Biomolecular condensates

A cross-cutting audit of how GO and this repository annotate membraneless compartments

AI Gene Review · projects/CONDENSATES · IN_PROGRESS · 2026

Bottom line

  • Being in a condensate is a location; making one is a function. The corpus records the first in 238 gene folders and the scaffold function in 9.
  • Reviewers already downgraded 146 of 399 (37%) condensate-space annotations, with no shared rule.
  • A full re-review of 59 GO:0034045 PAS-membrane assertions left none at ACCEPT; GO has since made the term obsolete.

The asymmetry

Three ontology problems

  1. No "biomolecular condensate" class. GO:0043228 membraneless organelle also contains the ribosome and the cytoskeleton.
  2. Condensates outside the grouping. GO:0000407 phagophore assembly site is a liquid-like condensate (PMID:32025038) but is not under membraneless organelle.
  3. Terms that assume a membrane. GO:0034045 PAS membrane shares its phagophore synonyms with GO:0061908.

The GO:0034045 audit

What the audit showed

  • First pass (through the term): every previously reviewed assertion had been ACCEPT; all 31 across 14 genes moved (26 MODIFY, 5 over-annotated).
  • Several prior justifications argued pathway membership, not localization (e.g. Rab7: "Consistent with the Rab7 role in autophagy").
  • Second pass: 7 genes reviewed in full (496 annotations, 28 on GO:0034045).
  • Fed into GO issue #29437; superseded in part by the new GO:7770114 phagophore membrane.

Working principles (drafts)

  1. Scaffold, client or regulator: say which in core_functions.
  2. Condensate CC alone is rarely a core function.
  3. Prefer the material claim over the compartment claim.
  4. Demand condensate-grade evidence (FRAP, hexanediol with controls, endogenous tags).
  5. Model condensates as modules, as modules/phagophore_assembly_site.yaml does.

Status and next steps

  • ✅ Corpus audit script and tables: projects/CONDENSATES/CONDENSATES-go-audit.md
  • ✅ GO:0034045 slice audit: projects/CONDENSATES/GO_0034045-annotation-audit.md
  • ⬜ Run the calibration batch of scaffold genes (SQSTM1, NFE2L2, LGALS3, TP53 orthologs, Ccnt1, mid1, TARDBP) against the principles.
  • ⬜ Decide whether to request a condensate grouping class and children of GO:0140693.

Related: projects/STRESS_GRANULES.md · projects/CAEEL_P_GRANULES.md · projects/SL.md