traces(32044/openai/gpt-5.4): run 25980138583

Author: github-actions[bot]

traces/25980138583/ISSUE_COMMENTS.md

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+Added the requested BP term `protein O-linked glycosylation via N-acetylglucosamine` as a child of `protein O-linked glycosylation`, with synonyms for `protein O-linked GlcNAcylation` and `protein O-linked-N-acetylglucosaminylation`.
+
+The definition was based on PMID:35536957 and explicitly notes that this modification adds a single beta-linked N-acetylglucosamine to serine or threonine and is not elongated into a larger oligosaccharide chain.
+
+Changes committed locally and ready for PR #<NN>.
+
+---
+🤖 **Generated by opencode agent**
+- Runtime: `opencode`
+- Model: `openai/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/25980138583)

traces/25980138583/PR_COMMENTS.md

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+Added a new biological process term to support annotation of Ogt/Eogt and orthologs at the requested level of granularity:
+
+- `GO:7770074` protein O-linked glycosylation via N-acetylglucosamine
+
+What changed:
+
+- Added the new term under `GO:0006493` protein O-linked glycosylation.
+- Added exact synonyms:
+  - `protein O-linked GlcNAcylation`
+  - `protein O-linked-N-acetylglucosaminylation`
+- Added `term_tracker_item` linking back to issue `#32044`.
+- Added `created_by` and `creation_date` metadata for the new term.
+
+Rationale:
+
+- The issue requests a BP term for O-GlcNAcylation so relevant gene products can be annotated more specifically than the generic parent `protein O-linked glycosylation`.
+- Existing GO precedent under `protein O-linked glycosylation` models sugar-specific child processes as direct `is_a` descendants without adding extra logical axioms.
+- PMID:35536957 supports the biology captured in the definition: O-GlcNAc is a distinct modification of serine/threonine residues by a single beta-linked N-acetylglucosamine.
+
+Validation and research performed:
+
+- Validated PMID:35536957 with `linkml-reference-validator cache reference PMID:35536957`.
+- Created temporary `RESEARCH.md` and `DESIGN_PATTERNS.md` notes to document literature support and GO modeling precedent.
+- Validated supporting text in `RESEARCH.md` with `linkml-reference-validator validate text-file`.
+- Ran `make travis_build` from `src/ontology`; build passed.
+
+Completed checklist:
+
+- [x] PLAN: The issue and all its context has been analyzed, the intent is clear, and a plan for addressing it has been created
+- [x] PRE-VALIDATION: Current state of the ontology validates prior to any changes
+- [x] RESEARCH: Necessary background research performed and captured in `RESEARCH.md`
+- [x] TERM-SEARCH: Relevant ontology terms were consulted in `src/ontology/go-edit.obo`
+- [x] DESIGN-PATTERNS: Existing design patterns and sibling terms were consulted and summarized in `DESIGN_PATTERNS.md`
+- [x] EDITS: Correct new-term procedure followed using a staging file in `terms/` and `obo-checkin.pl`
+- [x] RELATIONSHIPS: Appropriate parentage included
+- [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: `/chemical-entity` and `/design-pattern` consulted; no extra CHEBI axiom or DP logical definition was needed for this BP term
+- [x] METADATA: New-term metadata included and issue link added
+- [x] AUTOMATED-VALIDATION: Ontology validates with `make travis_build`
+- [x] REFERENCE-VALIDATION: PMID:35536957 validated and used for the definition
+- [x] CHANGES-COMMITTED
+- [x] RELEVANT-FILES: Only `src/ontology/go-edit.obo` was committed
+- [x] ACCURACY: The change is biologically aligned with the cited review and existing GO precedent
+- [x] ISSUE-ALIGNMENT: The change addresses the requested new term coherently
+- [ ] PR is created or amended
+- [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. Include checklists.
+
+---
+🤖 **Generated by opencode agent**
+- Runtime: `opencode`
+- Model: `openai/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/25980138583)

traces/25980138583/__issue_context__.json

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+{
+  "body": "Following the edits in https://github.com/geneontology/go-ontology/issues/29770 last year (June 2025), the current tree under 'protein O-linked glycosylation' looks like this:\n<img width=\"452\" height=\"131\" alt=\"Image\" src=\"https://github.com/user-attachments/assets/8cfbdafa-a21b-4555-97b3-7501c99211dc\" />\n\nHowever, is seems that one of the new terms requested in https://github.com/geneontology/go-ontology/issues/29770 was not made:\n**protein O-linked glycosylation via N-acetylglucosamine** (referred to as 'protein O-linked GlcNAcylation' in https://github.com/geneontology/go-ontology/issues/29770)\n\nThis term is needed to annotate fly Ogt and Eogt (see https://flybase.org/reports/FBgg0002104) and orthologs.\nThe term was also requested back in 2022 in #23575, but it was not made then because \"This corresponds to the MF protein GO:0097363 O-acetylglucosaminyltransferase activity, since it is a single reaction.\"\n\nIt's true that adding GlcNAc is a single-step event and the sugar isn't further extended - the process is actually reversible and seems more similar to phosphorylation than the other O-linked glycosylations (see PMID: 35536957). Nonetheless, I think we need a distinct BP term for this so that the relevant genes can be annotated to same level of granularity as (and thus be distinguished from) the current sister terms. (Currently, Ogt/Eogt are annotated to the generic parent term 'protein O-linked glycosylation')\n\n\n* **Suggested term label:**\nprotein O-linked glycosylation via N-acetylglucosamine\n\n* **Definition (free text)**\nA glycoprotein biosynthetic process in which a single N-acetylglucosamine is covalently linked via a beta-glycosidic bond to the oxygen atom of a serine or threonine side chain in a protein, resulting in the formation of a protein O-linked glycan. The sugar is not elongated into a larger oligosaccharide chain.\n\n* **Reference, in format PMID:#######**\nPMID: 35536957\n\n\n* **Gene product name and ID to be annotated to this term**\nDmel Ogt and Eogt, and orthologs\n\n* **Parent term(s)**\nprotein O-linked glycosylation\n\n\n* **Synonyms (please specify, EXACT, BROAD, NARROW or RELATED)**\nprotein O-linked GlcNAcylation [EXACT]\nprotein O-linked-N-acetylglucosaminylation  [EXACT]\n\n* **Any other information**\n",
+  "comments": [],
+  "title": "NTR: protein O-linked glycosylation via N-acetylglucosamine",
+  "url": "https://github.com/geneontology/go-ontology/issues/32044"
+}