InterPro mapping review — supporting material

Supporting material for the InterPro Mapping Review project.

Contents

• extract_suspect_interpro_mappings.py — reproducible extractor. Walks every
  genes/*/*/*-ai-review.yaml, finds the annotations sourced from InterPro2GO
  (original_reference_id: GO_REF:0000002), recovers the source InterPro entry id(s)
  from the matching *-goa.tsv (the WITH/FROM column), joins in the reviewer's
  action, and writes the two TSVs below.
• suspect_interpro_mappings.tsv — one row per reviewed InterPro2GO annotation
  (gene, InterPro id(s), GO term, action, suspect flag, proposed replacement, reason).
• interpro_family_priorities.tsv — one row per InterPro entry, aggregating how often
  it produced an accepted vs a suspect mapping across all reviewed genes. This is the
  ranked worklist for family-level deep research (entries that repeatedly produce
  suspect mappings first).

Proposed interpro2go edits (SSSOM)

• interpro2go.sssom.yaml — canonical SSSOM mapping set: the family-deep-research verdicts
  expressed as proposed edits to InterPro2GO (one row per reviewed (InterPro entry, GO term);
  exactMatch = sound, broadMatch = over-broad/demote, exactMatch + predicate_modifier: Not
  = remove). Source of truth.
• interpro2go.terms.yaml — generated nested term-tuple form (do not edit by hand) for GO
  label validation.
• sssom_to_terms.py — regenerates the .terms.yaml from the .sssom.yaml.

just validate-interpro-mappings   # SSSOM structure + GO term/label validation

Family deep research (generated process)

Family deep research is generated, not hand-written. It is wired the same way as gene
deep research:

• templates/interpro_family_research.md — the deep-research prompt template.
• scripts/deep_research_interpro_family.py — wrapper that loads the cached InterPro
  metadata as context and runs deep-research-client.
• just deep-research-interpro-family <IPR> [provider] — the recipe (in
  project.justfile); provider defaults to falcon (Edison). Output:
  interpro/<db>/<ID>/<ID>-deep-research-<provider>.md.

just deep-research-interpro-family IPR000719          # falcon (Edison) by default

Regenerate

uv run python projects/INTERPRO/extract_suspect_interpro_mappings.py

An annotation is counted "suspect" when its review action is anything other than
ACCEPT (MODIFY, REMOVE, MARK_AS_OVER_ANNOTATED, KEEP_AS_NON_CORE, UNDECIDED). The TSVs
are regenerated from the current state of the reviews, so re-run after new reviews land.