InterPro2GO mapping review

Finding the family-level mappings that put wrong GO terms on many genes at once

AI Gene Review · projects/INTERPRO · 2026

Bottom line

  • InterPro2GO copies each mapped GO term onto every protein that matches the entry, including members that lack the function.
  • We mined 3,652 InterPro2GO rows already judged in gene reviews, ranked 1,826 entries by flagged rows, and deep-researched the top families.
  • Output: 29 proposed mapping edits on 12 entries: 7 remove, 10 narrow, 12 endorse. Proposals only; InterPro has not adopted them.

The mechanism and the pipeline

Why mappings, not genes

  • A bad mapping is one error repeated on every matched gene; fixing it once fixes all of them.
  • Typical failure: fold is not function. A domain shared by enzymes and non-enzymes (pseudokinases, copper chaperones, RIG-I-like sensors) carries the enzyme's term.
  • A second pattern: name collision. IPR045122 "calcium permeable" channel mapped to GO:0005227 calcium-activated channel.

What reviewers already said about these rows

1,732 rows (47%) flagged. This is a priority signal, not a mapping error rate: it includes valid non-core rows and specificity refinements.

Proposed removals (7)

Entry GO term Reason
IPR000719 kinase domain GO:0005524, GO:0006468 pseudokinases
IPR001424 Cu/Zn SOD GO:0006801 superoxide metabolism copper chaperones
IPR012724 DnaJ GO:0005524 ATP binding ATP belongs to Hsp70 partner
IPR045122 CSC1-like GO:0005227 Ca-activated channel name collision; mechanosensitive
IPR042371 Z-binding GO:0003726 dsRNA deaminase deaminase is a separate ADAR1 domain
IPR006935 Helicase/UvrB N GO:0003677 DNA binding IFIH1 (MDA5) is an RNA sensor

Two intake paths

  • Ranked worklist: entries with many flagged rows. IPR000719 has 50 flagged of 112; IPR008271 34 of 55; IPR001128 26 of 44.
  • Gene-first: three removals (IPR045122, IPR042371, IPR006935) came from reading ~60 human genes one at a time.
  • The worklist is blind to wrong mappings that are rarely reviewed; IPR045122 has three human members.

Status and next steps

  • ✅ Extractor, worklist, 29-row SSSOM set; just validate-interpro-mappings
  • ⬜ Deferred family research: sigma-54, pseudouridine synthase, GAPDH
  • ⬜ Continue down the worklist; check accepted rows on exception members
  • ⬜ Summarize per-entry recommendations for InterPro2GO curators

Read more: projects/INTERPRO.md · projects/INTERPRO/interpro2go.sssom.yaml · projects/INTERPRO/interpro_family_priorities.tsv