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[DO NOT MERGE] eval #3533 i:1: Add articular cartilage zonal chondrocyte cell types (opencode/openai/gpt-5.4, .) #593

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[DO NOT MERGE] eval #3533 i:1: Add articular cartilage zonal chondrocyte cell types (opencode/openai/gpt-5.4, .) #593

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23916a2
Add zonal articular chondrocyte terms
github-actions[bot] May 17, 2026
45cf3e1
eval-agent: issue #3533 (openai/gpt-5.4, .)
github-actions[bot] May 17, 2026
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43 changes: 42 additions & 1 deletion src/ontology/cl-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -3301,6 +3301,10 @@ Declaration(Class(obo:CL_7770003))
Declaration(Class(obo:CL_7770004))
Declaration(Class(obo:CL_7770005))
Declaration(Class(obo:CL_7770006))
Declaration(Class(obo:CL_9900000))
Declaration(Class(obo:CL_9900001))
Declaration(Class(obo:CL_9900002))
Declaration(Class(obo:CL_9900003))
Declaration(Class(obo:CP_0000000))
Declaration(Class(obo:CP_0000025))
Declaration(Class(obo:CP_0000027))
Expand Down Expand Up @@ -35653,6 +35657,43 @@ SubClassOf(obo:CL_7770006 obo:CL_0002367)
SubClassOf(obo:CL_7770006 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_9606))
SubClassOf(obo:CL_7770006 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_Q9UIK5))

# Class: obo:CL_9900000 (superficial zone articular chondrocyte)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:23015907") Annotation(oboInOwl:hasDbXref "PMID:23124445") Annotation(oboInOwl:hasDbXref "PMID:41226342") obo:IAO_0000115 obo:CL_9900000 "An articular chondrocyte located in the most superficial zone of articular cartilage, characterized by flattened morphology and tangential alignment parallel to the joint surface, and residing within a matrix of fine collagen fibrils and relatively low proteoglycan content. In mice and humans, this cell typically expresses lubricin (PRG4) and contributes to lubrication and resistance to shear and tensile forces at the cartilage surface.")
AnnotationAssertion(terms:contributor obo:CL_9900000 <https://orcid.org/0000-0003-0098-4399>)
AnnotationAssertion(terms:date obo:CL_9900000 "2026-05-17T01:04:42Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:CL_9900000 "superficial zone articular chondrocyte")
SubClassOf(obo:CL_9900000 obo:CL_1001607)
SubClassOf(obo:CL_9900000 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000013208))

# Class: obo:CL_9900001 (middle zone articular chondrocyte)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:23015907") Annotation(oboInOwl:hasDbXref "PMID:23124445") Annotation(oboInOwl:hasDbXref "PMID:41226342") obo:IAO_0000115 obo:CL_9900001 "An articular chondrocyte located in the middle (transitional) zone of articular cartilage, characterized by round morphology and relatively random spatial organization, and residing in a matrix enriched in proteoglycans and thicker collagen fibrils oriented obliquely to the articular surface. This cell contributes to the largest volume fraction of articular cartilage and functions primarily in distributing and absorbing compressive loads between the superficial and deep zones.")
AnnotationAssertion(terms:contributor obo:CL_9900001 <https://orcid.org/0000-0003-0098-4399>)
AnnotationAssertion(terms:date obo:CL_9900001 "2026-05-17T01:04:42Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:23015907") oboInOwl:hasRelatedSynonym obo:CL_9900001 "transitional zone articular chondrocyte")
AnnotationAssertion(rdfs:label obo:CL_9900001 "middle zone articular chondrocyte")
SubClassOf(obo:CL_9900001 obo:CL_1001607)

# Class: obo:CL_9900002 (deep zone articular chondrocyte)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:23015907") Annotation(oboInOwl:hasDbXref "PMID:23124445") Annotation(oboInOwl:hasDbXref "PMID:41226342") obo:IAO_0000115 obo:CL_9900002 "An articular chondrocyte located in the deep (radial) zone of articular cartilage, characterized by columnar arrangement perpendicular to the joint surface and residence within a matrix containing the highest proteoglycan concentration and large-diameter collagen fibrils oriented radially. In humans, this cell expresses collagen type X (COL10A1) and provides maximal resistance to compressive forces. It is positioned adjacent to the tidemark, where collagen fibrils extend into the calcified cartilage to anchor the articular cartilage to subchondral bone.")
AnnotationAssertion(terms:contributor obo:CL_9900002 <https://orcid.org/0000-0003-0098-4399>)
AnnotationAssertion(terms:date obo:CL_9900002 "2026-05-17T01:04:42Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:23015907") oboInOwl:hasRelatedSynonym obo:CL_9900002 "radial zone articular chondrocyte")
AnnotationAssertion(rdfs:label obo:CL_9900002 "deep zone articular chondrocyte")
SubClassOf(obo:CL_9900002 obo:CL_1001607)
SubClassOf(obo:CL_9900002 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000005693))

# Class: obo:CL_9900003 (calcified zone articular chondrocyte)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:18455690") Annotation(oboInOwl:hasDbXref "PMID:23015907") Annotation(oboInOwl:hasDbXref "PMID:41226342") obo:IAO_0000115 obo:CL_9900003 "An articular chondrocyte located in the calcified cartilage zone below the tidemark at the interface between articular cartilage and subchondral bone, embedded within a mineralized extracellular matrix. In humans, this cell exhibits a hypertrophic-like phenotype and typically expresses collagen type X (COL10A1). Together with the surrounding calcified matrix, it forms a transitional region that mechanically couples the deep articular cartilage to the underlying subchondral bone.")
AnnotationAssertion(terms:contributor obo:CL_9900003 <https://orcid.org/0000-0003-0098-4399>)
AnnotationAssertion(terms:date obo:CL_9900003 "2026-05-17T01:04:42Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:CL_9900003 "calcified zone articular chondrocyte")
SubClassOf(obo:CL_9900003 obo:CL_1001607)
SubClassOf(obo:CL_9900003 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000005693))

# Class: obo:CP_0000000 (obsolete CP:0000000)

AnnotationAssertion(obo:IAO_0100001 obo:CP_0000000 obo:CL_0017500)
Expand Down Expand Up @@ -35732,4 +35773,4 @@ 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))
)
)