001034</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000021">
<obo:COB_based_on>http://purl.obolibrary.org/obo/CARO_0001008</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000022">
<obo:COB_based_on>http://purl.obolibrary.org/obo/OBI_0100026</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000025">
<obo:COB_based_on>http://purl.obolibrary.org/obo/OBI_0000245</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000026">
<obo:COB_based_on>http://purl.obolibrary.org/obo/OBI_0000047</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000031">
<obo:COB_based_on>http://purl.obolibrary.org/obo/BFO_0000141</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000033">
<obo:COB_based_on>http://purl.obolibrary.org/obo/BFO_0000017</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000034">
<obo:COB_based_on>http://purl.obolibrary.org/obo/BFO_0000015</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000035">
<obo:COB_based_on>http://purl.obolibrary.org/obo/OBI_0000011</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000037">
<obo:COB_based_on>http://purl.obolibrary.org/obo/GO_0008150</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000038">
<obo:COB_based_on>http://purl.obolibrary.org/obo/GO_0003674</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000042">
<obo:COB_based_on>http://purl.obolibrary.org/obo/CHEBI_24867</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000043">
<obo:COB_based_on>http://purl.obolibrary.org/obo/CHEBI_33250</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000049">
<obo:COB_based_on>http://purl.obolibrary.org/obo/CHEBI_33696</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000055">
<obo:COB_based_on>http://purl.obolibrary.org/obo/PCO_0000000</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000057">
<obo:COB_based_on>http://purl.obolibrary.org/obo/BFO_0000029</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000058">
<obo:COB_based_on>http://purl.obolibrary.org/obo/OBI_0001909</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000061">
<obo:COB_based_on>http://purl.obolibrary.org/obo/IAO_0000030</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000062">
<obo:COB_based_on>http://purl.obolibrary.org/obo/OGMS_0000073</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000063">
<obo:COB_based_on>http://purl.obolibrary.org/obo/OGMS_0000014</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000064">
<obo:COB_based_on>http://purl.obolibrary.org/obo/OGMS_0000063</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000065">
<obo:COB_based_on>http://purl.obolibrary.org/obo/ENVO_02500000</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000066">
<obo:COB_based_on>http://purl.obolibrary.org/obo/MOP_0000543</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000067">
<obo:COB_based_on>http://purl.obolibrary.org/obo/ENVO_01001110</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000068">
<obo:COB_based_on>http://purl.obolibrary.org/obo/ENVO_01000813</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000069">
<obo:COB_based_on>http://purl.obolibrary.org/obo/IAO_0000033</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000075">
<obo:COB_based_on>http://purl.obolibrary.org/obo/GO_0032991</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000076">
<obo:COB_based_on>http://purl.obolibrary.org/obo/IAO_0000005</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000079">
<obo:COB_based_on>http://purl.obolibrary.org/obo/IAO_0000104</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000088">
<obo:COB_based_on>http://purl.obolibrary.org/obo/DRON_0000005</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000101">
<obo:COB_based_on>http://purl.obolibrary.org/obo/IAO_0000310</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000102">
<obo:COB_based_on>http://purl.obolibrary.org/obo/IAO_0000027</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000103">
<obo:COB_based_on>http://purl.obolibrary.org/obo/GO_0005634</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000107">
<obo:COB_based_on>http://purl.obolibrary.org/obo/OBI_0000070</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000108">
<obo:COB_based_on>http://purl.obolibrary.org/obo/OBI_0200000</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000109">
<obo:COB_based_on>http://purl.obolibrary.org/obo/OBI_0000066</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000110">
<obo:COB_based_on>http://purl.obolibrary.org/obo/OBI_0000094</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000111">
<obo:COB_based_on>http://purl.obolibrary.org/obo/BFO_0000016</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000112">
<obo:COB_based_on>http://purl.obolibrary.org/obo/BFO_0000034</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000113">
<obo:COB_based_on>http://purl.obolibrary.org/obo/OBI_0000260</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000114">
<obo:COB_based_on>http://purl.obolibrary.org/obo/BFO_0000023</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000118">
<obo:COB_based_on>http://purl.obolibrary.org/obo/CARO_0010004</obo:COB_based_on>
<obo:COB_based_on>http://purl.obolibrary.org/obo/NCBITaxon_131567</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000123">
<obo:COB_based_on>http://purl.obolibrary.org/obo/SEPIO_0000048</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000502">
<obo:COB_based_on>http://purl.obolibrary.org/obo/BFO_0000020</obo:COB_based_on>
<obo:COB_based_on>http://purl.obolibrary.org/obo/PATO_0000001</obo:COB_based_on>
</rdf:Description>
</rdf:RDF>



<!-- Generated by the OWL API (version 4.5.29) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.29.2024-05-13T12:11:03Z) https://github.com/owlcs/owlapi -->

3 changes: 3 additions & 0 deletions src/ontology/components/cob-to-external.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -111,6 +111,9 @@ COB:0000118 cellular organism owl:equivalentClass NCBITaxon:131567 cellular orga
COB:0000118 cellular organism owl:equivalentClass CARO:0010004 cellular organism . semapv:ManualMappingCuration
COB:0000118 cellular organism sssom:superClassOf UBERON:0000468 multicellular organism . semapv:ManualMappingCuration
COB:0000118 cellular organism sssom:superClassOf PO:0000003 whole plant . semapv:ManualMappingCuration
COB:0000119 evaluant role owl:equivalentClass OBI:0000067 evaluant role . semapv:ManualMappingCuration
COB:0000120 information representation owl:equivalentClass IAO:0000015 information carrier . semapv:ManualMappingCuration
COB:0000121 measurement datum owl:equivalentClass IAO:0000109 measurement datum . semapv:ManualMappingCuration
COB:0000036 contains process owl:equivalentProperty BFO:0000067 contains process . semapv:ManualMappingCuration
COB:0000047 has part owl:equivalentProperty BFO:0000051 has part . semapv:ManualMappingCuration
COB:0000070 has participant owl:equivalentProperty RO:0000057 has participant . semapv:ManualMappingCuration
Expand Down
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