[DO NOT MERGE] eval #3588 i:1: Prevent contributors from relabelling imported annotation properties (opencode/openai/gpt-5.4, .)

[cmungall]

⚠️ EVALUATION ONLY - DO NOT MERGE ⚠️

Original Issue

#3588: Prevent contributors from relabelling imported annotation properties

Original PR (human solution)

#3589: Dont relabel imported annotation properties ter

Agent Commits

• Remove imported oboInOwl property relabels

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

Agent Response - PR Comments

This change addresses issue #3588 by removing imported annotation-property relabeling that had been reintroduced into src/ontology/cl-edit.owl.

What changed:

• Removed the redundant AnnotationAssertion(rdfs:label ...) axioms for imported oboInOwl:* annotation properties:
  SubsetProperty, consider, hasBroadSynonym, hasDbXref, hasExactSynonym, hasNarrowSynonym, hasRelatedSynonym, hasSynonymType, and inSubset.
• Added a short note to docs/annotation_properties.md stating that imported oboInOwl:* annotation properties already get labels from the import chain and should not be relabeled in src/ontology/cl-edit.owl because that causes spurious serialization diffs.

Rationale:

• The issue report explains that these labels come from the merged import module already.
• Reasserting those labels in cl-edit.owl is unnecessary and creates unstable diffs, especially for properties like hasDbXref that can serialize with conflicting imported labels.
• The ontology change was kept minimal by removing only the redundant relabeling axioms.
• Because this evaluation repo should be edited only in src/ontology/cl-edit.owl or docs/, the preventative follow-up was implemented as contributor documentation rather than a CI/script change.

Checks completed:

• Read the imported issue context from __issue_context__.json.
• Verified the exact redundant rdfs:label axioms present in src/ontology/cl-edit.owl.
• Removed those axioms.
• Confirmed there are no remaining AnnotationAssertion(rdfs:label oboInOwl:...) assertions in src/ontology/cl-edit.owl.
• Reviewed the final diff before committing.

Local commit:

• e22e743 - Remove imported oboInOwl property relabels

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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 commit e22e743.

I removed the redundant rdfs:label assertions for imported oboInOwl:* annotation properties from src/ontology/cl-edit.owl and added a short contributor note in docs/annotation_properties.md to discourage reintroducing them, since they cause spurious serialization diffs.

Changes committed 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-3588

See workflow artifacts for full agent trace.

[cmungall]

📋 Traces: traces/25977575607