Entner-Doudoroff Sub-pathway Obsoletion (GO:0009255, GO:0061679, GO:0061680, GO:0061681)

Bottom line: GO retired four Entner-Doudoroff (ED) sub-pathway terms,
GO:0009255, GO:0061679, GO:0061680 and GO:0061681, and replaced them with the
parent GO:0061678 Entner-Doudoroff pathway because the alternate gluconate
and 6-phosphogluconate routes are better distinguished by GO-CAM structure
than by nested pathway terms. PR #3232 applied the only direct fixes needed in this
repo: PSEPK edd now keeps its
GOA-sourced GO:0009255 row but marks it MODIFY to GO:0061678, PSEPK
eda now proposes a NEW row on
GO:0061678, and both reviews' core_functions point to GO:0061678. The same
PR fixed the related PSEPK glk
proposal for obsolete GO:0061688 by accepting its existing GO:0006096
glycolytic process row instead: Glk phosphorylates glucose upstream of the
ED dehydration and aldol-cleavage reactions, so it should not receive the ED
pathway process term. The remaining repo work is optional new E. coli edd,
eda and gnd coverage, tracked in #460.

Overview

GO retired four sub-variant terms under the Entner-Doudoroff pathway and
consolidated annotations to the parent term
GO:0061678 Entner-Doudoroff pathway:

• GO:0009255 Entner-Doudoroff pathway through 6-phosphogluconate
• GO:0061679 Entner-Doudoroff pathway through gluconate
• GO:0061680 Entner-Doudoroff pathway through gluconate to D-glyceraldehyde
• GO:0061681 Entner-Doudoroff pathway through gluconate to D-glyceraldehyde-3-phosphate

This flattened an over-specified sub-pathway hierarchy without changing the
biology: the key direct functions are still phosphogluconate dehydratase for
Edd and KDPG aldolase for Eda. The repo now carries those two ED enzymes on
the parent ED-pathway term, while the module
modules/entner_doudoroff_and_gluconeogenesis.yaml records the finer route
structure.

Upstream tickets

• Annotation tracker: geneontology/go-annotation#6390
• Ontology ticket: geneontology/go-ontology#31916

Obsoletion plan (per upstream)

Affected upstream groups (original issue snapshot)

External mappings flagged for review (per upstream)

Impact on this repo

The obsoletion affected two PSEPK gene reviews that were already on
GO:0009255:

The obsoletion was already present in GO release 2026-05-19; PR #3232
refreshed both reviews after the repo ontology cache had rolled to
2026-07-26 so that the author-supplied directly_involved_in references
and review actions point to GO:0061678 instead of GO:0009255.
GOA-sourced existing_annotations[].term.id values are never rewritten
(see CLAUDE.md); the change is carried in action plus
proposed_replacement_terms instead. The biology is
unchanged — Edd (phosphogluconate dehydratase) and Eda (KDPG aldolase) are
the canonical ED-pathway enzymes in P. putida KT2440.

The pathway modules are already updated.
modules/entner_doudoroff_and_gluconeogenesis.yaml grounds the committed
6-phosphogluconate branch in GO:0061678 and records the old GO:0009255 and
GO:0061688 variant terms as obsolete. modules/emp_glycolysis.yaml also
points readers to GO:0061678 for the Entner-Doudoroff route, keeping ED
separate from the fructose-6-phosphate-centered EMP glycolysis module.

Sibling term outside this page's scope. The same modules record that
GO:0061688 glycolytic process via Entner-Doudoroff Pathway was obsoleted in
the same obsoletion wave with replaced_by GO:0006096. PSEPK
glk had proposed GO:0061688 as a
MODIFY replacement and listed it in core_functions[].directly_involved_in.
PR #3232 dropped that target, accepted the GOA GO:0006096 row, and moved
core_functions to GO:0006096. GO:0061678 was rejected for Glk because the
enzyme phosphorylates glucose upstream of the ED branch rather than catalyzing
an ED step. PSEPK pgi2 mentions GO:0061688 only in prose, to reject it.

Negative control: PSEPK zwf. genes/PSEPK/zwf/ is a complete review of
glucose-6-phosphate 1-dehydrogenase, the entry step that feeds
6-phosphogluconate into the ED pathway. zwf-ai-review.yaml uses none of
GO:0009255, GO:0061678 or GO:0061688, so it needs no change and confirms that
only the edd and eda reviews (plus glk's proposed target) are affected.

Scope

• Organisms: bacteria (E. coli, Pseudomonas spp., other ED-using
  organisms). The repo's existing PSEPK coverage is the primary in-scope set.
• GO branch: BP (carbohydrate catabolism, glycolysis-alternative). The
  obsoletion is purely terminological — no MF terms are affected.
• Type of fix: lift annotations one level to the parent term GO:0061678.
  No enzyme-MF changes required.

Candidate genes for initial review

The two ED-enzyme reviews and the sibling glk fix are the completed PSEPK
check set; a small set of ortholog reviews would round out coverage of the
canonical ED pathway.

Existing PSEPK reviews checked

1. edd (PSEPK) — genes/PSEPK/edd/edd-ai-review.yaml. The GOA IEA row
   keeps its GOA term id GO:0009255 and moves from ACCEPT to MODIFY with
   proposed_replacement_terms GO:0061678; core_functions[].directly_involved_in
   now uses GO:0061678.
2. eda (PSEPK) — genes/PSEPK/eda/eda-ai-review.yaml. The curator-proposed
   NEW row (no GOA row) and core_functions now use GO:0061678.
3. glk (PSEPK) — genes/PSEPK/glk/glk-ai-review.yaml. Obsolete
   GO:0061688 MODIFY target dropped; GOA GO:0006096 glycolytic process row
   now ACCEPT and core_functions → GO:0006096. GO:0061678 was considered
   and rejected, since Glk performs no ED step.

New ortholog reviews (proactive)

Verify each with just fetch-gene <organism> <gene> before starting; do not
add files without confirming the UniProt accession from the UniProt API. This
optional follow-up batch is tracked in
#460.

1. edd (E. coli K-12) — phosphogluconate dehydratase; the founding
   organism for the ED pathway and likely the EcoCyc-affected entry upstream.
2. eda (E. coli K-12) — KDPG aldolase; companion to E. coli edd,
   completes the two-enzyme ED core.
3. gnd / 6PGD homologs — the diversion point between ED and the pentose
   phosphate pathway; a clean review here clarifies why annotations should
   sit at GO:0061678 rather than a sub-variant.

Proposed approach

1. Done in #3232: PSEPK edd and eda now use GO:0061678 for the
   author-supplied replacement or NEW process term and for
   core_functions[].directly_involved_in.
2. Done in #3232: PSEPK glk now stays on GO:0006096 after obsolete
   GO:0061688 was dropped as an attempted replacement.
3. Open in #460: E. coli edd, E. coli eda and a gnd/6PGD boundary
   review remain useful as one coherent ED-pathway follow-up batch, but they
   no longer block this obsoletion cleanup.

Priority

Low–Medium. The obsoletion is mechanical and only two existing reviews
are affected; both are updated in a single small PR, #3232, now that
the ontology release has shipped. Higher value is in using the moment to add E. coli ED
reviews, but those are independent of the obsoletion itself.

Status

• 2026-05-10 — Project file created. Tracking upstream issue #6390 (last
  active 2026-05-01). Obsoletion not yet merged. Two existing PSEPK reviews
  (edd, eda) flagged for term-ID update once the obsoletion ships.
• 2026-09-27 — PR #3232 applied the obsoletion after the repo ontology cache
  had rolled to 2026-07-26: edd's GOA row became MODIFY → GO:0061678,
  eda's NEW row now proposes GO:0061678, and both edd and eda
  core_functions were repointed to GO:0061678. The related obsolete
  GO:0061688 (glycolytic process via Entner-Doudoroff Pathway, replaced_by
  GO:0006096) was handled on PSEPK glk, which stays ACCEPT on GO:0006096.
  The E. coli edd/eda and gnd ortholog reviews remain as optional follow-up.
• 2026-10-04 — Project audit rechecked PSEPK edd, eda, glk, pgi2 and zwf
  against the project summary. No additional PSEPK review edits were needed;
  stale post-obsoletion wording in the project page and deck was collapsed,
  and #460 now
  tracks only the optional E. coli edd/eda/gnd follow-up batch.