Entner-Doudoroff sub-pathway obsoletion

Four variant terms → GO:0061678 Entner-Doudoroff pathway

AI Gene Review · projects/ENTNER_DOUDOROFF_OBSOLETION · 2026

Bottom line

  • GO obsoleted four ED sub-pathway terms (GO:0009255, GO:0061679, GO:0061680, GO:0061681) and folded them into GO:0061678.
  • Only two repo reviews needed direct fixes: P. putida edd and eda.
  • PR #3232 is merged: edd ACCEPT → MODIFY → GO:0061678, eda NEW → GO:0061678, and both core_functions now point to GO:0061678.

Old terms → replacement

Why the variants went

  • The four terms mirrored MetaCyc variant pathways: via 6-phosphogluconate, via gluconate, and two gluconate endpoints.
  • GO's obsoletion comment: variants are better captured as GO-CAMs than as nested ontology terms.
  • The parent GO:0061678 already covers both intermediates (gluconate or 6-phosphogluconate) and both endpoints.
  • No molecular function terms change.

What the variants described

The edd row before #3232

genes/PSEPK/edd/edd-ai-review.html: the ACCEPT on GO:0009255 (main, before #3232). GOA ids are not rewritten, so #3232 makes it MODIFY → GO:0061678 rather than keeping ACCEPT.

Repo impact

Gene Row on GO:0009255 Action Also in
PSEPK edd IEA, GO_REF:0000120 ACCEPT → MODIFY → GO:0061678 (#3232) core_functions.directly_involved_in
PSEPK eda proposed, from UniProt pathway line NEW, now GO:0061678 (#3232) core_functions.directly_involved_in
  • No review uses GO:0061679, GO:0061680 or GO:0061681.
  • The ED module and both PSEPK ED-enzyme reviews now use GO:0061678.
  • Sibling term GO:0061688 (obsoleted in the same GO release) was proposed by PSEPK glk; #3232 drops it and ACCEPTs glk's GOA GO:0006096 row, since Glk does no ED step.
  • Upstream issue snapshot: EcoCyc 1 and UniProt 3 annotations, plus 7 external mappings.

Next steps

  1. Done in #3232: edd, eda → GO:0061678 (rows and core_functions); glk → GO:0006096.
  2. Later, as one batch tracked in #460: E. coli edd, E. coli eda, and a pass over gnd.

Upstream: go-annotation#6390 · go-ontology#31916
Read more: projects/ENTNER_DOUDOROFF_OBSOLETION.md