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

IN_PROGRESS OBSOLETION

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

Overview

A GO obsoletion proposal will retire four sub-variant terms under the
Entner-Doudoroff pathway and consolidate annotations to the parent term
GO:0061678 Entner-Doudoroff pathway:

The intent is to flatten the over-specified sub-pathway hierarchy and let
biology be captured by the single parent ED-pathway term plus the relevant
enzyme MFs. This project tracks impact on the AI Gene Review repo and queues
follow-up edits to existing reviews and candidate gene reviews for the canonical
ED enzymes.

Upstream tickets

Obsoletion plan (per upstream)

Obsoleted term ID Replacement
Entner-Doudoroff pathway through 6-phosphogluconate GO:0009255 GO:0061678 Entner-Doudoroff pathway
Entner-Doudoroff pathway through gluconate GO:0061679 GO:0061678 Entner-Doudoroff pathway
Entner-Doudoroff pathway through gluconate to D-glyceraldehyde GO:0061680 GO:0061678 Entner-Doudoroff pathway
Entner-Doudoroff pathway through gluconate to D-glyceraldehyde-3-phosphate GO:0061681 GO:0061678 Entner-Doudoroff pathway

Affected upstream groups (from issue body)

Group Annotations Status
EcoCyc 1 pending
UniProt 3 pending

External mappings flagged for review (per upstream)

Source Mapping
MetaCyc:PWY-8004 → metacyc2go GO:0009255
InterPro:IPR004786 (6-phosphogluconate dehydratase) → interpro2go GO:0009255
HAMAP:MF_02094 → hamap2go GO:0009255
UniRule:UR000683091 → unirule2go GO:0009255
UniRule:UR001995752 → unirule2go GO:0009255
MetaCyc:NPGLUCAT-PWY → metacyc2go GO:0061680
MetaCyc:PWY-2221 → metacyc2go GO:0061681

Impact on this repo

The obsoletion directly affects existing reviews. Two PSEPK gene reviews
already use GO:0009255 in their existing_annotations and core_functions:

Gene File Current usage
PSEPK edd genes/PSEPK/edd/edd-ai-review.yaml IEA from GO_REF:0000120, accepted; also referenced under core_functions[].directly_involved_in
PSEPK eda genes/PSEPK/eda/eda-ai-review.yaml action: NEW annotation proposal (not in GOA) keyed off the UniProt pathway statement; also referenced under core_functions[].directly_involved_in

Both reviews will need a refresh once the obsoletion lands so that the
directly_involved_in references and the existing_annotations review
entries point to GO:0061678 instead of GO:0009255. The biology is
unchanged — Edd (phosphogluconate dehydratase) and Eda (KDPG aldolase) are
the canonical ED-pathway enzymes in P. putida KT2440.

Scope

Candidate genes for initial review

The two existing PSEPK reviews are the immediate work items; a small set of
ortholog reviews would round out coverage of the canonical ED pathway.

Existing reviews to refresh (post-obsoletion)

  1. edd (PSEPK) — genes/PSEPK/edd/edd-ai-review.yaml. Update
    GO:0009255 → GO:0061678 in both existing_annotations and the
    core_functions[].directly_involved_in block.
  2. eda (PSEPK) — genes/PSEPK/eda/eda-ai-review.yaml. Same edit pattern
    as edd.

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.

  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. zwf (PSEPK) — glucose-6-phosphate 1-dehydrogenase, the entry step into
    the ED pathway via 6-phosphogluconate. Already partially covered in the
    PSEPK gene set per projects/SPKW/SPKW-PSEPK.md; verify status before adding.
  4. 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. Wait for the obsoletion to land in a public GO release. The
    ontology ticket (#31916) has not yet been merged at the time of writing,
    so refreshing the PSEPK reviews now would need to be redone if labels
    change.
  2. Once the obsoletion is in a release, update the two PSEPK reviews in
    one PR — the change is mechanical (term ID swap + label update) and the
    review.summary text already justifies pathway-level annotation. The
    action differs by gene: for edd the existing IEA is ACCEPTed and
    stays ACCEPT on the lifted parent term; for eda the annotation is
    a curator-proposed NEW (no GOA row) and stays NEW on the lifted
    parent term. The review.summary text in eda also references the old
    label "Entner-Doudoroff pathway through 6-phosphogluconate" and should
    be updated to "Entner-Doudoroff pathway (GO:0061678)" alongside the
    term-ID swap.
  3. Re-run just validate PSEPK edd and just validate PSEPK eda after
    the edits to confirm the schema accepts the new term IDs.
  4. Defer new ortholog reviews (E. coli edd/eda, zwf, gnd) to a follow-up
    batch — the obsoletion does not block them, and they are best done as a
    coherent ED-pathway batch rather than ad hoc.

Priority

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

Status