Reactome black box events

Can gene reviews name the missing transporters in pathway reactions?

AI Gene Review · projects/REACTOME_GAP_FILLING · 2026 · scoping, one pilot

Bottom line

  • Reactome black box events are reactions that must happen but have no assigned catalyst or transporter, often at an organelle membrane.
  • Pilot done: ABCD3 (81 annotations reviewed) gets a NEW bile acid transmembrane transporter term for peroxisomal import of C27 bile-acid CoA esters.
  • Scoped, not started beyond that: no systematic black-box query yet; the other bile acid gaps have no candidate reviewed.

The pilot pathway

How ABCD3 was resolved

Workflow and expansion targets

  1. Identify black box events in a Reactome pathway; sort by reaction type and membrane.
  2. Candidates from GO, expression, domain architecture, deep research.
  3. Converge with a full gene review: activity, loss of function, structure, localization.
  4. Tier the result and report to Reactome curators.

Next areas: mitochondrial SLC25 carriers, cholesterol and sphingolipid trafficking, other ABC families, peroxisomal SLCs.

Status

  • One gene review (genes/human/ABCD3/), proposing NEW GO:0015125 (IMP).
  • Reactome R-HSA-382575 lists ABCD3 for LCFA transport but not for bile-acid CoA esters: an update to propose.
  • Collaboration with Reactome curators (P. D'Eustachio, L. Matthews).

Read more: projects/REACTOME_GAP_FILLING.md · genes/human/ABCD3/ABCD3-ai-review.yaml