GroEL annotation review notes

2026-08-29 qualifier-aware audit

• Reconciled all 62 grouped review signatures against the current GOA cache. The 96 physical GOA lines collapse to 62 signatures because multiple WITH/FROM partners share the same term, qualifier, evidence code, and reference. Qualifiers are 47 enables, 5 involved_in, 4 located_in, 4 acts_upstream_of_or_within, and 2 part_of; exact IPI partners are retained in supporting_entities.
• GroEL is the ATP-dependent folding subunit of the cytosolic GroEL-GroES chaperonin. Direct evidence describes chaperonins as “mediating ATP-dependent polypeptide folding” PMID:7935796, places folding intermediates “inside central cavities within individual chaperonin rings” PMID:8097882, and resolves the ATP/GroES-dependent folding chamber PMID:9285585. GO:0140662 is therefore the evidence-matched core molecular function, with GO:0006457, GO:0005829, and GO:1990220 as its central process, location, and complex context.
• Refreshed current PAINT provenance with just fetch-panther-paint PTHR45633 --extra-uniprot P0A6F5 on 2026-08-29. Current PAINT retains GO:0006457 at PTN000143677 and GO:0005524, GO:0009408, and GO:1990220 at PTN000143644. The legacy GO:0051082 IBA remains in GOA but is absent from refreshed PAINT; its propagation review therefore records SOURCE_STALE_OR_MISSING, while the row is biologically redirected to GO:0140662 rather than treated as a current node assertion.
• All four physical GO:0051082 signatures are MODIFY to GO:0140662. GroEL is an active ATP-dependent foldase, not merely a passive unfolded-protein binder, and the old term is obsolete. A general holdase NTR is not needed for the reviewed GroEL evidence because the cited experiments directly couple substrate capture to productive ATP/GroES-dependent folding [PMID:7935796; PMID:8097882].
• The GO:0051082 obsoletion and its inadequate blanket replacements are tracked upstream in go-ontology#30962, as recorded by projects/UNFOLDED_PROTEIN_BINDING.md; GroEL itself has the evidence-matched current foldase replacement GO:0140662.
• Generic GO:0005515 IPI rows were separated by evidence content. GroES-only interactions are MODIFY to GO:0051087. Single-client, sigma32, cross-system, and heterogeneous interactome signatures are retained as KEEP_AS_NON_CORE because an IPI observation cannot be rewritten as chaperone catalytic activity and no one replacement fits mixed partner sets. The anthrax PA interaction is MARK_AS_OVER_ANNOTATED: the full text explicitly uses GroEL as an experimental scaffold and aggregation suppressor rather than identifying a physiological E. coli client PMID:18568038.
• Accession labels were verified against repository records rather than inferred from memory: P60010 is yeast ACT1/actin; P00586 is bovine TST/rhodanese; P0A817 is E. coli MetK; P0A717 is ribose-phosphate pyrophosphokinase Prs; P0A7H0 is RecF; P0A9W0 is UlaR; P0AEX9 is MalE/MBP; P0AEY3 is MazG; and P39177 is UspG. This removes the prior duplicate/mistaken DegP, KasA, RpsA, MalZ, YjgF, and Gim/GroES descriptions.
• The single P39177 IPI remains KEEP_AS_NON_CORE, not MODIFY to GO:0051787: PMID:12071968 calls UspG/UP12 a putative GroEL substrate and confirms interaction, but does not establish that the assayed partner is misfolded, which GO:0051787 specifically requires. The two sole-partner sigma32 rows likewise remain non-core physical/regulatory context; an IPI row is not rewritten as catalytic chaperone activity.
• PMID:7935796 is treated differently because its IMP evidence is a mutational functional analysis linking the apical substrate-binding site to ATP hydrolysis and productive release. That row can be evidence-matched to GO:0140662 without the binding-to-activity category error that would affect a simple IPI.
• Experimental-curator restraint was applied. Most cached records are abstract-only; only PMID:18304323, PMID:18568038, and PMID:24561554 contain full text. No experimental annotation was removed because assay detail was inaccessible. The yeast TRiC/GimC paper with a heterologous chaperonin trap remains non-core rather than being rejected PMID:9878052.
• Broad electronic terms were made actionable where appropriate: GO:0000166 nucleotide binding is MODIFY to GO:0005524 ATP binding, and GO:0016853 isomerase activity is MODIFY to GO:0140662. Radiation survival, virion assembly, and membrane association remain valid non-core contexts; the cytosolic chaperonin function remains core.
• Final actions: 27 ACCEPT, 22 MODIFY, 12 KEEP_AS_NON_CORE, 1 MARK_AS_OVER_ANNOTATED, and no REMOVE, UNDECIDED, or PENDING. Status is COMPLETE because every current signature has a qualifier-aware evidence decision and every IBA has current PTN/source provenance.