TCDB to GO

Why transporter classifications never become GO annotations, and a scored starter set for a tc2go pipeline

AI Gene Review · projects/TCDB · 2026

Bottom line

  • GO already links TC numbers to 170 MF terms, but has no tc2go pipeline, so 50.6% of reviewed TCDB-linked transporters (4,431 of 8,758) lack any transporter-activity term.
  • We scored all 194 GO TC-to-GO leads against reviewed UniProt members: 80 safe to propagate (70 at single-system level), 18 over-propagate, 67 point to missing specific terms.
  • Four validated SSSOM sets, including 477 filtered rows from TCDB's own GO dump and 8 hand-backed exemplars.

A missing pipeline, and which TC level is safe

Why transporters

  • TCDB is the IUBMB-adopted transporter classification; class.subclass.family.subfamily.system.
  • EC and RHEA reach proteins via ec2go / rhea2go; TC has term xrefs only.
  • TCDB's own go.py dump (34,497 rows) is mostly CC/BP and noise: only 13% of rows are transporter-activity MF; protein binding appears 452 times.

Scoring the 194 leads

JUSTIFIED: ≥2 reviewed members and ≥70% carry the term. GAP_CANDIDATE: a specific system whose members all lack it (tested first).

Hand-backed exemplars (tc2go.sssom.yaml)

TC GO term Verdict Backing protein
2.A.22.1.1 SERT GO:0005335 exactMatch SLC6A4 P31645
3.A.3.1.1 Na⁺/K⁺-ATPase GO:0005391 exactMatch ATP1A1 P05023
2.A.69 AEC GO:0010329 auxin efflux exactMatch PIN1 Q9C6B8
1.A.8 MIP GO:0015250 water narrowMatch aquaglyceroporins differ
2.A.17 POT/PTR GO:0015112 nitrate narrowMatch CHL1/NRT1.1 Q05085
2.A.18 AAAP GO:0010328 auxin influx narrowMatch AUX1 Q96247

Two more narrowMatch rows: 2.A.36 CPA1 (SOS1) and 2.A.38 Trk (HKT1 as counter-example).

Status and next steps

  • ✅ GO xrefs extracted and scored; go.py characterised; reverse gap quantified
  • ✅ Four SSSOM sets pass just validate-tcdb-mappings
  • ⬜ Package the 80 JUSTIFIED leads as a proposed tc2go pipeline for GO
  • ⬜ Push the 67 GAP_CANDIDATE leads through gene review; closure-aware reverse gap
  • ⬜ Rebuild the generated set at subfamily/system level

Read more: projects/TCDB.md · projects/TCDB/tc2go.propagation.sssom.yaml · projects/TCDB/TCDB-METHODOLOGY.md