GOA changes since the original review:
- New rows (12, all resolved): GO:0005524 ATP binding IEA (InterPro); cytoplasm ISO (human
P11021) and ISS (mouse P20029); ER lumen ISO located_in and ISS (P11021); cell surface ISO;
melanosome ISO and ISS; GO:0044183 protein folding chaperone IEA (ARBA00029119) and IPI
(PMID:11884402, with thyroglobulin RGD:3848); GO:0009725 response to hormone IDA
(PMID:11884402); GO:0045732 positive regulation of protein catabolic process ISO (mouse).
- Retired rows (6, reviews kept, retirement sentence added): GO:0000166, GO:0005524 and
GO:0016787 IEA; GO:0005515 IPI PMID:18757373 (DMP1) and PMID:12514190 (TMEM132A);
GO:0051082 IPI PMID:11884402. QuickGO confirms GO:0051082 is obsolete ("should be replaced
by an activity term such as protein folding chaperone (GO:0044183) or unfolded protein
holdase activity (GO:0140309)"). GOA replaced it with GO:0044183 IPI from the same paper,
which is what the earlier review recommended. As in St13, the HSP70 chaperone activity has
a GO term (GO:0044183), so no proposed_new_terms entry is needed.
Action changes:
- GO:0005515 protein binding (5 IPI rows), MARK_AS_OVER_ANNOTATED is no longer allowed:
- PMID:7916014 (thyroglobulin) -> MODIFY to GO:0044183, because the binding is ATP-sensitive
client binding PMID:7916014. This matches the curators'
GO:0044183 IPI for the same interaction from PMID:11884402.
- PMID:17981125 (Sigmar1), PMID:9714535 (ERp29), PMID:18757373 (DMP1, retired) and
PMID:12514190 (TMEM132A, retired) -> REMOVE. None of the abstracts supports a specific BiP
MF; removal does not mean the interactions are false.
- GO:0006983 ER overload response ISO: ACCEPT -> MARK_AS_OVER_ANNOTATED, with a
propagation_review. The mouse source is Bip mRNA induction PMID:11854325, and the term is defined by NF-kappaB activation.
- GO:0042149 cellular response to glucose starvation ISO: ACCEPT -> KEEP_AS_NON_CORE. It is
an expression response (human source PMID:10085239), not BiP's own molecular role.
- GO:0031625 ubiquitin protein ligase binding ISO: ACCEPT -> KEEP_AS_NON_CORE. The human
source is an IPI from a Ro/SS-A (Ro52/TRIM21) study (PMID:8666824), not SYVN1/HRD1 as the
old text claimed; UniProt has "Interacts with TMEM132A and TRIM21".
- New GO:0045732 ISO -> MARK_AS_OVER_ANNOTATED. The mouse source IDA (PMID:18923430, full
text) shows substrate handover from P58 PMID:18923430 and reports no BiP degradation assay; BiP's
degradation role is participation in ERAD (GO:0036503).
- New GO:0009725 response to hormone IDA -> UNDECIDED. The abstract only says that ERp29 was
induced by TSH PMID:11884402, and the full text is not cached.
- Added verbatim supported_by to about 70 ACCEPT/KEEP rows that had none: current UniProt CC
lines, deep-research quotes, the IEP papers, and donor-side papers for ISO rows (mouse
conditional knockout PMID:19816510; Cripto/TGF-beta PMID:17991893; ERdj5 PMID:12411443;
Mtj1 PMID:12065409).
- core_functions: replaced three non-verbatim, paraphrased quotes (flagged
full_text_unavailable) with verbatim UniProt and paper quotes; added supported_by to the
ATP hydrolysis entry; removed project-rule wording and stated why GO:0044183 rather than
GO:0140309 fits. Description: typo fix only.
Open questions:
- GO:0009725 (IDA, PMID:11884402): does the full text show a TSH-induced change in BiP? If it
does, IEP is the more usual code.
- GO:0071353 cellular response to interleukin-4 (ISO from MGI IDA PMID:9798653) rests on a
cDNA-subtraction expression screen; kept non-core, but it is an expression observation.
Review follow-up 2026-10-19 (PR #4624): the GOA refresh retired every GO:0051082 unfolded protein
binding row for Hspa5 (GOA now carries GO:0044183 protein folding chaperone), so the BioReason-Pro
SFT prediction rationale "Term is in GOA" for GO:0051082 was no longer true; the CNN assessment
stands and the rationale now says so. Updated the GO:0036503 label to the current ontology label
"ERAD quality control pathway" (QuickGO and the refreshed GOA; the local ontology cache still
carries the old label, hence an advisory validator warning). Removed evidence-code commentary from
two core_functions descriptions and added a VERIFIED reference_review for PMID:11854325.