[DO NOT MERGE] eval #3597 i:1: [NTR] Add mouth terms for Hubmap (opencode/openai/gpt-5.4, .)

[cmungall]

⚠️ EVALUATION ONLY - DO NOT MERGE ⚠️

Original Issue

#3597: [NTR] Add mouth terms for Hubmap

Original PR (human solution)

#3598: Add 8 mouth/salivary gland cell type terms for HuBMAP (issue #3597)

Agent Commits

• Add new mouth and salivary gland cell terms

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

Agent Response - PR Comments

Implemented a set of new mouth and salivary gland cell type terms requested in issue #3597.

Added new terms:

• CL_9900001 serous demilune cell of salivary gland
• CL_9900002 basal duct cell of salivary gland
• CL_9900003 periductal fibroblast of salivary gland
• CL_9900004 junctional epithelial cell
• CL_9900005 tuft cell of parotid gland
• CL_9900006 tuft cell of sublingual gland
• CL_9900007 ionocyte of salivary gland
• CL_9900008 myoepithelial cell of salivary gland

What I changed:

• Added labels, text definitions, cited synonyms, contributor ORCID, creator, timestamps, and issue links for each new class.
• Used conservative modeling with asserted parentage and part_of restrictions aligned to existing salivary gland patterns already present in cl-edit.owl.
• Added function-related axioms only where they were directly supported by the issue text and existing local modeling patterns.

Rationale:

• The imported issue body bundled multiple clearly specified new-term requests under issue #3597.
• Existing local ontology content already included related salivary gland classes such as tuft cell of submandibular gland, salivary gland acinar cell subclasses, and salivary gland duct cell types, so these additions were modeled to stay consistent with that local structure.
• I avoided overcommitting to more specific logical definitions where the issue text was broad or anatomy-specific evidence was limited.

Validation and research:

• Read __issue_context__.json and repository guidance in AGENTS.md.
• Checked existing salivary gland and gingival terms in src/ontology/cl-edit.owl to align naming and axioms.
• Retrieved PubMed pages for key cited references used in the request.
• Ran syntax validation with:
  robot convert --input src/ontology/cl-edit.owl --output /tmp/opencode/cl-edit.ofn

Completed checklist:

• Read issue context
• Confirmed relevant existing ontology patterns
• Added new classes in src/ontology/cl-edit.owl
• Added references, ORCID contributor, dates, and issue links
• Validated ontology syntax with robot convert
• Committed only the ontology file locally

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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 ontology additions for issue #3597 locally and committed the ontology changes. Please see PR # for review.

---

🤖 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-3597

See workflow artifacts for full agent trace.

[cmungall]

📋 Traces: traces/25977628964