Vesicle Docking BP Subtree — Obsoletion & MF Refactor (GO:0048278)

IN_PROGRESS OBSOLETION

Warnings (1)

Vesicle Docking BP Subtree — Obsoletion & MF Refactor (GO:0048278)

Overview

A GO obsoletion proposal will retire the entire GO:0048278 vesicle docking
biological-process subtree plus its regulation terms, and redirect the
biology to two molecular-function terms:

The rationale is the same as the parallel
ER-PM,
mito-ER,
ciliary basal-body, and
synaptic vesicle docking
trackers in this repo: the docking step is best represented as a binding
activity (MF) rather than a process (BP).

This project is the parent tracker for the upstream
geneontology/go-annotation#6379
annotation-review issue, which covers the whole BP subtree. The
SYNAPTIC_VESICLE_DOCKING_OBSOLETION
tracker handles one sibling sub-issue (#6415, GO:0099148); the parallel
VESICLE_TETHERING_OBSOLETION tracker
covers the related vesicle-tethering obsoletions (#6375, GO:0099022 and
children).

Upstream tickets

Obsoletion plan (per upstream)

Obsoleted term ID Replacement (consider)
vesicle docking GO:0048278 MF: GO:0160321 vesicle docking activity (placeholder)
Golgi vesicle docking GO:0048211 MF: GO:0160321
phagosome-lysosome docking GO:0090384 MF: GO:0160321
regulation of vesicle docking GO:0106020 (likely retained regulatory BP)
positive regulation of vesicle docking GO:0106022 (likely retained regulatory BP)
negative regulation of vesicle docking GO:0106021 (likely retained regulatory BP)
vesicle docking involved in exocytosis GO:0006904 MF: GO:0160321
synaptic vesicle docking GO:0016081 MF: GO:0160321 (docking) or the proposed "vesicle tethering activity" MF (not yet minted; see Overview)
dense core granule docking GO:0061790 MF: GO:0160321

OLS check (2026-05-23): all nine BP terms are still active. The replacement
MF GO:0160321 is not yet resolvable in OLS — this is the same placeholder
state noted in the sibling synaptic-docking and ciliary-docking trackers, so
the obsoletion has not landed yet.

Affected upstream groups (from issue body)

Group Annotations Status (per upstream)
ComplexPortal 52 pending
SGD 15 pending
UniProt 12 pending
SynGO 10 pending (8 sit under GO:0099148 — see sibling tracker)
FlyBase 8 DONE
MGI 7 DONE
RGD 7 DONE
BHF-UCL 5 done
PINC 4 pending
ParkinsonsUK-UCL 4 done
SynGO-UCL 2 done
HGNC-UCL 1 done
dictyBase 1 pending
WB 1 pending
DisProt 1 pending

No InterPro2GO / UniProt-Keyword / UniRule mappings to the obsoleted terms
were listed in the upstream issue body.

Impact on this repo

Direct overlap with existing reviews is small — most of the affected
genes (syntaxins, SNAREs, RABs, exocyst, Munc18/STXBP, tomosyn, septins,
TRAPP/COG/GARP subunits, etc.) are not yet covered here.

Verified by greppings genes/*/*/*-goa.tsv and *-ai-review.yaml for the
nine obsoleted IDs:

Gene Organism File Affected row
USO1 human genes/human/USO1/USO1-ai-review.yaml GO:0048211 Golgi vesicle docking, IBA from PANTHER:PTN000000707 / SGD:S000002216, currently action: ACCEPT

Also tracked under the sibling project
SYNAPTIC_VESICLE_DOCKING_OBSOLETION:

Gene Organism Affected row
Camk2a mouse two GO:0099148 rows currently ACCEPT (see that tracker)

The USO1 annotation will need a refresh when the obsoletion lands. USO1
(p115) is a bona fide Golgi vesicle tether/docking factor, so this is one
of the cleaner candidates for a legitimate transfer onto the new
docking-activity MF — in contrast to e.g. CaMKIIα, which only regulates
docking. The current review text already notes that "the essential function
is SNARE assembly rather than tethering per se", so the refresh should
revisit whether the new MF (GO:0160321 vesicle docking activity) or the
proposed (not-yet-minted) "vesicle tethering activity" MF is the better fit.
(Note: GO:0099023 vesicle tethering complex is a CC term, not the
tethering-activity MF, and must not be used as the MF replacement here.)

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. USO1 (human, UniProt O60763) — genes/human/USO1/. The
    GO:0048211 IBA row is currently ACCEPT; refresh once the obsoletion
    lands. Likely a clean transfer to GO:0160321 vesicle docking activity
    or the proposed "vesicle tethering activity" MF (not yet minted; see
    Overview — not GO:0099023, which is the CC "vesicle tethering complex").
    p115 is the canonical Golgi tether — see existing notes mentioning
    GM130/giantin interactions and SNARE-assembly function.
  2. Camk2a (mouse, UniProt P11798) — covered by sibling tracker
    SYNAPTIC_VESICLE_DOCKING_OBSOLETION;
    listed here only for completeness because it sits under the same
    #6379 umbrella.

Tier 2 — clean new reviews for canonical docking factors

These are well-known docking/tethering proteins absent from the repo. Each
should be a relatively self-contained review (SNARE/tether biology is
well-characterised) and they collectively populate the new MF terms with
high-quality experimental anchors.

  1. STX1A (human, UniProt Q16623) — syntaxin-1A; SNARE-complex
    component, classic synaptic vesicle docking factor.
  2. STXBP1 (human, UniProt P61764) — Munc18-1; binds STX1A and is a
    primary docking/priming factor at synapses. Disease-relevant (epileptic
    encephalopathy) → high curation value.
  3. EXOC4 / Sec8 (human, UniProt Q96A65) — exocyst component; the
    GO:0090522 vesicle tethering involved in exocytosis annotation is
    already flagged in the sibling tethering obsoletion #6375 (InterPro2GO
    mapping IPR039682 → GO:0090522).
  4. EXOC6 / Sec15 (human, UniProt Q8TAG9) — exocyst component; same
    #6375 InterPro2GO route (IPR007225 → GO:0090522).
  5. SEC18 / NSF (human NSF, UniProt P46459) — ATPase that disassembles
    SNARE complexes after docking/fusion; a frequent annotation target for
    vesicle-fusion and docking terms.

Tier 3 — yeast / Dictyostelium / fly cross-organism cases

  1. Uso1 (yeast, UniProt P25386, SGD YDL058W) — yeast ortholog of
    human USO1; sits in the SGD "15 pending" bucket and provides a clean
    cross-organism comparison against Tier 1 (#1).
  2. Sec1 (yeast, UniProt P30619) — Munc18 family / STXBP1 ortholog;
    docking factor at the plasma membrane.
  3. tom-1 (C. elegans, UniProt A0A0K3ATN9) — tomosyn; already listed
    under the sibling synaptic-docking tracker as the canonical negative
    regulator (MODIFY test case).

Proposed approach

  1. Wait for the obsoletion to land. The replacement MF GO:0160321 is
    not yet minted (OLS check 2026-05-23). The ontology ticket
    #31880 is
    open and shared with the synaptic-docking and ciliary-docking trackers.
  2. Refresh USO1 first (Tier 1). p115 is the textbook Golgi vesicle
    tether/docking factor, so this is the cleanest test of "BP → new docking
    MF" transferability and most likely to be a straightforward MODIFY
    onto the new MF.
  3. Coordinate with the sibling tracker
    SYNAPTIC_VESICLE_DOCKING_OBSOLETION
    for Camk2a, Septin5, tom-1 — those genes belong to the same umbrella
    obsoletion (#6379) but are scoped under #6415 there to avoid duplicated
    work.
  4. Then queue Tier 2 (STX1A, STXBP1, EXOC4, EXOC6, NSF) as new reviews.
    STX1A + STXBP1 in particular pair with the existing Tier 1 USO1 review
    to populate the new MFs across both the Golgi-tether and the
    plasma-membrane-SNARE arms of the literature.
  5. Re-validate each affected review with
    just validate <organism> <gene> after editing.

The vesicle docking obsoletion in #6379 is part of a coordinated cluster of
"BP-tether/docking → MF binding activity" obsoletions. The other items in
the cluster:

Priority

Medium. Higher than purely-queueing obsoletion trackers because one
existing repo review (USO1) goes stale on obsoletion. Lower than
SYNAPTIC_VESICLE_DOCKING_OBSOLETION because USO1 is likely a clean
MODIFY onto the new MF (USO1 / p115 is a docking/tether factor),
whereas CaMKIIα is a regulator and forces a harder per-gene judgment.

Status