Antimicrobial resistance

Reviewing 30 resistance determinants and bridging CARD's ontology to GO

AI Gene Review · projects/ANTIMICROBIAL_RESISTANCE · 2026

Bottom line

  • Resistance enzymes are well understood, but GO usually holds only a generic term like transferase activity, or nothing.
  • We reviewed 30 determinants in 21 species (140 rows, 47 NEW) and built a validated ARO→GO mapping (23 mappings, 9 gaps).
  • Applied to 4,182 CARD-linked UniProt entries it yields 630 candidate GO annotations; a spot check found 4/6 correct, so they are curator leads.

Why AMR, and why CARD

  • Sparse GO, rich biochemistry: e.g. MphA and MphB had empty GOA records.
  • CARD / ARO already curates mechanism, drug class, gene family and PMIDs for each determinant (OBO Foundry, CC-BY 4.0).
  • ARO has no GO cross-references (zero GO: xrefs in 8,602 classes), so the bridge has to be built here.
  • response to antibiotic (GO:0046677) is usually present and true. The gain is the missing enzyme chemistry.

The pipeline

The mapping set

aro2go.html: curator view of the SSSOM mappings, gaps and UniProt impact. just validate-mappings checks every ARO/GO CURIE and label.

Where the gains are

Spot check of six candidates

# Entry Candidate GO Verdict
1 MCR-1 GO:0043838 pEtN transferase correct, high value
2 RmtE GO:0070043 rRNA guanine-N7 MTase correct refinement
3 ermZ/srm1 GO:0052910 23S A-N6 diMTase correct, more precise
4 AAC(6')-Ib8 GO:0034069 redundant: has child GO:0047663
5 OXA-1090 GO:0008800 beta-lactamase questionable: may be a PBP
6 FosK GO:0004364 mapping over-generalises (FosB)

Fixes that followed: subsumption filter (104 suppressed), fosfomycin mapping restricted to FosA, Erm mapped to family-safe GO:0008988.

Gene reviews: where GO has no term

Cfr review: generic rows marked over-annotated, tRNA carryover removed, and a new term proposed. Six such full reviews (tetX, fosB, arr, ereB, lnuA, cfr) each propose a missing leaf MF.

Results across 30 reviews

Action Rows
NEW 47
ACCEPT 46
MODIFY 34
KEEP_AS_NON_CORE 6
MARK_AS_OVER_ANNOTATED 5
REMOVE 2

140 existing-annotation rows. NEW dominates because many TrEMBL accessions had no GOA at all. The 20-gene focused batch is draft-level (curator leads).

Status and next steps

  • ✅ 30 gene reviews, SSSOM mapping set, pipeline, annotation-gain report and spot review.
  • ⬜ Submit the missing leaf MF terms (tetracycline monooxygenase, erythromycin esterase, rifampin ADP-ribosyltransferase, lincosamide nucleotidyltransferase, FosB, Cfr).
  • ⬜ Next families: mph(C/E/G), erm(B/C), mef(A/E), ere(A), CTX-M / KPC.

Read more: projects/ANTIMICROBIAL_RESISTANCE.md · projects/ANTIMICROBIAL_RESISTANCE/aro2go.sssom.yaml · uniprot2aro2go.py