[DO NOT MERGE] eval #3452 i:1: [NTR] Add new terms for stem cell memory T cells (TSCM): CD4+ and CD8+ subsets (opencode/openai/gpt-5.4, .)

[cmungall]

⚠️ EVALUATION ONLY - DO NOT MERGE ⚠️

Original Issue

#3452: [NTR] Add new terms for stem cell memory T cells (TSCM): CD4+ and CD8+ subsets

Original PR (human solution)

#3554: Add stem cell memory T cell terms: CD4+ and CD8+ subsets

Agent Commits

• Add CD4 and CD8 stem cell memory T cell terms for issue #3452

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

Agent Response - PR Comments

Added two new Cell Ontology terms requested in issue #3452:

• CL_9900001 stem cell memory CD4-positive, alpha-beta T cell
• CL_9900002 stem cell memory CD8-positive, alpha-beta T cell

What changed:

• Added declarations for both new classes in src/ontology/cl-edit.owl.
• Added labels, text definitions, issue tracking annotation, contributor ORCIDs, creator, and timestamps.
• Added requested exact synonyms for both CD4 and CD8 TSCM terms.
• Placed the new terms under the existing memory T-cell parents:
  • CD4 TSCM under CL_0000897 CD4-positive, alpha-beta memory T cell
  • CD8 TSCM under CL_0000909 CD8-positive, alpha-beta memory T cell

Rationale:

• The issue requested two new stem cell memory T-cell subset terms rather than species-specific subclasses.
• The comment thread raised broader species-specific modeling questions for memory T-cell subsets, but also noted that this should be handled in a separate ticket, so I kept this change scoped to the concrete NTR.
• The definitions follow the request text and are supported by the cited literature on T memory stem cells and their long-lived, self-renewing, multipotent properties.

References used in the definitions and/or synonym support:

• PMID:19525962
• PMID:21926977
• PMID:28060797

Validation performed:

• Confirmed the requested terms were not already present in src/ontology/cl-edit.owl.
• Checked the existing hierarchy for the CD4 and CD8 memory T-cell parent classes.
• Ran a ROBOT syntax conversion check:
  • robot convert -i src/ontology/cl-edit.owl -o /tmp/opencode/cl-edit-validated.owl

Checklist completed:

• Read imported issue context
• Verified existing parent terms in the ontology
• Added two new CL_99xxxxx terms
• Added definitions with literature references
• Added requested ORCID contributors
• Added issue tracker annotation
• Performed syntax validation with ROBOT
• Committed only the ontology edit

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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 new terms for stem cell memory T cells and committed the ontology changes locally.

Added:

• stem cell memory CD4-positive, alpha-beta T cell
• stem cell memory CD8-positive, alpha-beta T cell

These changes are committed in PR #.

I kept this ticket focused on the two requested new terms. The species-specific modeling questions raised in the thread were not folded into this edit.

---

🤖 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-3452

See workflow artifacts for full agent trace.

[cmungall]

📋 Traces: traces/25977400720