Add logical definitions and design patterns for squamous and cuboidal epithelial cells

[Copilot]

Formalizes cell shape characteristics for epithelial cells using PATO morphology terms. Adds logical definitions to enable automated classification of squamous (flattened) and cuboidal cells.

Ontology changes

• New term: cuboidal epithelial cell (CL_9900001) with logical definition epithelial cell ⊓ ∃has_characteristic.cuboidal
• Updated: squamous epithelial cell (CL_0000076) with logical definition epithelial cell ⊓ ∃has_characteristic.flattened
• Added axioms to cells explicitly described as having squamous or cuboidal morphology (9 cells total):
  • Squamous cells (has_characteristic some flattened):
    • CL_0002653 (squamous endothelial cell)
    • CL_4033083 (squamous granulosa cell)
    • CL_0002190 (squamous cell of epidermis)
    • CL_0002221 (keratinized squamous cell of esophagus)
  • Cuboidal cells (has_characteristic some cuboidal):
    • CL_4033084 (cuboidal granulosa cell)
    • CL_0002063 (pulmonary alveolar type 2 cell)
    • CL_0000634 (Claudius cell)
    • CL_0002223 (anterior lens cell)
    • CL_0002662 (luminal cell of lactiferous duct)
• Added PATO terms: PATO:0002254 (flattened), PATO:0002312 (cuboidal)

Cells were selected based on comprehensive search of the ontology, carefully reviewing definitions to ensure the morphological term describes the actual cell shape (not just mentioned in passing). Excluded cells with variable morphology that change between squamous and cuboidal states.

Example logical axiom:

EquivalentClasses(obo:CL_0000076 
  ObjectIntersectionOf(obo:CL_0000066 
    ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0002254)))

Design patterns

Created DOSDP patterns for automated term generation:

• squamousEpithelialCell.yaml - generates terms for squamous cell types
• cuboidalEpithelialCell.yaml - generates terms for cuboidal cell types

Both use bearer of (RO:0000053) relation consistent with existing cellBearerOfQuality pattern.

Documentation

• Extended relations_guide.md with "Recording cell shape" section
• Added pattern documentation showing example terms and data previews

Other squamous/cuboidal cells automatically inherit morphology characteristics through reasoning via subclass relationships.

Original prompt

---

This section details on the original issue you should resolve

<issue_title>Fix design patterns for columnar cuboidal and squamous epithelial cells</issue_title> <issue_description>## New term

cuboidal epithelial cell equivalent_to epithelial cell and has_characteristic some cuboidal SubClassOf: columnar cuboidal epithelial cell

New logical def

squamous epithelial cell equivalent_to epithelial cell and has_characteristic some flattened (PATO:0002254)

## Axiomatization:

• Find all cell types with squamous in name or stated to be squamous in definition and add 'relationship: has_characteristic some flattened (PATO:0002254)
• Find all cell types with cuboidal in name or stated to be squamous in definition and add 'relationship: has_characteristic some cuboidal

Documentation

• Extend relations_guide section on cell characteristics to include this
• Add DOSDPs for both patterns under src/patterns

</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes obophenotype/cell-ontology#3536

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