Vesicle Targeting (GO:0006903) & Descendants — Obsoletion & Replacement

Overview

A GO obsoletion is retiring GO:0006903 vesicle targeting and its
descendant hierarchy. These BP terms conflate a vesicle-mediated
transport process with a targeting/tethering step in a way that is
no longer considered meaningful, so each is being collapsed onto a
broader, well-defined vesicle-transport parent. The biology is
unchanged; the fix is terminological (move annotations to the
designated replacement transport term).

Upstream tickets

Annotation tracker: geneontology/go-annotation#6424
Ontology ticket: geneontology/go-ontology#31865 — closed 2026-05-16
Upstream review spreadsheet (curator-maintained): https://docs.google.com/spreadsheets/d/1o5T_b5I9RNLdWUgcnaHxv4lqiY88_Al3CvpC4ul3Sv8

Obsoletion plan (per upstream issue)

Obsoleted term	ID	Replacement
vesicle targeting	GO:0006903	GO:0016192 vesicle-mediated transport
vesicle targeting to fusome	GO:0045479	(no explicit replacement listed)
clathrin coating of Golgi vesicle, plasma membrane to endosome targeting	GO:0010785	(no explicit replacement listed)
vesicle targeting, plasma membrane to endosome	GO:0048201	(no explicit replacement listed)
vesicle targeting, to, from or within Golgi	GO:0048199	GO:0048193 Golgi vesicle transport
vesicle targeting, rough ER to cis-Golgi	GO:0048207	GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport
regulation of vesicle targeting, to, from or within Golgi	GO:0048209	(no explicit replacement listed)
vesicle targeting, cis-Golgi to rough endoplasmic reticulum	GO:0048206	GO:0006890 retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
vesicle targeting, inter-Golgi cisterna	GO:0048204	GO:0048219 inter-Golgi cisterna vesicle-mediated transport
vesicle targeting, trans-Golgi to endosome	GO:0048203	GO:0006895 Golgi to endosome transport

All ten source terms are still active (not yet obsolete) in
QuickGO / GO API as of 2026-05-17 — the ontology ticket is merged but
the obsoletion has not yet propagated to the released ontology or to
annotations. All six listed replacement targets are valid, active BP
terms.

Affected experimental / direct annotations

Pulled from QuickGO (goUsage=exact, experimental evidence
ECO:0000269 descendants) on 2026-05-17. 22 experimental
annotations fall on just 4 of the 10 obsoleted terms; the other
six terms (GO:0045479, GO:0010785, GO:0048201, GO:0048209,
GO:0048206, GO:0048204) have zero experimental annotations and
will be handled entirely by IEA/IBA auto-migration.

GO:0006903 vesicle targeting → GO:0016192 vesicle-mediated transport (12)

Group/ID	Gene	Species	Evidence	Reference
UniProtKB:O15498	YKT6	Homo sapiens (9606)	IDA	PMID:9211930
UniProtKB:Q7Z460	CLASP1	Homo sapiens (9606)	IMP	PMID:24859005
UniProtKB:O75122	CLASP2	Homo sapiens (9606)	IMP	PMID:24859005
UniProtKB:Q61161	Map4k2	Mus musculus (10090)	IDA	PMID:8643544
UniProtKB:Q8K3E5	Ahi1	Mus musculus (10090)	IMP (acts_upstream_of_or_within)	PMID:20592197
UniProtKB:P21707	Syt1	Rattus norvegicus (10116)	IDA	PMID:14715137
UniProtKB:P61023	Chp1	Rattus norvegicus (10116)	IDA	PMID:8626580
UniProtKB:Q258K2	MYH9	Canis lupus familiaris (9615)	IMP	PMID:18504258
UniProtKB:P53141	MLC1	S. cerevisiae S288C (559292)	IMP	PMID:12456647
ComplexPortal:CPX-3188	polarisome	S. cerevisiae S288C (559292)	IMP	PMID:16166638
UniProtKB:P0CY31	SEC4	Candida albicans SC5314 (237561)	IGI	PMID:9639314
UniProtKB:Q9C744	DELTA-ADR	Arabidopsis thaliana (3702)	IEP (acts_upstream_of_or_within)	PMID:28559361

GO:0048203 vesicle targeting, trans-Golgi to endosome → GO:0006895 Golgi to endosome transport (7)

Group/ID	Gene	Species	Evidence	Reference
UniProtKB:Q5MNZ9	WIPI1	Homo sapiens (9606)	IDA	PMID:15020712
UniProtKB:Q63HQ0	AP1AR	Homo sapiens (9606)	IDA	PMID:19706427
UniProtKB:P35181	APS1	S. cerevisiae S288C (559292)	IMP	PMID:17003107
UniProtKB:P36000	APL2	S. cerevisiae S288C (559292)	IMP	PMID:17003107
UniProtKB:P38700	APM2	S. cerevisiae S288C (559292)	IMP	PMID:17003107
UniProtKB:Q12028	APL4	S. cerevisiae S288C (559292)	IMP	PMID:17003107
ComplexPortal:CPX-533	AP-1 complex	S. cerevisiae S288C (559292)	IMP	PMID:17003107

GO:0048199 vesicle targeting, to, from or within Golgi → GO:0048193 Golgi vesicle transport (2)

Group/ID	Gene	Species	Evidence	Reference
UniProtKB:Q63584	Tmed10	Rattus norvegicus (10116)	IEP	PMID:17101722
UniProtKB:Q9D1D4	Tmed10	Mus musculus (10090)	IEP	PMID:17101722

GO:0048207 vesicle targeting, rough ER to cis-Golgi → GO:0006888 ER to Golgi vesicle-mediated transport (1)

Group/ID	Gene	Species	Evidence	Reference
UniProtKB:Q9NZD2	GLTP	Homo sapiens (9606)	IMP	DOI:10.1101/2025.06.17.657375 (preprint)

A large pool of IEA annotations (~2,470 across these terms in
QuickGO) and any IBA propagations will be remapped automatically
once the obsoletion lands and the next pipeline runs. These do not
need per-annotation work here.

Mapping cleanup (per upstream issue)

InterPro2GO: InterPro:IPR031483 (AP-1 complex-associated
regulatory protein) → GO:0048203 — needs remapping to the
replacement GO:0006895 by the InterPro2GO maintainers. This is an
InterPro mapping concern, not a per-gene review item.
No ARBA / UniRule mappings to the obsoleted terms were listed
(UniRule appears in the upstream template header only).

Impact on this repo

No genes annotated to any of the obsoleted terms are currently
reviewed in this repo. Checked all 9606/yeast symbols above
(YKT6, CLASP1, CLASP2, WIPI1, AP1AR, GLTP, MLC1,
SYT1, CHP1, MAP4K2, AHI1, TMED10, MYH9, SEC4, AP-1
subunits) against genes/**/*-ai-review.yaml — no matches.

So no existing reviews need refresh for the obsoletion itself.
This differs from the synaptic-vesicle-docking tracker
(go-annotation#6415), where mouse Camk2a had to be queued for a
refresh. Here the project is purely a forward-looking opportunity
to add high-value, currently-unreviewed human trafficking genes.

Scope

Organisms: human (12 of 22 EXP rows, 6 distinct human genes)
and S. cerevisiae (8 rows, all the AP-1 / polarisome / MLC1
complex annotations) carry essentially all the experimental
signal. Rat/mouse/dog/Candida/Arabidopsis rows are orthologs that
will largely follow automatically once the model-organism groups
remap.
GO branches: BP only — a transport-vs-targeting collapse onto
broader vesicle-transport parents. No MF or CC changes.
Type of fix: terminological. Reviews should ask whether the
designated replacement is the most informative available term
for the gene's core role, or whether a more specific extant BP
(or an MF) better captures the function — e.g. YKT6 is a SNARE
whose core MF (SNARE binding / SNAP receptor activity) is more
informative than any generic transport BP.

Candidate genes for initial review

Verify each with just fetch-gene <organism> <gene> and confirm the
UniProt accession before starting. None are currently in the repo.

Tier 1 — human, well-characterized, strong direct evidence

YKT6 / O15498 (Homo sapiens) — longin-domain R-SNARE central
to ER–Golgi and autophagosome–lysosome fusion. IDA on GO:0006903
(PMID:9211930). Best single candidate: heavily studied, core MF
anchor (SNARE / SNAP receptor activity) is far more informative
than the generic GO:0016192 replacement, so this is a good test
of MODIFY-vs-transfer judgement.
CLASP1 / Q7Z460 and CLASP2 / O75122 (Homo sapiens) —
microtubule plus-end tracking proteins; both IMP on GO:0006903
from the same study (PMID:24859005) implicating them in
Golgi-derived vesicle transport. Reviewable as a pair.
WIPI1 / Q5MNZ9 (Homo sapiens) — PI3P-binding autophagy
effector; IDA on GO:0048203 (PMID:15020712, trans-Golgi to
endosome). Review should weigh the GO:0006895 replacement against
WIPI1's better-characterized autophagy/PI3P-binding roles.

Tier 2 — human, adaptor / less direct

AP1AR / Q63HQ0 (Homo sapiens) — AP-1 complex-associated
regulatory protein (gadkin); IDA on GO:0048203 (PMID:19706427).
Note this gene is also the subject of the InterPro2GO mapping
cleanup (IPR031483 → GO:0048203).

Tier 3 — opportunistic / lower value

GLTP / Q9NZD2 (Homo sapiens) — glycolipid transfer protein;
IMP on GO:0048207 but the only reference is an unpublished
preprint (DOI:10.1101/2025.06.17.657375). Lower priority until a
peer-reviewed reference exists.
S. cerevisiae AP-1 clathrin-adaptor subunits (APL2/APL4/
APM2/APS1, PMID:17003107) — a coherent yeast complex set, but
all IMP from a single study; consider only if extending yeast
coverage. The Reactome/SGD groups will likely remap these
directly.

Proposed approach

Hold as a tracking project — do not action yet. The ontology
ticket (#31865) is merged/closed but all ten source terms are
still active in the released ontology and QuickGO as of
2026-05-17. Wait for the obsoletion to propagate before pulling
GOA, so just fetch-gene reflects the remapped terms.
When the obsoletion lands, start with human YKT6. Run
just fetch-gene human YKT6, confirm the GOA pull shows
GO:0006903 as obsolete / remapped to GO:0016192, then review per
CLAUDE.md. Expect the right call to be MODIFY toward a more
informative SNARE MF rather than a literal transfer to the
generic transport BP.
Follow with CLASP1/CLASP2 (as a pair), then WIPI1, then
AP1AR. Each review evaluates whether the designated
replacement BP is the most informative term or whether a
narrower extant BP / cognate MF is warranted.
Defer Tier 3 (GLTP preprint-only; yeast AP-1 subunits) unless
they surface via other workstreams.
Do not create reviews for the ortholog rows (rat/mouse/dog/
Candida/Arabidopsis) or the IEA/IBA pool — these auto-migrate.

Priority

Medium. 22 experimental annotations across 6 organisms — larger
than most obsoletion trackers in this repo — and several affected
human genes (YKT6, CLASP1/2, WIPI1) are biologically important
trafficking proteins with no review yet in this repo. The
obsoletion is a good trigger to add them, but the work should wait
until the obsoletion propagates to released annotations.

Status

2026-05-17 — Project file created. Upstream annotation issue
go-annotation#6424 open (last updated 2026-05-15); ontology ticket
go-ontology#31865 closed 2026-05-16. All ten source terms still
active in QuickGO/GO API; all six replacement targets valid. No
affected gene is reviewed in this repo, so nothing needs refresh —
held as a forward-looking tracking project. No gene reviews
started.

Warnings (1)