traces(31961/gpt-5.4): run 25610627574

Author: github-actions[bot]

traces/25610627574/ISSUE_COMMENTS.md

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+Obsoleted GO:0008785 `alkyl hydroperoxide reductase activity` with direct replacement to GO:0102039 `NADH-dependent peroxiredoxin activity`, and committed the change locally for PR #<NN>.
+
+I also cleaned up the remaining GO-internal references to the obsolete term by rewiring the `GO:0009321 alkyl hydroperoxide reductase complex` see-also comment to GO:0102039 and removing an unrelated stray comment on GO:0070937.
+
+---
+🤖 **Generated by codex agent**
+- Runtime: `codex`
+- Model: `gpt-5.4`
+- Agent config: `ai4curation/go-ontology-agent-config@v9:.`
+- Iteration: `1`
+- Run: [View workflow run](https://github.com/ai4curation/eval-ont-agent-go/actions/runs/25610627574)

traces/25610627574/PR_COMMENTS.md

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+Obsoletes GO:0008785 `alkyl hydroperoxide reductase activity` with a direct `replaced_by` link to GO:0102039 `NADH-dependent peroxiredoxin activity`.
+
+Rationale:
+
+The issue request is clear and the replacement target already exists in GO with the expected peroxiredoxin/EC/RHEA grounding. The existing term GO:0008785 encoded a substrate-specific octane hydroperoxide reaction, but the issue discussion and supporting literature indicate that known Ahp/AhpC gene products support the broader NADH-dependent peroxiredoxin activity term instead. I therefore converted GO:0008785 into a standard obsolete term, preserved its historical definition provenance, added an obsoletion reason, added the tracker item for issue #31961, and set `replaced_by: GO:0102039`.
+
+I also removed remaining GO-internal references to GO:0008785. The `GO:0009321 alkyl hydroperoxide reductase complex` see-also comment was rewired to the surviving active MF term GO:0102039. A stray and unrelated `GO:0070937 CRD-mediated mRNA stability complex` comment that referenced GO:0008785 was removed rather than rewired.
+
+Research and review:
+
+I created `RESEARCH.md` and `DESIGN_PATTERNS.md` locally to document the biological rationale and the applicable obsoletion pattern. `RESEARCH.md` covers:
+
+* PMID:12517450, the peroxiredoxin review already used on GO:0102039, supporting the broader peroxide-reducing/peroxiredoxin framing.
+* PMID:11717276, one of the issue-cited experimental annotation PMIDs for E. coli Ahp, supporting Ahp-mediated peroxide scavenging rather than an octane-specific function.
+* PMID:21674802, the issue-cited Pseudomonas annotation PMID, explicitly describing AhpC as a 2-Cys peroxiredoxin involved in peroxide removal.
+
+I attempted PMID validation with `linkml-reference-validator`, but NCBI returned HTTP 429 from this environment; I verified PMID/title/abstract metadata directly via the Europe PMC API instead. No new references were introduced into the ontology file.
+
+Validation:
+
+* Pre-validation passed: `cd src/ontology && make travis_build`
+* Post-change validation passed: `cd src/ontology && make travis_build`
+
+Completed checklist:
+
+- [x] PLAN: The issue and all context were analyzed and the intent was clear.
+- [x] PRE-VALIDATION: Current ontology state validated before changes.
+- [x] RESEARCH: Background research performed and summarized in `RESEARCH.md`.
+- [x] TERM-SEARCH: Relevant GO terms and usages were checked in `src/ontology/go-edit.obo`.
+- [x] DESIGN-PATTERNS: Relevant local obsoletion precedent documented in `DESIGN_PATTERNS.md`.
+- [x] EDITS: Standard `obo-checkout.pl` / `obo-checkin.pl` workflow used with local term files.
+- [x] RELATIONSHIPS: Obsolete term stripped of active relationships/logical axioms; replacement handled via `replaced_by`.
+- [x] logical definitions are appropriate, and are not over-specified, and conform to DESIGN_PATTERNS.md doc.
+- [x] relationships conform to other similar terms in the ontology.
+- [x] is_a is not over-asserted.
+- [x] is_a, part_of, and other relationships specified appropriately.
+- [x] SPECIALIZED-EDITS: /term-obsoletion guidance applied.
+- [x] SPECIALIZED-EDITS: /reaction guidance applied.
+- [x] SPECIALIZED-EDITS: /chemical-entity not applicable.
+- [x] SPECIALIZED-EDITS: /taxon-constraint not applicable.
+- [x] METADATA: Obsoletion metadata and tracker item are correct for the edited term.
+- [x] AUTOMATED-VALIDATION: `make travis_build` passed after changes.
+- [x] REFERENCE-VALIDATION: Supporting PMIDs were checked for title/abstract consistency; no new ontology references were added.
+- [x] CHANGES-COMMITTED
+- [x] RELEVANT-FILES: Only `src/ontology/go-edit.obo` was committed.
+- [x] ACCURACY: The change is biologically aligned with the issue rationale and literature review.
+- [x] ISSUE-ALIGNMENT: The change is a coherent direct-replacement obsoletion for issue #31961.
+- [x] Issue update prepared in `ISSUE_COMMENTS.md` for posting back to the original issue.
+- [x] PR description prepared in `PR_COMMENTS.md` for posting to the PR by automation.
+
+Commit:
+
+* `d7eb245` Obsolete GO:0008785 alkyl hydroperoxide reductase activity
+
+---
+🤖 **Generated by codex agent**
+- Runtime: `codex`
+- Model: `gpt-5.4`
+- Agent config: `ai4curation/go-ontology-agent-config@v9:.`
+- Iteration: `1`
+- Run: [View workflow run](https://github.com/ai4curation/eval-ont-agent-go/actions/runs/25610627574)

traces/25610627574/__issue_context__.json

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+{
+  "body": "This entry has no EC/RHEA/MetaCyc/KEGG xref:\n\nid: GO:0008785\nname: alkyl hydroperoxide reductase activity\nnamespace: molecular_function\ndef: \"Catalysis of the reaction: octane hydroperoxide + NADH + H+ = H2O + NAD+ + 1-octanol.\" [GOC:curators]\nis_a: GO:0016668 ! oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor\nproperty_value: term_tracker_item \"https://github.com/geneontology/go-ontology/issues/28261\" xsd:anyURI\nproperty_value: term_tracker_item \"https://github.com/geneontology/go-ontology/issues/28340\" xsd:anyURI\n\nDespite the generic-sounding name, this is actually a substrate-specific version of the following term (and note that \"alkyl hydroperoxide reductase\" is listed as synonym of EC 1.11.1.26 at Expasy):\n\nid: GO:0102039\nname: NADH-dependent peroxiredoxin activity\nnamespace: molecular_function\ndef: \"Catalysis of the reaction: a hydroperoxide + H+ + NADH = an alcohol + H2O + NAD+.\" [GOC:pz, PMID:12517450, RHEA:62628]\nsynonym: \"alkylhydroperoxide reductase activity\" EXACT []\nxref: EC:1.11.1.26 {source=\"skos:exactMatch\"}\nxref: MetaCyc:R4-RXN\nxref: RHEA:62628 {source=\"skos:exactMatch\"}\nis_a: GO:0051920 ! peroxiredoxin activity\nproperty_value: term_tracker_item \"https://github.com/geneontology/go-ontology/issues/30193\" xsd:anyURI\n\n\nSo, GO:0008785 should be obsoleted and replaced with GO:0102039.\n\nThere are only 3 annotations (2 EXP) to GO:0008785  alkyl hydroperoxide reductase activity:\n- E.coli AhpF from PMID:11717276 by EcoliWiki\n- Pseudomonas PA3529 from PMID:21674802 by PseudoCAP\n\n\n",
+  "comments": [
+    {
+      "id": "IC_kwDOAkAHws8AAAABAyI_4Q",
+      "author": {
+        "login": "raymond91125"
+      },
+      "authorAssociation": "MEMBER",
+      "body": "Dear all, \n\nThe proposal has been made to obsolete GO:0008785 alkyl hydroperoxide reductase activity.\n\n* The reason for obsoletion is that it is more specific than the specificity of any known gene product.\n\nExperimental annotations\nEcoliWiki 1\nPseudoCAP 1\n\nNo InterPro2GO/UniRule/UniProtKW mappings.\n\nAnnotations can be viewed here: \nhttps://github.com/geneontology/go-annotation/issues/6396\n\nThis term is being replaced by GO:0102039 NADH-dependent peroxiredoxin activity\n\nAny comments can be  added to the issue: https://github.com/geneontology/go-ontology/issues/31961\n\n\nThanks, \n",
+      "createdAt": "2026-04-29T21:11:56Z",
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+      "reactionGroups": [],
+      "url": "https://github.com/geneontology/go-ontology/issues/31961#issuecomment-4347543521",
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+    },
+    {
+      "id": "IC_kwDOAkAHws8AAAABAyJLkg",
+      "author": {
+        "login": "raymond91125"
+      },
+      "authorAssociation": "MEMBER",
+      "body": "@dragon-ai-agent please obsolete GO:0008785 alkyl hydroperoxide reductase activity.",
+      "createdAt": "2026-04-29T21:12:29Z",
+      "includesCreatedEdit": false,
+      "isMinimized": false,
+      "minimizedReason": "",
+      "reactionGroups": [
+        {
+          "content": "EYES",
+          "users": {
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+      "url": "https://github.com/geneontology/go-ontology/issues/31961#issuecomment-4347546514",
+      "viewerDidAuthor": false
+    },
+    {
+      "id": "IC_kwDOAkAHws8AAAABAyJU3g",
+      "author": {
+        "login": "dragon-ai-agent"
+      },
+      "authorAssociation": "MEMBER",
+      "body": "🤖 Working on it...\n\nFollow along: [View workflow run](https://github.com/geneontology/go-ontology/actions/runs/25134164454)\n\n*— @dragon-ai-agent*",
+      "createdAt": "2026-04-29T21:12:54Z",
+      "includesCreatedEdit": false,
+      "isMinimized": false,
+      "minimizedReason": "",
+      "reactionGroups": [],
+      "url": "https://github.com/geneontology/go-ontology/issues/31961#issuecomment-4347548894",
+      "viewerDidAuthor": true
+    }
+  ],
+  "title": "obsolete GO:0008785  alkyl hydroperoxide reductase activity",
+  "url": "https://github.com/geneontology/go-ontology/issues/31961"
+}