[DO NOT MERGE] eval #31961 i:2: obsolete GO:0008785 alkyl hydroperoxide reductase activity (openai/gpt-5.4, .)

[dragon-ai-agent]

⚠️ EVALUATION ONLY - DO NOT MERGE ⚠️

Original Issue

#31961: obsolete GO:0008785 alkyl hydroperoxide reductase activity

Original PR (human solution)

#32015: Obsolete GO:0008785 alkyl hydroperoxide reductase activity (#31961)

Agent Commits

• obsolete GO:0008785 as overly specific catalytic activity

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

Agent Response - PR Comments

Obsoleted GO:0008785 alkyl hydroperoxide reductase activity and replaced it with GO:0102039 NADH-dependent peroxiredoxin activity as requested in issue #31961.

Changes made:

• Converted GO:0008785 to an obsolete term with replaced_by: GO:0102039.
• Added a new term_tracker_item for issue #31961 and recorded the obsoletion reason on the obsolete term.
• Updated the GO:0009321 alkyl hydroperoxide reductase complex see-also comment to reference GO:0102039 instead of the obsolete MF term.
• Removed a stray comment on GO:0070937 CRD-mediated mRNA stability complex that still pointed to GO:0008785.

Rationale:

• The issue already identified GO:0008785 as an overly substrate-specific activity term with GO:0102039 as the correct replacement.
• Obsoleting the term without cleaning up remaining internal references would leave stale ontology comments pointing at an obsolete MF term.

Validation:

• Ran make travis_build in src/ontology.
• Build completed successfully, including ROBOT verification and obsolete-reference checks.

Checklist:

• PLAN: Reviewed the imported issue title, body, and comments.
• PRE-VALIDATION: N/A as a separate baseline run was not performed; post-change full validation passed.
• RESEARCH: N/A; no new biological assertions or literature-backed definitions were added.
• TERM-SEARCH: Reviewed GO:0008785, GO:0102039, and all internal GO:0008785 references in go-edit.obo.
• DESIGN-PATTERNS: N/A; no new terms or logical definitions were added.
• EDITS: Used obo-checkout.pl and obo-checkin.pl with local files in terms/.
• RELATIONSHIPS: Removed active axioms from the obsolete term and rewired or removed stale internal references.
• SPECIALIZED-EDITS: Applied /term-obsoletion guidance; /reaction was consulted because this is a catalytic activity term.
• METADATA: Preserved existing provenance, added the new issue tracker item, and did not add creation metadata to existing terms.
• AUTOMATED-VALIDATION: make travis_build passed.
• REFERENCE-VALIDATION: N/A; no new PMIDs, RHEA IDs, EC IDs, or other reference IDs were introduced.
• CHANGES-COMMITTED: Local commit created: 10e9bf4 (obsolete GO:0008785 as overly specific catalytic activity).

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🤖 Generated by opencode agent

• Runtime: opencode
• Model: openai/gpt-5.4
• Agent config: ai4curation/go-ontology-agent-config@v9:.
• Iteration: 2
• Run: View workflow run

Agent Response - Issue Comments

Implemented locally in PR #.

GO:0008785 alkyl hydroperoxide reductase activity has been obsoleted and replaced by GO:0102039 NADH-dependent peroxiredoxin activity, consistent with the issue discussion that the obsolete term was more specific than any supported gene product annotation. I also updated the GO:0009321 see-also comment to point at GO:0102039 and removed one stray obsolete-term comment from GO:0070937.

Validation passed with make travis_build.

---

🤖 Generated by opencode agent

• Runtime: opencode
• Model: openai/gpt-5.4
• Agent config: ai4curation/go-ontology-agent-config@v9:.
• Iteration: 2
• Run: View workflow run

Experiment Config

Parameter	Value
Model	openai/gpt-5.4
Agent config	ai4curation/go-ontology-agent-config@v9:.
Iteration	2
URL prefix	https://href.li/?
Base branch	eval-base-issue-31961

See workflow artifacts for full agent trace.

[dragon-ai-agent]

📋 Traces: traces/25613564661

[dragon-ai-agent]

Superseded by new run (force_new_branch=true)