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‎traces/25978840224/ISSUE_COMMENTS.md‎

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Obsoleted `GO:0061817` as requested and mapped it to `GO:0160214 endoplasmic reticulum-plasma membrane adaptor activity`.
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Validation passed locally.
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One follow-up point: direct annotations to `GO:0061817` are still present in AmiGO, with many remaining `IBA` annotations, so annotation migration/review should still be completed on the annotation side.
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Changes committed locally and ready for PR #<NN>.
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---
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🤖 **Generated by opencode agent**
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- Runtime: `opencode`
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- Model: `openai/gpt-5.4`
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- Agent config: `ai4curation/go-ontology-agent-config@v9:.`
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- Iteration: `1`
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- Run: [View workflow run](https://github.com/ai4curation/eval-ont-agent-go/actions/runs/25978840224)

‎traces/25978840224/PR_COMMENTS.md‎

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Obsoleted `GO:0061817 endoplasmic reticulum-plasma membrane tethering` because the issue correctly identified it as representing a molecular function rather than a biological process.
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Changes made:
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- Converted `GO:0061817` to an obsolete term in `src/ontology/go-edit.obo`
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- Updated the label to `obsolete endoplasmic reticulum-plasma membrane tethering`
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- Preserved the original definition provenance and converted the definition to the required `OBSOLETE.` form
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- Removed the synonym and biological process parentage from the obsolete stanza
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- Added an obsoletion comment explaining the reason
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- Added `property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31873" xsd:anyURI`
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- Added `is_obsolete: true`
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- Added `replaced_by: GO:0160214` (`endoplasmic reticulum-plasma membrane adaptor activity`)
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Rationale:
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- The original BP term described membrane tethering accomplished by a tether/adaptor molecule, which is better modeled as the MF term `GO:0160214`.
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- The issue discussion explicitly requested obsoletion and identified `GO:0160214` as the annotation target to use.
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- `GO:0051643 endoplasmic reticulum localization` remains broader, but the direct replacement used here is the more specific MF requested in the issue comments.
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Validation and checks:
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- Checked the imported issue context and local repo guidance
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- Used the term obsoletion workflow and edited the term through `obo-checkout.pl` / `obo-checkin.pl`
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- Confirmed there were no internal GO ontology references to `GO:0061817` outside its own stanza
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- Ran `make travis_build` in `src/ontology`; build passed
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- Queried direct annotation usage with `runoak -i amigo: associations GO:0061817`
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Annotation impact note:
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- Direct annotations to `GO:0061817` are still present in AmiGO, including many `IBA` annotations, so annotation migration remains necessary after the ontology obsoletion.
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- This matches the issue history noting that annotation review/migration is part of the follow-up work.
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Checklist:
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- [x] PLAN: analyzed issue context and intent
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- [x] PRE-VALIDATION: validated ontology state as part of local `make travis_build`
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- [x] TERM-SEARCH: reviewed `GO:0061817`, `GO:0160214`, and `GO:0051643`
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- [x] DESIGN-PATTERNS: not applicable beyond standard obsoletion pattern
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- [x] EDITS: used checkout/checkin workflow via `terms/`
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- [x] RELATIONSHIPS: removed obsolete-term logical/structural axioms
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- [x] SPECIALIZED-EDITS: used obsoletion workflow
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- [x] METADATA: added correct obsoletion metadata and issue tracker link
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- [x] AUTOMATED-VALIDATION: `make travis_build` passed
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- [x] REFERENCE-VALIDATION: preserved existing definition provenance only; no new references introduced
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- [x] CHANGES-COMMITTED: committed local ontology change
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---
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🤖 **Generated by opencode agent**
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- Runtime: `opencode`
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- Model: `openai/gpt-5.4`
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- Agent config: `ai4curation/go-ontology-agent-config@v9:.`
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- Iteration: `1`
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- Run: [View workflow run](https://github.com/ai4curation/eval-ont-agent-go/actions/runs/25978840224)

‎traces/25978840224/__issue_context__.json‎

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{
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"body": "\n\nTransferred from\nhttps://github.com/geneontology/go-ontology/issues/22181\n\nPlease provide as much information as you can:\n\n* **GO term ID and Label**\n* \nGO:0061817 endoplasmic reticulum-plasma membrane tethering\nThe attachment of an endoplasmic reticulum membrane to the plasma membrane via molecular tethers.\n\n* **Reason for deprecation** Put an x in the appropriate box: \n\n - [x] The reason for obsoletion is that this term represents a molecular function.\n\n* **\"Replace by\" term (ID and label)**\nIf all annotations can safely be moved to that term\n\n* **\"Consider\" term(s) (ID and label)**\n\nThis is an MF and should use\n[GO:0160214] endoplasmic reticulum-plasma membrane adaptor activity\npart_of GO:0051643 endoplasmic reticulum localization\n\nGO:0061817 endoplasmic reticulum-plasma membrane tethering\ncould have direct replacemnt GO:0051643 endoplasmic reticulum localization\nbut curators should check that the correct MF term is annotated\n\n\n\n\n* **Are there annotations to this term?**\n- How many EXP: 15\n\n* **Are there mappings and cross references to this term? (InterPro, Keywords; check QuickGO cross-references section)**\n\n* **Is this term in a subset? (check the AmiGO page for that term)**\n\n* **Any other information**\n\n\n----\nChecklist for ontology editor\n\n***Check term usage and metadata in Protégé***\n- [ ] check term usage in the ontology \n- [ ] check internal mappings: RHEA, EC, MetaCyc\n- [ ] check subset usage\n- [ ] check taxon constraints \n\n***Check annotations***\n- [ ] create Annotation Review spreadsheet \n- * Annotation Review template: https://docs.google.com/spreadsheets/d/1izV3q1jnq_Ybg5MJ53O_b5BCTkGtjl_Fi-cOg3-7eBE/edit#gid=0\n- * Instructions: https://wiki.geneontology.org/Annotation_Review_Request\n- [ ] create annotation review ticket: https://github.com/geneontology/go-annotation/issues/new?assignees=&labels=annotation+review&template=annotation-review-for-obsoletion.md&title=Review+annotations+to+%5BINSERT+GO+TERM%5D\n- [ ] find external mappings (via IEAS), include in obsoletion notice \n- [ ] tag curators in Annotation Review ticket. Responsible annotator for each group: https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv\n\n***Notification***\n- [ ] create [obsoletion announcement](https://github.com/geneontology/go-announcements/issues/new?assignees=&labels=obsoletion&template=obsoletion-notice.md&title=Obsoletion+notice%3A+%5BGO+ID%3A+term+label%5D)\n- [ ] announce to GO friends (go-friends@mailman.stanford.edu)\n- [ ] paste the text in the ontology ticket\n",
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"comments": [
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"id": "IC_kwDOAkAHws8AAAABBKemAA",
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"author": {
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"login": "raymond91125"
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},
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"authorAssociation": "MEMBER",
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"body": "The proposal has been made to obsolete GO:0061817 endoplasmic reticulum-plasma membrane tethering.\n\n\n* The reason for obsoletion is that this term represents a molecular function.\n\nExperimental annotations\nCGD 4\nPomBase 13 DONE\nTAIR 2\nUniProt 2 DONE\n\n8 InterPro2GO mappings have been removed.\n\nAnnotations can be viewed here: https://github.com/geneontology/go-annotation/issues/6383\n\nAnnotations can be transferred to\nGO:0160214 endoplasmic reticulum-plasma membrane adaptor activity.\n\nAny comments can be added to the issue: https://github.com/geneontology/go-ontology/issues/31873\n\n\nThanks, ",
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"createdAt": "2026-05-04T17:27:40Z",
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"author": {
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"authorAssociation": "MEMBER",
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"body": "@dragon-ai-agent please obsolete GO:0061817 endoplasmic reticulum-plasma membrane tethering.",
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"createdAt": "2026-05-04T17:28:08Z",
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"login": "dragon-ai-agent"
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"body": "🤖 Working on it...\n\nFollow along: [View workflow run](https://github.com/geneontology/go-ontology/actions/runs/25333221838)\n\n*— @dragon-ai-agent*",
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"createdAt": "2026-05-04T17:28:31Z",
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"title": "Obsoletion request: GO:0061817 endoplasmic reticulum-plasma membrane tethering",
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"url": "https://github.com/geneontology/go-ontology/issues/31873"
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}

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