Nitrogen cycle metabolic process: do_not_annotate and regulation obsoletion

GO:0071941 → annotate its child pathways · GO:1903314/5/6 obsolete

AI Gene Review · projects/NITROGEN_CYCLE_OBSOLETION · 2026

Bottom line

  • GO:0071941 is an ecosystem grouping term; its three regulation children are now obsolete and the parent is proposed as do_not_annotate.
  • Of 6 experimental rows, 5 are mouse kidney/liver genes we recommend removing; napA should move to GO:0019333 denitrification pathway.
  • Scoped. The one in-repo hit, A. vinelandii nifA, used the now-obsolete GO:1903316; replacement tracked in #3235 (open).

Old terms → where annotations should go

What the term is for

Why five of six rows are wrong

  • Pkd1, Prkcsh, Sec63 (IGI, PMID:21685914): the polycystic kidney and liver disease network; glucosidase II, translocon, polycystin.
  • Apc (IMP, PMID:16740478): liver metabolic zonation; urea-cycle enzymes sit downstream, but APC has no nitrogen-cycle role.
  • All five use acts_upstream_of_or_within, assigned by MGI.
  • The term is about microbial nitrogen transformations; mammalian nitrogen excretion is a different process.
  • napA (IMP, PMID:10227138) is a real denitrification gene, just on the parent term.

In this repo

Review Relation State
genes/AZOVI/nifA used GO:1903316 (obsolete) MODIFY target, NEW row and core_functions; replacement tracked in #3235 (open)
genes/human/SEC63 ortholog of affected mouse Sec63 reviewed; no GO:0071941 row in its GOA file
mouse Pkd1, Prkcsh, Apc, Sec63; napA affected upstream not reviewed

GO has no "regulation of nitrogen fixation" term, so a replacement must be chosen per row.

Status and next steps

  • 2026-05-13: project created; 6 rows matched the upstream count.
  • 2026-09-26: OLS lists GO:1903314/5/6 obsolete; GO:0071941 still live.
  • 2026-09-26 (later): nifA replacement tracked in #3235 (open).
  • Next: review human PKD1, PRKCSH, APC and flag the mouse rows; add the pattern to projects/OVER_ANNOTATION_PATTERNS.md.

Upstream: go-annotation#6411 · go-ontology#27220
Read more: projects/NITROGEN_CYCLE_OBSOLETION.md