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‎traces/25979820856/ISSUE_COMMENTS.md‎

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Implemented locally and committed.
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I obsoleted `GO:1905353` and `GO:0097711`, both with `replaced_by: GO:1905349` as agreed in the issue thread. I also rewired the internal `starts_with` reference from `GO:0060271 cilium assembly` to `GO:1905349` so the obsolete term is no longer referenced in the ontology.
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Validation passed with `make travis_build`.
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Changes committed in 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/25979820856)

‎traces/25979820856/PR_COMMENTS.md‎

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Summary
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This change obsoletes the two ciliary process terms discussed in issue `#31882`:
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- `GO:0097711` `ciliary basal body-plasma membrane docking`
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- `GO:1905353` `ciliary transition fiber assembly`
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Both obsolete terms now carry:
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- `name: obsolete ...`
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- `def: "OBSOLETE. ..."` preserving the original definition provenance
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- `property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31882" xsd:anyURI`
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- `is_obsolete: true`
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- `replaced_by: GO:1905349`
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I also rewired the only GO-internal reference I found to an obsolete term:
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- `GO:0060271 cilium assembly`
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- changed `relationship: starts_with GO:0097711` to `relationship: starts_with GO:1905349 ! ciliary transition zone assembly`
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Rationale
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The issue discussion reached a final decision to obsolete both terms as redundant with `GO:1905349 ciliary transition zone assembly`, specifically the final decision noted in `https://github.com/geneontology/go-ontology/issues/31882#issuecomment-4235254498`. The imported issue context also records that curator-side annotation cleanup had already been handled or reviewed as part of the obsoletion discussion.
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Validation
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- Pre-validation: `make travis_build` passed before edits
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- Post-edit validation: `make travis_build` passed after edits
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- Checked GO-internal references with `obo-grep.pl`; the only in-ontology reference requiring rewiring was the `starts_with` edge from `GO:0060271`
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Checklist
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- [x] PLAN: Issue context reviewed and final requested action was clear
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- [x] PRE-VALIDATION: Current ontology validated before edits
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- [x] TERM-SEARCH: Relevant GO terms and references inspected with `obo-grep.pl`
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- [x] SPECIALIZED-EDITS: `/term-obsoletion` guidance followed
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- [x] EDITS: Used `obo-checkout.pl` / edited in `terms/` / `obo-checkin.pl`
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- [x] RELATIONSHIPS: Removed obsolete term usage and rewired the affected internal relationship
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- [x] METADATA: Added obsoletion metadata and issue tracker links; preserved original provenance
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- [x] AUTOMATED-VALIDATION: `make travis_build` passed after changes
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- [x] ISSUE-ALIGNMENT: Changes match the explicit final decision in the issue thread
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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/25979820856)

‎traces/25979820856/__issue_context__.json‎

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"body": "\n\n**Final decision: see https://github.com/geneontology/go-ontology/issues/31882#issuecomment-4235254498\n(obsolete and replace)**\n\n- obsolete GO:1905353 ciliary transition fiber assembly >> replace by GO:1905349 ciliary transition zone assembly \n- obsolete GO:0097711 ciliary basal body-plasma membrane docking >> replace by GO:1905349 ciliary transition zone assembly\n\n\n~GO:0097711 ciliary basal body-plasma membrane docking\nThe docking of a cytosolic centriole/basal body to the plasma membrane via the ciliary transition fibers. In some species this may happen via an intermediate step, by first docking to the ciliary vesicle via the ciliary transition fibers. The basal body-ciliary vesicle then relocates to the plasma membrane, followed by the ciliary vesicle fusing with the plasma membrane, effectively attaching the basal body to the plasma membrane.\nThis sounds MUCH broader than \nremove parent\nGO:0140056 organelle localization by membrane tethering\nThe aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.\nand it has other is_a parents\n(this term will be obsoleted once descendants are removed or rehoused)~\n\n",
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"body": "@ValWood \n\nThis term doesn't have other is_a parents: \n\n<img width=\"645\" height=\"469\" alt=\"Image\" src=\"https://github.com/user-attachments/assets/c98cee6d-a721-4176-a554-466bc2cc3b76\" />\n\n\nDidn't we say that tethering was a MF ? ",
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"body": "GO:0051640 organelle localization ?\n",
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"body": "This is docking. Docking and tethering are separate steps in vesicle -mediated transport.\n\nThis seems to be referring to a broader processs, this isn't just describing docking:\n\nThe docking of a cytosolic centriole/basal body to the plasma membrane via the ciliary transition fibers. In some species this may happen via an intermediate step, by first docking to the ciliary vesicle via the ciliary transition fibers. The basal body-ciliary vesicle then relocates to the plasma membrane, followed by the ciliary vesicle fusing with the plasma membrane, effectively attaching the basal body to the plasma membrane.\n\nIt's a bit vague, so I was going to park it until somebody models this process.....\n\nIf it really is describing \"docking\" it can be obsoleted with the rest of the docking terms\nhttps://github.com/geneontology/go-ontology/issues/31880\n\n",
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"body": "There are only 6 EXP annotations, 3 are fly\n@hattrill do you know the intended scope of \"ciliary basal body-plasma membrane docking\"?\nIs this single step or a multistep process?\n\nIs it analogous to vesicle dociking?\n\nthanks\nVal",
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"body": "It seems to involve the entire centriole:\nhttps://link.springer.com/article/10.1186/s13630-016-0030-8/figures/1",
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"body": "From \"PMID:27646273\" TZ assembly is a complex process starting with the docking of the mother centriole to cytoplasmic vesicles and the timely and spatially ordered assembly of multiple proteins.\n\nSo, looking at the redundancy in annotation, \"ciliary transition zone assembly\" covers this and we can get rid of \"ciliary basal body-plasma membrane docking\", for flies at least. ",
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"body": "right, I wondered if these two terms were related.\n\nI suggest we do that, and if a specific docking activity is required it can be added later.",
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"body": "With you there. I will revise our annotations now.",
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"body": "Done - no Dmel ones left!",
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"body": "To be clear, the final decision is \n> Obsolete GO:0097711 ciliary basal body-plasma membrane docking and replace by GO:1905349 ciliary transition zone assembly\n\n\nRight ? ",
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"body": "I think as the process of basal body assembly and TZ assemblt can vary between species, I would not add \"replace by\" but \"consider\" GO:1905349 ciliary transition zone assembly. \n\nI think that ciliary transition fiber assembly may also be a consider option in some species, but it is vaguely described and is only a child of protein-containing complex assembly. Just going to look at that with claude...",
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"body": "Ok, ciliary transition fiber assembly has no annotations and is part of docking/TZ assembly. So I would suggest that we obsolete GO:1905353 ciliary transition fiber assembly and GO:0097711 ciliary basal body-plasma membrane docking\nand **replace** by GO:1905349 ciliary transition zone assembly (rather than consider) ",
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"body": "Dear all, \n\nThe proposal has been made to obsolete\nGO:1905353 ciliary transition fiber assembly\nGO:0097711 ciliary basal body-plasma membrane docking\n\n* The reason for obsoletion is that this term is redundant with GO:1905349 ciliary transition zone assembly.\n\nExperimental annotations\nFlyBase 2 DONE\nMGI 1 DONE\nReactome 1 DONE\nUniProt 1\nXenbase 1 DONE\nZFIN 1\n\n0 InterPro2GO/UniRule/UniProtKW mappings.\n\nAnnotations can be viewed here: https://github.com/geneontology/go-annotation/issues/6405.\n\nThe terms are replaced by GO:1905349 ciliary transition zone assembly.\n\nAny comments can be added to the issue: https://github.com/geneontology/go-ontology/issues/31882\n\nThanks, ",
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"body": "@dragon-ai-agent please obsolete GO:1905353 and GO:0097711.",
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"createdAt": "2026-05-05T20:09:29Z",
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"body": "🤖 Working on it...\n\nFollow along: [View workflow run](https://github.com/geneontology/go-ontology/actions/runs/25399618844)\n\n*— @dragon-ai-agent*",
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"createdAt": "2026-05-05T20:09:58Z",
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"title": "Obsolete: GO:0097711 ciliary basal body-plasma membrane docking Biological Process",
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"url": "https://github.com/geneontology/go-ontology/issues/31882"
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}

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