traces(31961/gpt-5.4): run 25592435780

Author: github-actions[bot]

traces/25592435780/ISSUE_COMMENTS.md

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+Obsoleted `GO:0008785` and replaced it with `GO:0102039` in PR #<NN>.
+
+I also updated the related `GO:0009321` comment to point to `GO:0102039` and removed one stale copied comment elsewhere that still referenced `GO:0008785`, so the ontology no longer points at the obsolete MF term.
+
+Local validation passed with `cd src/ontology && make travis_build`.
+
+---
+🤖 **Generated by codex agent**
+- Runtime: `codex`
+- Model: `gpt-5.4`
+- Agent config: `ai4curation/go-ontology-agent-config@v8-noskills:.`
+- Iteration: `1`
+- Run: [View workflow run](https://github.com/ai4curation/eval-ont-agent-go/actions/runs/25592435780)

traces/25592435780/PR_COMMENTS.md

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+Obsoleted `GO:0008785` (`alkyl hydroperoxide reductase activity`) and replaced it with `GO:0102039` (`NADH-dependent peroxiredoxin activity`) as requested in issue #31961.
+
+Changes made:
+- Marked `GO:0008785` obsolete, prefixed the definition with `OBSOLETE.`, added an obsoletion comment, added a tracker link to issue `#31961`, and set `replaced_by: GO:0102039`.
+- Updated `GO:0009321` (`alkyl hydroperoxide reductase complex`) so its see-also comment now points to `GO:0102039`.
+- Removed an unrelated stale copied comment on `GO:0070937` that still referenced `GO:0008785`, preventing an obsolete-term reference from remaining in the ontology.
+
+Rationale:
+- The issue discussion indicates `GO:0008785` is an over-specific substrate instance of the broader, already-curated `GO:0102039`, and the requested migration target is exact.
+- Cleaning the remaining ontology comments avoids leaving dangling references to an obsolete MF term.
+
+Validation:
+- Pre-validation: `cd src/ontology && make travis_build`
+- Post-edit validation: `cd src/ontology && make travis_build`
+- Result: passed, including `replacedby-obsolete-violation.sparql`, `replacedby-namespace-violation.sparql`, and `obsolete-reference-violation.sparql`
+
+Checklist:
+- [x] PLAN: Issue and comments reviewed; intent was clear.
+- [x] PRE-VALIDATION: `make travis_build` passed before edits.
+- [x] RESEARCH: N/A, no new references introduced.
+- [x] TERM-SEARCH: Checked `GO:0008785`, `GO:0102039`, and ontology-wide references to `GO:0008785`.
+- [x] DESIGN-PATTERNS: N/A for a straightforward obsoletion/replacement.
+- [x] EDITS: Used checkout/checkin workflow for edited GO terms.
+- [x] RELATIONSHIPS: Obsoletion used `replaced_by: GO:0102039`; no new logical axioms added.
+- [x] SPECIALIZED-EDITS: Obsoletion cleanup completed, including removal/update of stale references to the obsolete term.
+- [x] METADATA: Preserved existing metadata and added the new `term_tracker_item` for issue `#31961`.
+- [x] AUTOMATED-VALIDATION: `make travis_build` passed after changes.
+- [x] REFERENCE-VALIDATION: No new PMIDs or other references introduced.
+- [x] CHANGES-COMMITTED: Committed locally.
+
+---
+🤖 **Generated by codex agent**
+- Runtime: `codex`
+- Model: `gpt-5.4`
+- Agent config: `ai4curation/go-ontology-agent-config@v8-noskills:.`
+- Iteration: `1`
+- Run: [View workflow run](https://github.com/ai4curation/eval-ont-agent-go/actions/runs/25592435780)

traces/25592435780/__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",
+      "includesCreatedEdit": false,
+      "isMinimized": false,
+      "minimizedReason": "",
+      "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",
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+    }
+  ],
+  "title": "obsolete GO:0008785  alkyl hydroperoxide reductase activity",
+  "url": "https://github.com/geneontology/go-ontology/issues/31961"
+}