Vesicle Tethering BP Subtree — Obsoletion & MF Refactor (GO:0099022)

IN_PROGRESS OBSOLETION

Vesicle Tethering BP Subtree — Obsoletion & MF Refactor (GO:0099022)

Overview

A GO obsoletion proposal will retire GO:0099022 vesicle tethering and four
children (BPs), redirecting the biology to a single molecular-function term:

The rationale matches the parallel
vesicle docking,
ER-PM tethering,
mito-ER tethering,
ciliary basal-body docking, and
synaptic vesicle docking trackers:
the tethering step is best represented as a binding activity (MF) rather
than a process (BP). Note that the existing GO:0099023 vesicle tethering
complex is a cellular-component term, not the MF — it must not be reused as
the MF replacement.

Per @ValWood on the upstream issue, the recommended post-obsoletion pattern is
the new MF in a part_of annotation extension to the relevant transport BP,
e.g. GO:7770062 vesicle membrane tethering activity part_of GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport. Curators may also
fall back to existing or expanded "fusion" descendant BPs where they cover the
full tethering→docking→fusion pathway.

Upstream tickets

Obsoletion plan (per upstream)

Obsoleted term ID Replacement (consider)
vesicle tethering GO:0099022 MF: GO:7770062 vesicle membrane tethering activity (placeholder)
synaptic vesicle tethering involved in synaptic vesicle exocytosis GO:0099069 MF: GO:7770062
vesicle tethering involved in exocytosis GO:0090522 MF: GO:7770062
vesicle tethering to endoplasmic reticulum GO:0099044 MF: GO:7770062
vesicle tethering to Golgi GO:0099041 MF: GO:7770062

OLS check (2026-05-25): all five BP terms are still active (not yet
obsoleted). The replacement MF GO:7770062 is not yet resolvable in OLS —
the obsoletion has not landed yet.

Affected upstream groups (from issue body, 2026-04-15)

Group Annotations Status (per upstream)
ComplexPortal 95 pending
UniProt 11 pending
PomBase 8 DONE
SGD 6 pending
FlyBase 5 DONE
UOS_MCB 3 pending
WB 1 DONE
MGI 1 DONE

Mappings flagged by upstream for review (InterPro2GO / UniRule):

Term Source Mapping
GO:0090522 InterPro2GO InterPro:IPR007225 Exocyst complex component EXOC6/Sec15 → GO:0090522
GO:0090522 InterPro2GO InterPro:IPR039682 Exocyst complex component Sec8/EXOC4 → GO:0090522
GO:0090522 UniRule UniRule:UR000459766 → GO:0090522
GO:0090522 UniRule UniRule:UR001419783 → GO:0090522
GO:0099041 InterPro2GO InterPro:IPR028280 Protein Njmu-R1 → GO:0099041

InterPro has already removed the GO:0090522 mappings from IPR007225, IPR039682
and the UniRule entries (per @sarach06's 2026-04-22 comment); the new GO term
will be added once minted.

Impact on this repo

Two genes currently in the repo have annotation-level or core_function-level
references to the obsoleted terms:

Gene Organism File Affected row Notes
TMF1 human genes/human/TMF1/TMF1-ai-review.yaml GO:0099041 NAS row (line ~331); also referenced in core_functions (line ~615) and proposed_new_terms (line ~656, GO:0099022 / GO:7770062) The review already requests "vesicle tethering activity" as a new MF — this is the direct motivating use case for the obsoletion plan.
USO1 human genes/human/USO1/USO1-ai-review.yaml No direct rows under the 5 obsoleted IDs, but USO1 is a Golgi tether/docking factor (p115) and is already affected by the sibling VESICLE_DOCKING_OBSOLETION (#6379) via its GO:0048211 IBA row. Refresh under that tracker; coordinate here only if a tethering MF annotation is added on refresh.

Verified by grep -r "GO:00990(22\|41\|44\|69)\|GO:0090522" genes/ across
-goa.tsv and -ai-review.yaml files.

TMF1 is the highest-priority follow-up here. Its review explicitly cites
this obsoletion plan and uses GO:0060090 molecular adaptor activity as a
stand-in for the not-yet-minted tether MF (see TMF1-ai-review.yaml:600-668).
Once GO:7770062 lands, TMF1 should be refreshed to (a) update the
proposed_new_terms entry to reference the minted MF, (b) replace or annotate
the GO:0099041 NAS row, and (c) reconsider whether GO:0060090 is still the
best stand-in MF for core_functions.

Scope

Candidate genes for initial review

Verify each with just fetch-gene <organism> <gene> and confirm UniProt
accessions before starting.

Tier 1 — refresh required (already in repo)

  1. TMF1 (human, UniProt P82094) — genes/human/TMF1/. Direct
    GO:0099041 NAS row + proposed_new_terms already references GO:0099022 and
    GO:7770062. The single cleanest test case for transferring an existing
    review onto the new tether MF.

Tier 2 — InterPro2GO–flagged tether subunits (high-priority new reviews)

These genes are directly implicated in the upstream issue's flagged mapping
table — they are the most defensible new reviews because the obsoletion
spreadsheet will name them explicitly.

  1. EXOC4 / Sec8 (human, UniProt Q96A65) — exocyst component. Flagged
    in #6375 via InterPro2GO mapping IPR039682 → GO:0090522. Also listed as a
    Tier 2 candidate in the sibling VESICLE_DOCKING_OBSOLETION;
    pick one tracker to host the review when it is started.
  2. EXOC6 / Sec15 (human, UniProt Q8TAG9) — exocyst component. Flagged
    in #6375 via InterPro2GO mapping IPR007225 → GO:0090522.
  3. NJMU-R1 / RIPPLY3 family — flagged in #6375 via InterPro2GO mapping
    IPR028280 → GO:0099041. The InterPro family is small and rodent/human-only;
    pick a representative once UniProt accessions are checked. (Note: confirm
    the human gene symbol before fetch — the InterPro family name "Protein
    Njmu-R1" is older; current HGNC symbol is RIPPLY3 if matched, but the
    identification needs verification at fetch time.)

Tier 3 — canonical golgin / tether complex subunits

These are well-known tethers absent from the repo. They sit in the
ComplexPortal (95) and UniProt (11) buckets and would substantially populate
the new MF with high-quality experimental anchors.

  1. GMAP-210 / TRIP11 (human, UniProt Q15643) — golgin; tethers
    COPI-derived vesicles to the cis-Golgi via N-terminal amphipathic helix.
  2. Golgin-84 / GOLGA5 (human, UniProt Q8TBA6) — golgin tether for
    intra-Golgi transport vesicles; shares the N-terminal motif noted in
    TMF1-ai-review.yaml as conserved across golgin tethers.
  3. GORAB (human, UniProt Q5T7V8) — GRIP-domain golgin tether involved
    in retrograde trafficking; disease-relevant (gerodermia osteodysplastica).
  4. RAB6A (human, UniProt P20340) — recruits TMF1 and other golgin
    tethers via GTP-bound state; central upstream node for several of the
    genes above.

Proposed approach

  1. Wait for the obsoletion to land. The replacement MF GO:7770062 is
    not yet minted (OLS check 2026-05-25). The cluster of ontology tickets
    (#31868, #31871, #31872, #31881) is open and shared with the wider
    tether/docking refactor.
  2. Refresh TMF1 first (Tier 1). It is the only existing review in this
    repo with a direct annotation to one of the five obsoleted terms, and the
    review's proposed_new_terms block already names this exact obsoletion
    plan — so a refresh will close the loop cleanly.
  3. Coordinate with sibling trackers:
  4. VESICLE_DOCKING_OBSOLETION (#6379) —
    EXOC4 is a shared Tier 2 candidate; pick one tracker to host the new
    review when started.
  5. ER_PM_TETHERING_OBSOLETION (#6383),
    MITO_ER_TETHERING_OBSOLETION (#6397),
    CILIARY_BASAL_BODY_DOCKING_OBSOLETION (#6405),
    SYNAPTIC_VESICLE_DOCKING_OBSOLETION (#6415) —
    parallel BP→MF refactors; review-text wording should stay consistent
    across the cluster.
  6. Then queue Tier 2 (EXOC4, EXOC6, NJMU-R1/RIPPLY3) as new reviews —
    these are the genes upstream curators will inevitably touch when working
    through the InterPro2GO mapping fix.
  7. Re-validate each affected review with
    just validate <organism> <gene> after editing.

This is one item in a coordinated cluster of "BP-tether/docking → MF binding
activity" obsoletions. Cross-reference the parallel trackers:

Priority

Medium. Higher than purely-queueing obsoletion trackers because one
existing repo review (TMF1) explicitly references this obsoletion plan in
its proposed_new_terms and will need a follow-up edit once GO:7770062 is
minted. Lower than SYNAPTIC_VESICLE_DOCKING_OBSOLETION because the affected
existing-review count is small (1 vs 2+), and TMF1 is likely a clean MODIFY
onto the new MF (TMF1 is a Golgi vesicle tether), with no awkward
regulator-vs-effector judgment calls of the kind that complicate the docking
trackers.

Status