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

IN_PROGRESS OBSOLETION

Species: human

Genes: USO1 STX12

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

Bottom line: A transport vesicle is first tethered at a distance,
then docked against its target membrane, then fused. GO has retired the
whole GO:0048278 vesicle docking process subtree (nine terms).
Direct docking/tethering annotations now need a molecular function such
as GO:0160321 vesicle docking activity or GO:7770062 vesicle membrane
tethering activity, while regulatory rows need curator judgement because
GO:0106020/21/22 carry only a consider pointer to GO:0160321 and no
one-to-one MF replacement. This is the parent tracker for
go-annotation#6379; we recorded the upstream plan and group tallies,
found the affected reviews in this repo, and queued canonical docking
factors (STX1A, STXBP1, exocyst, NSF) as new reviews. The obsoletion has
landed: OLS shows all nine terms obsolete (GO:0048278, GO:0048211,
GO:0090384, GO:0006904, GO:0016081, GO:0061790 and the regulation
terms GO:0106020/21/22) and both MFs minted. Both affected human reviews
are fixed in #3237 (merged): the USO1
IBA row on GO:0048211 Golgi vesicle docking moves from ACCEPT to
MODIFY → GO:7770062 vesicle membrane tethering activity (p115 is the
canonical Golgi tether), and the STX12 IBA row on GO:0048278 moves from
ACCEPT to MODIFY → GO:0005484 SNAP receptor activity, with the
obsolete BP dropped from its core_functions. STX12 was reviewed after
this page was written. The new-review queue (STX1A, STXBP1, exocyst,
NSF) has not started.

Sibling trackers split the rest of the refactor:
SYNAPTIC_VESICLE_DOCKING_OBSOLETION
handles the regulation sub-issue (#6415, mouse Camk2a),
VESICLE_TETHERING_OBSOLETION the
tethering step (#6375), and
VESICLE_TARGETING_OBSOLETION the
targeting terms that fold into transport processes (#6424).

Overview

A GO obsoletion proposal retired 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
Golgi vesicle docking GO:0048211 MF: GO:0160321
phagosome-lysosome docking GO:0090384 MF: GO:0160321
regulation of vesicle docking GO:0106020 obsolete; OLS consider GO:0160321 (no direct replacement)
positive regulation of vesicle docking GO:0106022 obsolete; OLS consider GO:0160321 (no direct replacement)
negative regulation of vesicle docking GO:0106021 obsolete; OLS consider GO:0160321 (no direct replacement)
vesicle docking involved in exocytosis GO:0006904 MF: GO:0160321
synaptic vesicle docking GO:0016081 MF: GO:0160321 (docking) or GO:7770062 (tethering)
dense core granule docking GO:0061790 MF: GO:0160321

At project creation, all nine BP terms were still active in OLS on
2026-05-23 and the replacement MF GO:0160321 was not yet resolvable. By
the 2026-09-26 audit, the nine BP terms were obsolete and both GO:0160321 and
GO:7770062 were minted.

Affected upstream groups (from issue body)

Group Annotations Status (per upstream)
ComplexPortal 52 pending
SGD 15 DONE
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; was ACCEPT, MODIFY → GO:7770062 vesicle membrane tethering activity, fixed in #3237 (merged)
STX12 human genes/human/STX12/STX12-ai-review.yaml GO:0048278 vesicle docking, IBA; was ACCEPT and in core_functions, row MODIFY → GO:0005484 SNAP receptor activity and core BP dropped, fixed in #3237 (merged)

Also tracked under the sibling project
SYNAPTIC_VESICLE_DOCKING_OBSOLETION:

Gene Organism Affected row
Camk2a mouse two GO:0099148 rows, was ACCEPT, MODIFY → GO:0048172 regulation of short-term neuronal synaptic plasticity, fixed in #3237 (merged; see that tracker)

The USO1 annotation refresh chose GO:7770062 rather than GO:0160321. USO1
(p115) is a bona fide Golgi vesicle tether, and the obsoleted GO:0048211 row
was supported by long-range tethering to GM130/giantin upstream of docking and
fusion. That contrasts with STX12, where the SNARE role is better captured by
GO:0005484 SNAP receptor activity, and with CaMKIIα, which only regulates
docking and is handled under the synaptic sibling tracker.

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 was ACCEPT; fixed in #3237 (merged), which chose
    the tethering MF GO:7770062. p115 is the canonical Golgi tether upstream
    of docking/fusion — 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. NSF (human, UniProt P46459; yeast ortholog SEC18) — ATPase that
    disassembles SNARE complexes after docking/fusion; a frequent annotation
    target for vesicle-fusion and docking terms.

Tier 3 — yeast / worm cross-organism cases

  1. USO1 (yeast, UniProt P25386, SGD S000002216 / YDL058W) —
    yeast ortholog of human USO1; was in the SGD "15" bucket, now marked done
    upstream 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. Tier 1 refreshes are done. #3237 re-reviewed USO1 and STX12 after the
    obsoletion landed, choosing GO:7770062 for USO1 and GO:0005484 for STX12.
  2. Keep the USO1/STX12 split visible. p115/USO1 performs long-range
    Golgi vesicle tethering, while STX12 is a syntaxin-family SNARE better
    captured by SNAP receptor activity than by a broad docking BP.
  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. Use #639 to 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. The Tier 1 rows that made existing repo reviews stale are fixed,
so the remaining value is seeding canonical STX1A/STXBP1/exocyst/NSF
anchors through #639 for the new docking and tethering molecular functions and
coordinating EXOC4/EXOC6 with the sibling vesicle-tethering queue.

Status