traces(31961/gpt-5.5): run 25614460056

Author: github-actions[bot]

traces/25614460056/ISSUE_COMMENTS.md

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+GO:0008785 has been obsoleted and marked as replaced by GO:0102039. The two `go-edit.obo` comments that pointed to GO:0008785 were updated to point to GO:0102039.
+
+Changes committed in PR #<NN>.
+
+---
+🤖 **Generated by codex agent**
+- Runtime: `codex`
+- Model: `gpt-5.5`
+- Agent config: `ai4curation/go-ontology-agent-config@v9:.`
+- Iteration: `1`
+- Run: [View workflow run](https://github.com/ai4curation/eval-ont-agent-go/actions/runs/25614460056)

traces/25614460056/PR_COMMENTS.md

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+# Summary
+
+Obsoleted GO:0008785 `alkyl hydroperoxide reductase activity` and added `replaced_by: GO:0102039` (`NADH-dependent peroxiredoxin activity`).
+
+The obsolete stanza now follows GO obsoletion metadata conventions: obsolete label, `OBSOLETE.` definition prefix, obsoletion comment, issue #31961 term tracker item, `is_obsolete: true`, and no asserted `is_a`.
+
+Also updated two `go-edit.obo` comments that referenced GO:0008785 so they now point to GO:0102039:
+
+* GO:0009321 `alkyl hydroperoxide reductase complex`
+* GO:0070937 `CRD-mediated mRNA stability complex`
+
+# Rationale
+
+The issue requested direct obsoletion with replacement because GO:0008785 is a substrate-specific version of the broader, already cross-referenced GO:0102039 term. Rhea confirms RHEA:62628 as the reaction for GO:0102039 and EC:1.11.1.26.
+
+Reference checks were recorded in `RESEARCH.md`. PMID:12517450 and PMID:11717276 were cached and support text validated with `linkml-reference-validator`. PMID:21674802 was checked via EPA HERO because the NCBI request through the validator returned HTTP 429.
+
+# Validation
+
+* Pre-change `cd src/ontology && make travis_build`: passed
+* Post-change `cd src/ontology && make travis_build`: passed
+* `linkml-reference-validator validate text-file -r 'SUPPORT: (\S+:\S+) "(.*)"' -t 2 -R 1 RESEARCH.md`: passed
+* `obo-grep.pl --noheader -r 'GO:0008785' src/ontology/go-edit.obo`: only the obsolete stanza remains
+
+# Checklist
+
+* [x] PLAN: Issue context and comments reviewed; intent was clear.
+* [x] PRE-VALIDATION: Ontology validated before edits with `make travis_build`.
+* [x] RESEARCH: `RESEARCH.md` created; relevant PMIDs and Rhea replacement checked.
+* [x] TERM-SEARCH: GO:0008785, GO:0102039, and GO references to GO:0008785 checked in `go-edit.obo`.
+* [x] DESIGN-PATTERNS: `DESIGN_PATTERNS.md` created; obsoletion pattern applied; no new logical definitions added.
+* [x] EDITS: Terms were edited via `obo-checkout.pl` and `obo-checkin.pl`.
+* [x] RELATIONSHIPS: Obsolete term has no asserted `is_a`, `relationship`, or `intersection_of`; replacement is asserted with `replaced_by`.
+* [x] SPECIALIZED-EDITS: `/term-obsoletion`, `/reaction`, `/chemical-entity`, and `/design-pattern` checks applied as relevant.
+* [x] METADATA: Added issue #31961 `term_tracker_item`; no `created_by` or `creation_date` added because no new term was created.
+* [x] AUTOMATED-VALIDATION: Post-change `make travis_build` passed.
+* [x] REFERENCE-VALIDATION: PMID support lines in `RESEARCH.md` validated where cache access was available; no new definition references introduced.
+* [x] CHANGES-COMMITTED: Local commit `44e13a0` contains only `src/ontology/go-edit.obo`.
+
+---
+🤖 **Generated by codex agent**
+- Runtime: `codex`
+- Model: `gpt-5.5`
+- Agent config: `ai4curation/go-ontology-agent-config@v9:.`
+- Iteration: `1`
+- Run: [View workflow run](https://github.com/ai4curation/eval-ont-agent-go/actions/runs/25614460056)

traces/25614460056/__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",
+      "viewerDidAuthor": false
+    },
+    {
+      "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": {
+            "totalCount": 1
+          }
+        }
+      ],
+      "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"
+}