Condensates: GO and annotation audit

Supporting page for Biomolecular Condensates. Every table below is
generated, not hand-written:

uv run python projects/CONDENSATES/scripts/scan_condensate_annotations.py

Rerun it after corpus changes and replace the tables wholesale. The script takes ~4 minutes
over the full genes/ tree.

Scope of the term list

The script scans a hand-curated list of condensate-space GO terms. It has to: GO has no
biomolecular condensate class to enumerate descendants from. The obvious substitute,
GO:0043228 membraneless organelle, is too broad — checking hierarchical ancestors via OLS
confirms that both the ribosome (GO:0005840) and the cytoskeleton (GO:0005856) are
descendants of GO:0043232 intracellular membraneless organelle. Neither is a
phase-separated condensate.

The same check shows GO:0000407 phagophore assembly site is not a descendant of
GO:0043228, despite the PAS being a liquid-like Atg-protein condensate. It is included in
the list on biological grounds, not ontological ones.

Two parent terms (GO:0043228, GO:0043232) are scanned only to show how rarely they are
used directly.

Reading the tables

GOA coverage counts gene folders whose *-goa.tsv mentions the term, not
annotations — a gene with four nucleolus annotations counts once.
Review outcomes counts annotations in *-ai-review.yaml, so the totals are larger.
It includes NEW annotations proposed by reviewers, which is why some terms show more
reviewed annotations than GOA-annotated genes.
Term labels are as of the scan date; the audit does not resolve them live.

GOA coverage

Term	Label	Gene folders
GO:0005730	nucleolus	89
GO:0016607	nuclear speck	40
GO:0016604	nuclear body	39
GO:0000407	phagophore assembly site	23
GO:0016605	PML body	22
GO:0043186	P granule	20
GO:0010494	cytoplasmic stress granule	19
GO:0036464	cytoplasmic ribonucleoprotein granule	16
GO:0000932	P-body	15
GO:0140693	molecular condensate scaffold activity (MF)	9
GO:0035770	ribonucleoprotein granule	2
GO:0140694	membraneless organelle assembly (BP)	1
GO:0043232	intracellular membraneless organelle (parent)	1
GO:0042382	paraspeckles	0
GO:0140168	nuclear ribonucleoprotein granule	0
GO:0045495	pole plasm	0
GO:0043228	membraneless organelle (parent)	0

Review outcomes (399 reviewed annotations)

Term	Label	Actions
GO:0005730	nucleolus	ACCEPT 70, KEEP_AS_NON_CORE 45, MARK_AS_OVER_ANNOTATED 9, REMOVE 3, UNDECIDED 2
GO:0016607	nuclear speck	ACCEPT 22, KEEP_AS_NON_CORE 14, MARK_AS_OVER_ANNOTATED 2, REMOVE 1, NEW 1, UNDECIDED 1
GO:0016604	nuclear body	KEEP_AS_NON_CORE 18, ACCEPT 16, MARK_AS_OVER_ANNOTATED 1
GO:0000407	phagophore assembly site	ACCEPT 29, KEEP_AS_NON_CORE 3, UNDECIDED 1
GO:0016605	PML body	KEEP_AS_NON_CORE 19, ACCEPT 4, REMOVE 2, MODIFY 2
GO:0036464	cytoplasmic ribonucleoprotein granule	ACCEPT 14, KEEP_AS_NON_CORE 8, MARK_AS_OVER_ANNOTATED 3, NEW 1
GO:0000932	P-body	ACCEPT 20, KEEP_AS_NON_CORE 4, NEW 1
GO:0010494	cytoplasmic stress granule	ACCEPT 19, KEEP_AS_NON_CORE 6
GO:0043186	P granule	ACCEPT 20, REMOVE 2, KEEP_AS_NON_CORE 2, NEW 1
GO:0140693	molecular condensate scaffold activity (MF)	ACCEPT 13, NEW 5, MARK_AS_OVER_ANNOTATED 2, KEEP_AS_NON_CORE 2
GO:0140694	membraneless organelle assembly (BP)	ACCEPT 5
GO:0043232	intracellular membraneless organelle (parent)	ACCEPT 5
GO:0035770	ribonucleoprotein granule	ACCEPT 1

All actions combined: ACCEPT 238, KEEP_AS_NON_CORE 121, MARK_AS_OVER_ANNOTATED 17, NEW 9, REMOVE 8, UNDECIDED 4, MODIFY 2

GO:0140693 roster (22 annotations)

Species	Gene	Evidence	Action
EUPSC	Q6WDN4	ISS	NEW
SCHPO	mid1	IDA	ACCEPT
human	LGALS3	IDA	ACCEPT
human	LGALS3	IDA	ACCEPT
human	NFE2L2	IDA	ACCEPT
human	SQSTM1	IDA	ACCEPT
human	SQSTM1	IDA	ACCEPT
human	SQSTM1	IDA	ACCEPT
human	SQSTM1	IDA	ACCEPT
human	SQSTM1	IDA	ACCEPT
human	SQSTM1	IEA	ACCEPT
mouse	Ccnt1	IEA	ACCEPT
mouse	Ccnt1	ISO	ACCEPT
mouse	Ccnt1	ISS	ACCEPT
mouse	Trp53	IEA	KEEP_AS_NON_CORE
mouse	Trp53	ISS	KEEP_AS_NON_CORE
rat	Tp53	ISO	MARK_AS_OVER_ANNOTATED
rat	Tp53	ISS	MARK_AS_OVER_ANNOTATED
worm	meg-2	IGI	NEW
worm	meg-3	IDA	NEW
worm	meg-4	IDA	NEW
worm	pgl-2	IC	NEW