[DO NOT MERGE] eval #31961 i:1: obsolete GO:0008785 alkyl hydroperoxide reductase activity (openai/gpt-5.5, .)

[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 alkyl hydroperoxide reductase activity

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

Agent Response - PR Comments

Summary

Addresses geneontology/go-ontology#31961.

Changes made in src/ontology/go-edit.obo:

• Obsoleted GO:0008785 alkyl hydroperoxide reductase activity.
• Added replaced_by: GO:0102039 for NADH-dependent peroxiredoxin activity.
• Added the issue tracker link for #31961.
• Removed the asserted is_a from the obsolete term, per obsolete-term metadata practice.
• Rewired the GO:0009321 alkyl hydroperoxide reductase complex see-also comment from GO:0008785 to GO:0102039.
• Removed an unrelated see-also comment from GO:0070937 CRD-mediated mRNA stability complex that referenced GO:0008785.

Rationale

The issue identifies GO:0008785 as a substrate-specific version of GO:0102039 and requests obsoletion with direct replacement. GO:0102039 already carries the appropriate EC/RHEA/MetaCyc mappings and the exact synonym alkylhydroperoxide reductase activity.

The obsolete term now retains only historical/provenance metadata plus obsoletion metadata. Remaining GO-internal textual references to GO:0008785 were removed or updated so that no non-obsolete stanza points users to the obsolete MF term.

Research / reference checks

Reference IDs mentioned in the issue and on the replacement term were checked with linkml-reference-validator cache reference:

• PMID:11717276 — Alkyl hydroperoxide reductase is the primary scavenger of endogenous hydrogen peroxide in Escherichia coli.
• PMID:21674802 — Proteomics of the oxidative stress response induced by hydrogen peroxide and paraquat reveals a novel AhpC-like protein in Pseudomonas aeruginosa.
• PMID:12517450 — Structure, mechanism and regulation of peroxiredoxins.

Support excerpts recorded in RESEARCH.md were validated with:

linkml-reference-validator validate text-file -r 'SUPPORT: (\S+:\S+) "(.*)"' -t 2 -R 1 RESEARCH.md

All 6 support excerpts validated successfully.

Annotation impact was based on the issue summary because runoak -i amigo: associations GO:0008785 failed in this environment with an OAK/LinkML dependency error (AttributeError: type object 'Format' has no attribute 'JSON'). The issue reports 3 direct annotations, including 2 experimental annotations from EcoliWiki and PseudoCAP, and no InterPro2GO/UniRule/UniProtKW mappings.

Validation

Pre-validation syntax conversion before edits passed:

cd src/ontology && robot convert -i go-edit.obo -f obo -o /tmp/go-edit.prevalidation.obo

Post-edit ontology validation passed:

cd src/ontology && make travis_build

All reported SPARQL checks passed, including obsolete-reference and replaced-by checks.

Checklist

• PLAN: Issue context and comments analyzed; direct obsoletion with replacement was clear.
• PRE-VALIDATION: Current ontology parsed before changes with robot convert.
• RESEARCH: Reference IDs and support excerpts checked; annotation impact reviewed from issue context because OAK/Amigo access failed locally.
• TERM-SEARCH: GO:0008785, GO:0102039, and remaining GO:0008785 references were checked with obo-grep.pl.
• DESIGN-PATTERNS: Obsolete-term metadata pattern applied; no new logical definitions were added.
• EDITS: Terms were checked out to terms/, edited there, and checked back into src/ontology/go-edit.obo.
• RELATIONSHIPS: Obsolete term has no is_a, relationship, or intersection_of; direct replacement uses replaced_by: GO:0102039.
  • Logical definitions N/A; none added.
  • Relationships conform to obsolete-term practice.
  • is_a removed from obsolete term.
• SPECIALIZED-EDITS: /term-obsoletion and /reaction guidance consulted for catalytic activity obsoletion.
• METADATA: Obsolete name, definition prefix, comment, tracker link, is_obsolete: true, and replaced_by are present.
• AUTOMATED-VALIDATION: make travis_build passed.
• REFERENCE-VALIDATION: PMIDs used in research notes were validated; no new definition references were introduced.
• CHANGES-COMMITTED: Only src/ontology/go-edit.obo was committed.

---

🤖 Generated by pi agent

• Runtime: pi
• Model: openai/gpt-5.5
• Agent config: ai4curation/go-ontology-agent-config@v9:.
• Iteration: 1
• Run: View workflow run

Agent Response - Issue Comments

GO:0008785 has been obsoleted with direct replacement GO:0102039 NADH-dependent peroxiredoxin activity in PR #.

I also removed the remaining ontology comments that referenced GO:0008785: the alkyl hydroperoxide reductase complex comment now points to GO:0102039, and an unrelated comment on the CRD-mediated mRNA stability complex was removed.

Validation passed with cd src/ontology && make travis_build.

---

🤖 Generated by pi agent

• Runtime: pi
• Model: openai/gpt-5.5
• Agent config: ai4curation/go-ontology-agent-config@v9:.
• Iteration: 1
• Run: View workflow run

Experiment Config

Parameter	Value
Model	openai/gpt-5.5
Agent config	ai4curation/go-ontology-agent-config@v9:.
Iteration	1
URL prefix	https://href.li/?
Base branch	eval-base-issue-31961

See workflow artifacts for full agent trace.

[dragon-ai-agent]

📋 Traces: traces/25614487254

[dragon-ai-agent]

Superseded by new run (force_new_branch=true)