Mevalonate pathway terms: obsoletion

GO:1902767 and GO:0010142 → GO:0019287 (to IPP) or GO:0045337 (IPP → FPP)

AI Gene Review · projects/MEVALONATE_PATHWAY_OBSOLETION · 2026

Bottom line

  • GO obsoleted two overlapping mevalonate-route terms; each old row must go to GO:0019287 or GO:0045337 depending on the step the gene catalyses.
  • The human pathway is now reviewed here (HMGCS1, HMGCR, MVK, PMVK, MVD, IDI1, FDPS; PRs #1998, #2153): MVK, PMVK, MVD accept GO:0019287 and FDPS accepts GO:0045337.
  • 3 obsolete-term rows resolved in #3232: yeast ERG19 (1 RCA row, now REMOVE, since GO:0019287 is already accepted) and rat Hmgcs2 (2 rows, stay UNDECIDED, obsoletion recorded).

Old terms → replacements

One route, two replacement terms

Why it is a judgement, not a relabel

  • Both obsolete terms covered the whole route from acetyl-CoA through mevalonate to FPP.
  • The replacements split it at IPP: GO:0019287 for the upper steps, GO:0045337 for FDPS chemistry.
  • A kinase or decarboxylase row belongs on GO:0019287; an FDPS row on GO:0045337; some genes may need both.
  • Upstream lists: 2 EXP on GO:1902767 (1 EcoCyc left), 21 EXP on GO:0010142 across 16 genes.
  • E. coli uses the MEP pathway, so the yajO row is a removal candidate, not a remap.

What is in the repo

Gene Relevant rows Action
human MVK, PMVK, MVD GO:0019287 IBA + IEA ACCEPT
human FDPS GO:0045337 IBA + IEA ACCEPT
human HMGCS1, HMGCR, IDI1 reviewed; no row on either replacement –
rat Hmgcs2 GO:0010142 IBA + IEA UNDECIDED, obsoletion noted (#3232)
yeast ERG19 GO:0010142 RCA; GO:0019287 IEA REMOVE (#3232); ACCEPT

Modules: modules/mevalonate_pathway.yaml (grounded on GO:0019287) and modules/isoprenoid_diphosphate_biosynthesis.yaml.

Status and next steps

  • 2026-06-06: project created; only rat Hmgcs2 then carried an obsolete-term row.
  • 2026-07: human pathway reviews and modules added (PRs #1998, #2153).
  • 2026-09-26: OLS lists both terms obsolete.
  • 2026-09-27: #3232 applied the obsoletion: ERG19 RCA row REMOVE; Hmgcs2 rows UNDECIDED with the obsoletion in reason.
  • Next: identify the remaining EcoCyc row (possibly yajO).

Upstream: go-annotation#6440, #6439 · go-ontology#32082
Read more: projects/MEVALONATE_PATHWAY_OBSOLETION.md