[DO NOT MERGE] eval #3454 i:1: [Class hierarchy] Remove CD44-high and CD122-high from CD45RO-positive memory T cells (opencode/openai/gpt-5.4, .)

[cmungall]

⚠️ EVALUATION ONLY - DO NOT MERGE ⚠️

Original Issue

#3454: [Class hierarchy] Remove CD44-high and CD122-high from CD45RO-positive memory T cells

Original PR (human solution)

#3555: Remove CD44-high and CD122-high from CD45RO-positive memory T cells

Agent Commits

• Update CD45RO-positive memory T cell markers

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

Agent Response - PR Comments

Updated the two human CD45RO-positive memory T cell parent classes requested in issue #3454.

Changes made:

• Edited CL_0001203 (CD8-positive, alpha-beta memory T cell, CD45RO-positive) to remove the CD44-high and CD122-high constraints from its EquivalentClasses axiom.
• Edited CL_0001204 (CD4-positive, alpha-beta memory T cell, CD45RO-positive) to remove the same two constraints from its EquivalentClasses axiom.
• Revised both textual definitions so they now describe these classes as CD45RO-positive, CD127-positive, and CD25-negative, without asserting CD44-high or CD122-high.
• Preserved the existing definition xrefs and added the requested supporting PMIDs: 21926977, 24258910, and 41254224.

Rationale:

• The issue requested removal of CD44-high and CD122-high from the parent classes so subclasses inheriting from these human memory T-cell terms are not overconstrained by markers that are not intended to define the broader parent classes.
• The textual definitions were updated to stay aligned with the revised logical axioms.

Validation performed:

• Checked the exact ontology diff to ensure only the two targeted class stanzas changed.
• Ran git diff --check -- src/ontology/cl-edit.owl to confirm there were no whitespace or patch-formatting issues.

Completed checklist:

• Read imported issue context.
• Located the two target class stanzas in src/ontology/cl-edit.owl.
• Removed the CD44-high and CD122-high logical restrictions from both parent classes.
• Updated both definitions to match the revised class meaning.
• Added the requested references alongside the existing xrefs.
• Validated the resulting diff.
• Committed only the ontology file that was edited.

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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

Addressed in local changes committed for PR #.

Summary:

• Removed the CD44-high and CD122-high phenotype constraints from CL_0001203 and CL_0001204.
• Updated the textual definitions for both classes so they retain CD45RO-positive, CD127-positive, and CD25-negative but no longer describe the removed markers.
• Added the requested supporting references: PMID:21926977, PMID:24258910, and PMID:41254224.

---

🤖 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-3454

See workflow artifacts for full agent trace.

[cmungall]

📋 Traces: traces/25977402311