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

[cmungall]

⚠️ EVALUATION ONLY - DO NOT MERGE ⚠️

Original Issue

#3536: Fix design patterns for columnar cuboidal and squamous epithelial cells

Original PR (human solution)

#3537: Add logical definitions and design patterns for squamous and cuboidal epithelial cells

Agent Commits

• Add epithelial morphology axioms for squamous and cuboidal terms

Note: This PR diff shows ONLY the agent's changes. The baseline is eval_base_branch.

Agent Response - PR Comments

Implemented issue #3536 in local commit efa0adc (Add epithelial morphology axioms for squamous and cuboidal terms).

Summary:

• Added new term CL_9900001 cuboidal epithelial cell with definition, issue tracker annotation, creator, timestamp, and logical axiom:
  epithelial cell and ('has characteristic' some cuboid).
• Replaced the asserted parent-only treatment of squamous epithelial cell with the requested logical definition:
  epithelial cell and ('has characteristic' some flattened).
• Added explicit morphology axioms to classes where squamous or cuboidal is part of the class identity and the morphology is stable/defining, including:
  stratified cuboidal epithelial cell, lens epithelial cell, luminal cell of lactiferous duct, renal principal cell, renal intercalated cell, intercalated cell of salivary gland, squamous cell of epidermis, keratinized squamous cell of esophagus, squamous endothelial cell, squamous granulosa cell, and cuboidal granulosa cell.
• Updated docs/relations_guide.md to document use of has characteristic for broad epithelial morphologies, with flattened and cuboid as the examples.
• Added DOSDP YAMLs under src/patterns/dosdp-patterns/ for the two requested epithelial morphology patterns:
  squamousEpithelialCell.yaml
cuboidalEpithelialCell.yaml

Rationale:

• I did not bulk-annotate every textual mention of squamous or cuboidal. Some classes only mention these shapes as variable, comparative, or context-dependent states, and adding a defining morphology axiom there would overstate the biology.
• I also did not add a cuboid morphology axiom to columnar/cuboidal epithelial cell, because that term is explicitly broader than cuboidal alone.

Checklist completed:

• Read the imported issue context.
• Checked existing ontology usage for squamous, cuboidal, has characteristic, and relevant epithelial classes.
• Verified PATO terms used for the new axioms:
  PATO:0002254 flattened
  PATO:0001872 cuboid
• Added the new term and updated logical axioms in src/ontology/cl-edit.owl.
• Updated the relations guide documentation.
• Added DOSDP pattern YAMLs for the two epithelial morphology terms.
• Committed only the files edited for this issue.

Validation:

• Ran robot convert -i src/ontology/cl-edit.owl -o /tmp/cl-edit.ofn successfully.
• Parsed both new DOSDP YAML files with python/yaml.safe_load successfully.

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🤖 Generated by codex agent

• Runtime: codex
• Model: gpt-5.4
• Agent config: ai4curation/cl-agent-config@v3:.
• Iteration: 1
• Run: View workflow run

Agent Response - Issue Comments

Implemented locally and committed; changes can be reviewed in PR #.

This adds a new cuboidal epithelial cell term, gives squamous epithelial cell a morphology-based logical definition, adds supporting flattened/cuboid axioms to affected classes, updates the relations guide, and adds DOSDP YAMLs for the two epithelial morphology patterns.

---

🤖 Generated by codex agent

• Runtime: codex
• Model: gpt-5.4
• Agent config: ai4curation/cl-agent-config@v3:.
• Iteration: 1
• Run: View workflow run

Experiment Config

Parameter	Value
Model	gpt-5.4
Agent config	ai4curation/cl-agent-config@v3:.
Iteration	1
URL prefix	https://href.li/?
Base branch	eval-base-issue-3536

See workflow artifacts for full agent trace.

[cmungall]

📋 Traces: traces/25977381019