[DO NOT MERGE] eval #3453 i:1: [NTR] CD4-positive exhausted alpha-beta T cell / CD8-positive exhausted alpha-beta T cell (opencode/openai/gpt-5.4, .)

[cmungall]

⚠️ EVALUATION ONLY - DO NOT MERGE ⚠️

Original Issue

#3453: [NTR] CD4-positive exhausted alpha-beta T cell / CD8-positive exhausted alpha-beta T cell

Original PR (human solution)

#3556: Add CD4-positive and CD8-positive exhausted alpha-beta T cell terms

Agent Commits

• Add exhausted CD4 and CD8 alpha-beta T cell terms

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

Agent Response - PR Comments

Added two new CL terms in src/ontology/cl-edit.owl:

• CL_9900001 CD4-positive exhausted alpha-beta T cell
• CL_9900002 CD8-positive exhausted alpha-beta T cell

Rationale:

• The issue requested lineage-specific exhausted T-cell terms.
• Following the issue notes and existing CL organization, these were placed directly under CL_0000624 CD4-positive, alpha-beta T cell and CL_0000625 CD8-positive, alpha-beta T cell.
• I did not use CL_0011025 exhausted T cell as the parent because that term is an abstract lineage-free class, and the issue discussion explicitly called out that these new lineage-defined subsets should not be modeled under it.

What changed:

• Added class declarations for both new IDs.
• Added text definitions with PMID-backed xrefs.
• Added requested synonyms with literature xrefs.
• Added issue tracking with obo:IAO_0000233 pointing to issue #3453.
• Added both ORCID contributors from the issue body.
• Added terms:creator "GitHub Copilot" and terms:date annotations for the new terms.
• Added subclass axioms to the lineage parents.
• Added a PD-1 marker restriction for each term using ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001919) to capture the required shared marker.

Background checks completed:

• Read the imported issue context from __issue_context__.json.
• Checked src/ontology/cl-edit.owl to confirm the requested terms did not already exist.
• Confirmed the exact parent labels and IDs for CL_0000624 and CL_0000625.
• Reviewed the existing CL_0011025 exhausted T-cell term and local annotation style for new term blocks.
• Used the issue references and avoided the incorrect PMID noted in the imported discussion.

Validation performed:

• Reviewed the exact ontology diff after editing.
• Confirmed only src/ontology/cl-edit.owl was staged and committed.

Commit created locally:

• d998967 Add exhausted CD4 and CD8 alpha-beta T cell terms

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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

Changes committed in PR #.

Added new terms for CD4-positive exhausted alpha-beta T cell and CD8-positive exhausted alpha-beta T cell, placed directly under the corresponding CD4-positive and CD8-positive alpha-beta T-cell parents rather than under the abstract exhausted T cell class, consistent with the issue discussion.

---

🤖 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-3453

See workflow artifacts for full agent trace.

[cmungall]

📋 Traces: traces/25977413743