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[DO NOT MERGE] eval #3536 i:1: Fix design patterns for columnar cuboidal and squamous epithelial cells (codex/gpt-5.4, .) #591

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[DO NOT MERGE] eval #3536 i:1: Fix design patterns for columnar cuboidal and squamous epithelial cells (codex/gpt-5.4, .) #591

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efa0adc
Add epithelial morphology axioms for squamous and cuboidal terms
invalid-email-address May 17, 2026
2bef770
eval-agent: issue #3536 (gpt-5.4, .)
github-actions[bot] May 17, 2026
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9 changes: 8 additions & 1 deletion docs/relations_guide.md
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Expand Up @@ -230,6 +230,14 @@ For example, [erythrocyte](http://purl.obolibrary.org/obo/CL_0000765)
subClassOf [**'has characteristic'**](http://purl.obolibrary.org/obo/RO_0000053)
*some* [biconcave](http://purl.obolibrary.org/obo/PATO_0002039)

This relation is also the correct way to capture broad epithelial
morphologies. For example,
[squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076)
can be defined as an epithelial cell with
[flattened](http://purl.obolibrary.org/obo/PATO_0002254) morphology,
and cuboidal epithelial cells can be defined using
[cuboid](http://purl.obolibrary.org/obo/PATO_0001872).

PATO also has a set of terms for [<u>specific cell morphologies</u>](https://www.ebi.ac.uk/ols4/ontologies/pato) (mostly
neuronal), e.g.

Expand Down Expand Up @@ -259,4 +267,3 @@ some nucleus

See
<https://oboacademy.github.io/obook/explanation/taxon-constraints-explainer/>.

25 changes: 23 additions & 2 deletions src/ontology/cl-edit.owl
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Expand Up @@ -4522,11 +4522,21 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GO:0002065") Annotation(oboIn
AnnotationAssertion(rdfs:label obo:CL_0000075 "columnar/cuboidal epithelial cell")
SubClassOf(obo:CL_0000075 obo:CL_0000066)

# Class: obo:CL_9900001 (cuboidal epithelial cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "ISBN:0721662544") obo:IAO_0000115 obo:CL_9900001 "An epithelial cell that has a cuboidal morphology.")
AnnotationAssertion(obo:IAO_0000233 obo:CL_9900001 "https://github.com/obophenotype/cell-ontology/issues/3536")
AnnotationAssertion(terms:creator obo:CL_9900001 "GitHub Copilot")
AnnotationAssertion(terms:date obo:CL_9900001 "2026-05-17T01:02:50Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:CL_9900001 "cuboidal epithelial cell")
EquivalentClasses(obo:CL_9900001 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001872)))
SubClassOf(obo:CL_9900001 obo:CL_0000075)

# Class: obo:CL_0000076 (squamous epithelial cell)

AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000076 "CALOHA:TS-1249")
AnnotationAssertion(rdfs:label obo:CL_0000076 "squamous epithelial cell")
SubClassOf(obo:CL_0000076 obo:CL_0000066)
EquivalentClasses(obo:CL_0000076 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0002254)))

# Class: obo:CL_0000077 (mesothelial cell)

Expand Down Expand Up @@ -6103,6 +6113,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30422572") Annotation(ob
AnnotationAssertion(rdfs:label obo:CL_0000241 "stratified cuboidal epithelial cell")
EquivalentClasses(obo:CL_0000241 ObjectIntersectionOf(obo:CL_0000079 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0010077)))
SubClassOf(obo:CL_0000241 obo:CL_0000075)
SubClassOf(obo:CL_0000241 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001872))

# Class: obo:CL_0000242 (Merkel cell)

Expand Down Expand Up @@ -16052,6 +16063,7 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002190 "FMA:86925")
AnnotationAssertion(rdfs:label obo:CL_0002190 "squamous cell of epidermis")
SubClassOf(obo:CL_0002190 obo:CL_0000312)
SubClassOf(obo:CL_0002190 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001003))
SubClassOf(obo:CL_0002190 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0002254))

# Class: obo:CL_0002191 (granulocytopoietic cell)

Expand Down Expand Up @@ -16394,6 +16406,7 @@ AnnotationAssertion(rdfs:label obo:CL_0002221 "keratinized squamous cell of esop
SubClassOf(obo:CL_0002221 obo:CL_0000237)
SubClassOf(obo:CL_0002221 obo:CL_0002252)
SubClassOf(obo:CL_0002221 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001976))
SubClassOf(obo:CL_0002221 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0002254))

# Class: obo:CL_0002222 (vertebrate lens cell)

Expand Down Expand Up @@ -16425,6 +16438,7 @@ AnnotationAssertion(rdfs:label obo:CL_0002224 "lens epithelial cell")
EquivalentClasses(obo:CL_0002224 ObjectIntersectionOf(obo:CL_0000075 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001803)))
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0002224 obo:CL_0000075)
SubClassOf(obo:CL_0002224 obo:CL_0002222)
SubClassOf(obo:CL_0002224 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001872))

# Class: obo:CL_0002225 (secondary lens fiber)

Expand Down Expand Up @@ -20769,6 +20783,7 @@ AnnotationAssertion(terms:contributor obo:CL_0002653 <https://orcid.org/0000-000
AnnotationAssertion(oboInOwl:creation_date obo:CL_0002653 "2011-07-08T03:31:25Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:CL_0002653 "squamous endothelial cell")
SubClassOf(obo:CL_0002653 obo:CL_0000115)
SubClassOf(obo:CL_0002653 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0002254))

# Class: obo:CL_0002654 (epithelial cell of stratum corneum of esophageal epithelium)

Expand Down Expand Up @@ -20858,6 +20873,7 @@ AnnotationAssertion(oboInOwl:creation_date obo:CL_0002662 "2011-07-11T01:44:48Z"
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002662 "FMA:74504")
AnnotationAssertion(rdfs:label obo:CL_0002662 "luminal cell of lactiferous duct")
SubClassOf(obo:CL_0002662 obo:CL_0002326)
SubClassOf(obo:CL_0002662 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001872))

# Class: obo:CL_0002663 (myocardial endocrine cell of atrium)

Expand Down Expand Up @@ -22442,6 +22458,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "CL:CVS") obo:IAO_0000115 obo:
AnnotationAssertion(rdfs:label obo:CL_0005009 "renal principal cell")
SubClassOf(obo:CL_0005009 obo:CL_0000075)
SubClassOf(obo:CL_0005009 obo:CL_0002518)
SubClassOf(obo:CL_0005009 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001872))

# Class: obo:CL_0005010 (renal intercalated cell)

Expand All @@ -22454,6 +22471,7 @@ SubClassOf(obo:CL_0005010 obo:CL_0000075)
SubClassOf(obo:CL_0005010 obo:CL_0002078)
SubClassOf(obo:CL_0005010 obo:CL_0002518)
SubClassOf(obo:CL_0005010 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001285))
SubClassOf(obo:CL_0005010 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001872))

# Class: obo:CL_0005011 (renal alpha-intercalated cell)

Expand Down Expand Up @@ -33101,6 +33119,7 @@ SubClassOf(obo:CL_4033083 obo:CL_0000501)
SubClassOf(obo:CL_4033083 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0003981))
SubClassOf(obo:CL_4033083 ObjectSomeValuesFrom(obo:RO_0002207 obo:CL_4033066))
SubClassOf(obo:CL_4033083 ObjectSomeValuesFrom(obo:RO_0002210 obo:CL_4033084))
SubClassOf(obo:CL_4033083 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0002254))

# Class: obo:CL_4033084 (cuboidal granulosa cell)

Expand All @@ -33115,6 +33134,7 @@ AnnotationAssertion(rdfs:label obo:CL_4033084 "cuboidal granulosa cell")
SubClassOf(obo:CL_4033084 obo:CL_0000501)
SubClassOf(obo:CL_4033084 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001305))
SubClassOf(obo:CL_4033084 ObjectSomeValuesFrom(obo:RO_0002207 obo:CL_4033083))
SubClassOf(obo:CL_4033084 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001872))

# Class: obo:CL_4033085 (diffuse bipolar 5 cell)

Expand Down Expand Up @@ -34652,6 +34672,7 @@ AnnotationAssertion(rdfs:label obo:CL_4052048 "intercalated cell of salivary gla
SubClassOf(obo:CL_4052048 obo:CL_1001596)
SubClassOf(obo:CL_4052048 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0014727))
SubClassOf(obo:CL_4052048 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0015766))
SubClassOf(obo:CL_4052048 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001872))

# Class: obo:CL_4052049 (striated cell of salivary gland)

Expand Down Expand Up @@ -35599,4 +35620,4 @@ 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))
)
)
24 changes: 24 additions & 0 deletions src/patterns/dosdp-patterns/cuboidalEpithelialCell.yaml
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@@ -0,0 +1,24 @@
pattern_name: cuboidalEpithelialCell
pattern_iri: http://purl.obolibrary.org/obo/cl/cuboidalEpithelialCell

description: An epithelial cell that has a cuboidal morphology.

contributors:
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0002-6601-2165

classes:
epithelial cell: "CL:0000066"
cuboid: "PATO:0001872"

relations:
has characteristic: "RO:0000053"

name:
text: "cuboidal epithelial cell"

def:
text: "An epithelial cell that has a cuboidal morphology."

equivalentTo:
text: "'epithelial cell' and ('has characteristic' some 'cuboid')"
24 changes: 24 additions & 0 deletions src/patterns/dosdp-patterns/squamousEpithelialCell.yaml
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pattern_name: squamousEpithelialCell
pattern_iri: http://purl.obolibrary.org/obo/cl/squamousEpithelialCell

description: An epithelial cell that has a flattened morphology.

contributors:
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0002-6601-2165

classes:
epithelial cell: "CL:0000066"
flattened: "PATO:0002254"

relations:
has characteristic: "RO:0000053"

name:
text: "squamous epithelial cell"

def:
text: "An epithelial cell that has a flattened morphology."

equivalentTo:
text: "'epithelial cell' and ('has characteristic' some 'flattened')"