traces(31961/openai/gpt-5.4): run 25614306977

Author: github-actions[bot]

traces/25614306977/ISSUE_COMMENTS.md

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+Obsoleted GO:0008785 and set GO:0102039 (NADH-dependent peroxiredoxin activity) as the replacement in PR #<NN>.
+
+I also updated the remaining internal reference from GO:0009321 to point to GO:0102039 and removed an unrelated stale comment that still mentioned GO:0008785, so there are no remaining GO-internal references to the obsolete term.
+
+I validated the two annotation PMIDs mentioned in the issue (PMID:11717276 and PMID:21674802); both are consistent with annotation to the broader NADH-dependent peroxiredoxin activity term rather than retaining a separate substrate-specific GO:0008785 term.
+
+---
+🤖 **Generated by pi agent**
+- Runtime: `pi`
+- Model: `openai/gpt-5.4`
+- Agent config: `ai4curation/go-ontology-agent-config@v9:.`
+- Iteration: `2`
+- Run: [View workflow run](https://github.com/ai4curation/eval-ont-agent-go/actions/runs/25614306977)

traces/25614306977/PR_COMMENTS.md

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+Summary
+
+This PR obsoletes GO:0008785 "alkyl hydroperoxide reductase activity" and replaces it with GO:0102039 "NADH-dependent peroxiredoxin activity", as requested in issue #31961.
+
+Changes made
+
+- Obsoleted GO:0008785.
+  - name -> "obsolete alkyl hydroperoxide reductase activity"
+  - definition -> prefixed with "OBSOLETE."
+  - removed active classification
+  - added obsoletion comment
+  - added `is_obsolete: true`
+  - added `replaced_by: GO:0102039`
+  - added `term_tracker_item` for issue #31961
+- Updated GO:0102039.
+  - transferred the original GO:0008785 label as an EXACT synonym: "alkyl hydroperoxide reductase activity"
+  - added `term_tracker_item` for issue #31961
+- Removed remaining GO-internal references to GO:0008785.
+  - updated GO:0009321 comment to point to GO:0102039
+  - removed an unrelated stale comment on GO:0070937 that still referenced GO:0008785
+
+Rationale
+
+The issue rationale is sound: GO:0008785 is an over-specific substrate-level molecular function term, while GO:0102039 already captures the NADH-dependent peroxiredoxin/alkylhydroperoxide reductase activity and carries the EC/RHEA/MetaCyc cross-references.
+
+I validated the two PMIDs cited in the issue context:
+
+- 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."
+
+Both support annotation to the broader NADH-dependent peroxiredoxin activity term rather than retaining GO:0008785 as a distinct substrate-specific activity.
+
+Validation and research notes
+
+- Pre-validation: `cd src/ontology && make travis_build` passed before edits.
+- Post-validation: `cd src/ontology && make travis_build` passed after edits.
+- PMID validation: performed with `linkml-reference-validator cache reference ...`
+- Research notes captured in `RESEARCH.md` (not committed).
+- I attempted to use `runoak` for annotation/usages lookup per the obsoletion workflow, but the local environment has an oaklib/linkml import error. I therefore relied on the annotation counts given in the issue context and separately validated the cited PMIDs.
+
+Checklist
+
+- [x] PLAN: The issue and context were analyzed and the requested obsoletion/replacement path was clear.
+- [x] PRE-VALIDATION: Current ontology state validated before edits (`make travis_build`).
+- [x] RESEARCH: Annotation-supporting PMIDs reviewed and summarized in `RESEARCH.md`.
+- [x] TERM-SEARCH: Relevant GO terms searched in `src/ontology/go-edit.obo` with `obo-grep.pl`/`grep`.
+- [ ] DESIGN-PATTERNS: N/A for this obsoletion; no new logical definitions or compositional term design added.
+- [x] EDITS: Used checkout/checkin workflow via `obo-checkout.pl` and `obo-checkin.pl` with edits staged through `terms/`.
+- [x] RELATIONSHIPS: Obsolete term stripped of active axioms; remaining internal references rewired appropriately.
+  - [x] logical definitions are appropriate, and are not over-specified, and conform to DESIGN_PATTERNS.md doc (N/A; none added)
+  - [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:
+  - [x] /term-obsoletion skill used
+  - [x] /reaction skill consulted (catalytic activity / EC-RHEA context)
+  - [ ] /chemical-entity skill: N/A
+  - [ ] /taxon-constraint skill: N/A
+- [x] METADATA: Obsolete-term metadata and replacement metadata updated appropriately.
+- [x] AUTOMATED-VALIDATION: `make travis_build` passed after changes.
+- [x] REFERENCE-VALIDATION: PMIDs introduced in the issue context and research notes were validated.
+- [x] CHANGES-COMMITTED
+  - [x] RELEVANT-FILES: committed only `src/ontology/go-edit.obo`
+  - [x] ACCURACY: changes align with the issue rationale and validated literature context
+  - [x] ISSUE-ALIGNMENT: changes form a coherent direct-replacement obsoletion
+  - [ ] PR is created or amended: N/A here; handled by the evaluation harness
+  - [x] Communicate high level summary of changes on original issue(s), and any requests for further info
+  - [x] Communicated on PR detailed description of changes made, and rationale
+
+---
+🤖 **Generated by pi agent**
+- Runtime: `pi`
+- Model: `openai/gpt-5.4`
+- Agent config: `ai4curation/go-ontology-agent-config@v9:.`
+- Iteration: `2`
+- Run: [View workflow run](https://github.com/ai4curation/eval-ont-agent-go/actions/runs/25614306977)

traces/25614306977/__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"
+}