This report is retained as a review-integrity QA artifact, not as curated
biological evidence for AFP-ai-review.yaml. audit_afp_claims.py checks that
the finished AFP review covers every GOA row, keeps file quotes verbatim, avoids
duplicate YAML-key loss, and preserves or rejects claim phrasings that were
already adjudicated in review. A clean run verifies consistency of the curated
files; it does not establish AFP secretion, ligand binding, or interaction
biology independently of the cited sources.
Generated by audit_afp_claims.py. Run from the repository root:
uv run python genes/human/AFP/AFP-bioinformatics/audit_afp_claims.py
These are mechanical checks on AFP-ai-review.yaml, not biological analyses.
They cover three things the repository validators do not: that every GOA row has
its own reviewed entry (the fetch-gene stub collapses rows that differ only by
assigner), that file: quotes are verbatim (CI checks only PMID: quotes), and
that no duplicated YAML key has silently discarded data.
PASS - all checks clean.
| quantity | value |
|---|---|
| GOA data rows | 8 |
existing_annotations entries |
11 |
| - derived from GOA | 8 |
- proposed here (action: NEW) |
3 |
| distinct GO terms in GOA | 6 |
| GOA rows with an experimental evidence code | 3 |
| GOA assigners | AgBase, Ensembl, GO_Central, IntAct, Reactome, UniProt |
supporting_text quotes verified |
71 |
- in supported_by |
42 |
- in references[].findings[] |
29 |
of which cite a file: source (unchecked by CI) |
5 |
| retracted phrasings swept for (review + notes) | 13 |
| required corrections asserted with minimum counts | 6 |
The GOA TSV has 8 data rows while the generated stub seeded 7: the two
GO:0005515 rows for PMID:26808496 differ only in assigner, IntAct versus
AgBase, and were collapsed into one. They are restored as separate entries so
each assigner gets its own verdict, and so that one co-immunoprecipitation is not
counted as two independent supports.
All 3 experimentally-coded GOA rows are IPI protein-binding rows. There is
no experimental molecular-function row of any other kind and no experimental
biological-process row, which is why this review's diagnosis is under-annotation
rather than over-annotation.