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[DO NOT MERGE] eval #3521 i:1: Add reference dataset and NS-Forest marker for human bipolar neuron types (opencode/openai/gpt-5.4, .) #595

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[DO NOT MERGE] eval #3521 i:1: Add reference dataset and NS-Forest marker for human bipolar neuron types (opencode/openai/gpt-5.4, .) #595

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1afaede
Add CAP dataset links for human bipolar neuron types
May 17, 2026
6132791
eval-agent: issue #3521 (openai/gpt-5.4, .)
github-actions[bot] May 17, 2026
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15 changes: 14 additions & 1 deletion src/ontology/cl-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -10273,6 +10273,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:14689473") obo:IAO_00001
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1038/s41598-020-66092-9") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_0000748 "BC")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1038/s41598-020-66092-9") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) Annotation(oboInOwl:hasSynonymType obo:OMO_0003004) oboInOwl:hasRelatedSynonym obo:CL_0000748 "BCs")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "geo:GSE137537") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) Annotation(oboInOwl:hasSynonymType obo:OMO_0003004) oboInOwl:hasRelatedSynonym obo:CL_0000748 "BPs")
AnnotationAssertion(Annotation(rdfs:label "reference transcriptomic data on Cell Annotation Platform") rdfs:seeAlso obo:CL_0000748 "https://celltype.info/project/544/dataset/1157")
AnnotationAssertion(rdfs:label obo:CL_0000748 "retinal bipolar neuron")
EquivalentClasses(obo:CL_0000748 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001791)))
SubClassOf(obo:CL_0000748 obo:CL_0009004)
Expand All @@ -10296,6 +10297,7 @@ SubClassOf(obo:CL_0000750 obo:CL_0000748)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "PMID:14689473") obo:IAO_0000115 obo:CL_0000751 "A bipolar neuron found in the retina that is synapsed by rod photoreceptor cells but not by cone photoreceptor cells. These neurons depolarize in response to light.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38627529") obo:RO_0002175 obo:CL_0000751 obo:NCBITaxon_32443)
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000751 "FMA:67750")
AnnotationAssertion(Annotation(rdfs:label "reference transcriptomic data on Cell Annotation Platform") rdfs:seeAlso obo:CL_0000751 "https://celltype.info/project/544/dataset/1157")
AnnotationAssertion(rdfs:label obo:CL_0000751 "rod bipolar cell")
SubClassOf(obo:CL_0000751 obo:CL_0000749)
SubClassOf(obo:CL_0000751 ObjectSomeValuesFrom(obo:RO_0002102 obo:UBERON_0008925))
Expand Down Expand Up @@ -32722,6 +32724,7 @@ AnnotationAssertion(terms:contributor obo:CL_4033019 <https://orcid.org/0000-000
AnnotationAssertion(terms:date obo:CL_4033019 "2023-04-04T09:48:15Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32032773") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033019 "BB cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32032773") rdfs:comment obo:CL_4033019 "The axons of a blue cone bipolar cell terminate close to the ganglion cell layer, where they transfer the S-cone ON signal to small bistratified ganglion cells. Other targets of a blue cone bipolar cell include amacrine cells and possibly large bistratified ganglion cells.")
AnnotationAssertion(Annotation(rdfs:label "reference transcriptomic data on Cell Annotation Platform") rdfs:seeAlso obo:CL_4033019 "https://celltype.info/project/544/dataset/1157")
AnnotationAssertion(rdfs:label obo:CL_4033019 "ON-blue cone bipolar cell")
SubClassOf(obo:CL_4033019 obo:CL_0000749)

Expand Down Expand Up @@ -32803,6 +32806,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:22006647") Annotation(ob
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:22006647") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033027 "DB1 bipolar cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32032773") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033027 "DB1 cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:22006647") Annotation(oboInOwl:hasDbXref "PMID:32032773") rdfs:comment obo:CL_4033027 "In primates, a diffuse bipolar 1 cell on average makes 81 ribbon (output) synapses, 13 contacts are with OFF parasol cells and 47 contacts are with OFF midget cells. This cell might make flat contacts at both triad-associated and non-triad-associated positions on the cone pedicle.")
AnnotationAssertion(Annotation(rdfs:label "reference transcriptomic data on Cell Annotation Platform") rdfs:seeAlso obo:CL_4033027 "https://celltype.info/project/544/dataset/1157")
AnnotationAssertion(rdfs:label obo:CL_4033027 "diffuse bipolar 1 cell")
SubClassOf(obo:CL_4033027 obo:CL_0000750)

Expand All @@ -32813,6 +32817,7 @@ AnnotationAssertion(terms:contributor obo:CL_4033028 <https://orcid.org/0000-000
AnnotationAssertion(terms:date obo:CL_4033028 "2023-04-04T10:49:07Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32032773") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033028 "DB2 cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32032773") rdfs:comment obo:CL_4033028 "In primates, a diffuse bipolar 2 cell makes an average of 133 ribbon synapses, 47 contacts are with OFF parasol cells and 4 contacts are with OFF midget cells.")
AnnotationAssertion(Annotation(rdfs:label "reference transcriptomic data on Cell Annotation Platform") rdfs:seeAlso obo:CL_4033028 "https://celltype.info/project/544/dataset/1157")
AnnotationAssertion(rdfs:label obo:CL_4033028 "diffuse bipolar 2 cell")
SubClassOf(obo:CL_4033028 obo:CL_0000750)

Expand All @@ -32824,6 +32829,7 @@ AnnotationAssertion(terms:date obo:CL_4033029 "2023-04-04T10:53:33Z"^^xsd:dateTi
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.3389/fnana.2015.00122") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033029 "DB3 cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32032773") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033029 "DB3a cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.3389/fnana.2015.00122") Annotation(oboInOwl:hasDbXref "PMID:32032773") rdfs:comment obo:CL_4033029 "Originally, DB3a cells were termed diffuse bipolar 3 (DB3) cells. When an additional bipolar type which stratifies slightly more vitread and is calbindin negative was detected, this cell was renamed diffuse bipolar 3a cell. The axons of neighboring DB3a cells make homologous gap junctions. The DB3a cells provide the majority of their output to OFF parasol cells.")
AnnotationAssertion(Annotation(rdfs:label "reference transcriptomic data on Cell Annotation Platform") rdfs:seeAlso obo:CL_4033029 "https://celltype.info/project/544/dataset/1157")
AnnotationAssertion(rdfs:label obo:CL_4033029 "diffuse bipolar 3a cell")
SubClassOf(obo:CL_4033029 obo:CL_0000750)

Expand All @@ -32834,6 +32840,7 @@ AnnotationAssertion(terms:contributor obo:CL_4033030 <https://orcid.org/0000-000
AnnotationAssertion(terms:date obo:CL_4033030 "2023-04-04T10:53:42Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32032773") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033030 "DB3b cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24107939") Annotation(oboInOwl:hasDbXref "PMID:32032773") Annotation(oboInOwl:hasDbXref "PMID:33009001") rdfs:comment obo:CL_4033030 "In humans, a DB3b cell is CD15 positive. A DB3b cell might make sparse contacts to rod photoreceptors.")
AnnotationAssertion(Annotation(rdfs:label "reference transcriptomic data on Cell Annotation Platform") rdfs:seeAlso obo:CL_4033030 "https://celltype.info/project/544/dataset/1157")
AnnotationAssertion(rdfs:label obo:CL_4033030 "diffuse bipolar 3b cell")
SubClassOf(obo:CL_4033030 obo:CL_0000750)

Expand All @@ -32843,6 +32850,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:27833534") Annotation(ob
AnnotationAssertion(terms:contributor obo:CL_4033031 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(terms:date obo:CL_4033031 "2023-04-04T09:51:10Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32032773") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033031 "DB4 cell")
AnnotationAssertion(Annotation(rdfs:label "reference transcriptomic data on Cell Annotation Platform") rdfs:seeAlso obo:CL_4033031 "https://celltype.info/project/544/dataset/1157")
AnnotationAssertion(rdfs:label obo:CL_4033031 "diffuse bipolar 4 cell")
SubClassOf(obo:CL_4033031 obo:CL_0000749)

Expand All @@ -32852,6 +32860,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32032773") Annotation(ob
AnnotationAssertion(terms:contributor obo:CL_4033032 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(terms:date obo:CL_4033032 "2023-04-04T09:51:22Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32032773") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033032 "DB6 cell")
AnnotationAssertion(Annotation(rdfs:label "reference transcriptomic data on Cell Annotation Platform") rdfs:seeAlso obo:CL_4033032 "https://celltype.info/project/544/dataset/1157")
AnnotationAssertion(rdfs:label obo:CL_4033032 "diffuse bipolar 6 cell")
SubClassOf(obo:CL_4033032 obo:CL_0000749)

Expand All @@ -32861,6 +32870,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32032773") Annotation(ob
AnnotationAssertion(terms:contributor obo:CL_4033033 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(terms:date obo:CL_4033033 "2023-04-04T10:54:00Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32032773") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033033 "FMB cell")
AnnotationAssertion(Annotation(rdfs:label "reference transcriptomic data on Cell Annotation Platform") rdfs:seeAlso obo:CL_4033033 "https://celltype.info/project/544/dataset/1157")
AnnotationAssertion(rdfs:label obo:CL_4033033 "flat midget bipolar cell")
SubClassOf(obo:CL_4033033 obo:CL_0000750)

Expand All @@ -32870,6 +32880,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32032773") Annotation(ob
AnnotationAssertion(terms:contributor obo:CL_4033034 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(terms:date obo:CL_4033034 "2023-04-04T09:51:44Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32032773") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033034 "IMB cell")
AnnotationAssertion(Annotation(rdfs:label "reference transcriptomic data on Cell Annotation Platform") rdfs:seeAlso obo:CL_4033034 "https://celltype.info/project/544/dataset/1157")
AnnotationAssertion(rdfs:label obo:CL_4033034 "invaginating midget bipolar cell")
SubClassOf(obo:CL_4033034 obo:CL_0000749)

Expand All @@ -32880,6 +32891,7 @@ AnnotationAssertion(terms:contributor obo:CL_4033035 <https://orcid.org/0000-000
AnnotationAssertion(terms:date obo:CL_4033035 "2023-04-04T09:54:15Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32032773") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033035 "GB cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32032773") rdfs:comment obo:CL_4033035 "A giant bipolar cell is usually monostratified, although, very rarely, it can be bistratified.")
AnnotationAssertion(Annotation(rdfs:label "reference transcriptomic data on Cell Annotation Platform") rdfs:seeAlso obo:CL_4033035 "https://celltype.info/project/544/dataset/1157")
AnnotationAssertion(rdfs:label obo:CL_4033035 "giant bipolar cell")
SubClassOf(obo:CL_4033035 obo:CL_0000749)

Expand All @@ -32889,6 +32901,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30712875") Annotation(ob
AnnotationAssertion(obo:RO_0002175 obo:CL_4033036 obo:NCBITaxon_9443)
AnnotationAssertion(terms:contributor obo:CL_4033036 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(terms:date obo:CL_4033036 "2023-04-04T10:54:15Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(rdfs:label "reference transcriptomic data on Cell Annotation Platform") rdfs:seeAlso obo:CL_4033036 "https://celltype.info/project/544/dataset/1157")
AnnotationAssertion(rdfs:label obo:CL_4033036 "OFFx cell")
SubClassOf(obo:CL_4033036 obo:CL_0000750)
SubClassOf(obo:CL_4033036 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001786))
Expand Down Expand Up @@ -35780,4 +35793,4 @@ SubClassOf(ObjectIntersectionOf(obo:CL_0000163 ObjectSomeValuesFrom(obo:BFO_0000
SubClassOf(ObjectIntersectionOf(obo:CL_0000163 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000945)) obo:CL_0000164)
SubClassOf(ObjectIntersectionOf(obo:CL_0000163 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001264)) obo:CL_0000164)
SubClassOf(Annotation(oboInOwl:hasDbXref <https://github.com/obophenotype/cell-ontology/issues/757>) ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_7742)) ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000031))
)
)