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

[cmungall]

⚠️ EVALUATION ONLY - DO NOT MERGE ⚠️

Original Issue

#3533: Add articular cartilage zonal chondrocyte cell types

Original PR (human solution)

#3571: Add articular cartilage zonal chondrocyte cell types

Agent Commits

• Add zonal articular chondrocyte terms

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

Agent Response - PR Comments

Added four new subclasses of articular chondrocyte to represent the major depth-dependent zones of articular cartilage:

• CL:9900000 superficial zone articular chondrocyte
• CL:9900001 middle zone articular chondrocyte
• CL:9900002 deep zone articular chondrocyte
• CL:9900003 calcified zone articular chondrocyte

What changed:

• Added new class declarations for the four CL_99xxxxx terms.
• Added labels, textual definitions, contributor ORCID, and terms:date annotations.
• Added the requested zonal synonyms where applicable:
  • transitional zone articular chondrocyte for middle zone articular chondrocyte
  • radial zone articular chondrocyte for deep zone articular chondrocyte
• Placed all four terms under articular chondrocyte (CL:1001607 in this file).
• Added marker-based axioms only where they were well supported by the referenced literature and already fit existing CL modeling style:
  • PRG4 for superficial zone articular chondrocyte
  • COL10A1 for deep zone articular chondrocyte
  • COL10A1 for calcified zone articular chondrocyte

Rationale:

• The issue requested conservative, well-established zonal subclasses for articular cartilage.
• I used a minimal modeling approach because specific UBERON classes for each articular cartilage zone were not readily available from the ontology lookup performed here.
• The definitions reflect the established morphology, matrix environment, and functional distinctions across superficial, middle/transitional, deep/radial, and calcified zones.

References used during curation:

• PMID:41226342
• PMID:18455690
• PMID:23124445
• PMID:23015907

Validation performed:

• Reviewed the existing articular chondrocyte neighborhood in src/ontology/cl-edit.owl for parent consistency.
• Checked the exact git diff to confirm the change was limited to the intended ontology additions.
• Ran robot convert -i src/ontology/cl-edit.owl -o /tmp/opencode/cl-edit.ofn successfully as a syntax-level validation.

Completed checklist:

• Read imported issue context
• Confirmed parent term and existing neighboring terms
• Reviewed cited PubMed sources available in this environment
• Added four new CL_99xxxxx terms with references and metadata
• Validated the edited ontology file
• Committed only src/ontology/cl-edit.owl

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🤖 Generated by opencode agent

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

Agent Response - Issue Comments

Implemented the requested zonal articular chondrocyte terms and committed the changes locally. Ready for review in PR #.

---

🤖 Generated by opencode agent

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

Experiment Config

Parameter	Value
Model	openai/gpt-5.4
Agent config	ai4curation/cl-agent-config@v3:.
Iteration	1
URL prefix	https://href.li/?
Base branch	eval-base-issue-3533

See workflow artifacts for full agent trace.

[cmungall]

📋 Traces: traces/25977506170