Reparent Fermentation under metabolism, not respiration (#472)#478
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Reparent Fermentation under metabolism, not respiration (#472)#478turbomam wants to merge 1 commit into
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#472) METPO:1002005 Fermentation was a child of `respiration` with a self-contradictory definition ("A respiration that … without using an external electron acceptor"). Fermentation is canonically distinct from respiration (cf. GO:0006113 vs GO:0009060). Reparented to `metabolism` (respiration's own parent, making Fermentation a sibling of respiration) and reworded the genus to match: "A metabolism in which energy is generated through the oxidation of organic compounds without using an external electron acceptor …". Edited in the Sheet (SoT) and rebuilt. Fixes #472. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Pull request overview
Reparents METPO:1002005 (Fermentation) from respiration to metabolism and updates its definition genus accordingly, addressing the QC finding that the prior placement/definition was self-contradictory.
Changes:
- Updated the Fermentation row in
src/templates/metpo_sheet.tsvto parent it undermetabolismand reword the definition to “A metabolism in which …”. - Propagated the same parent + definition updates into the generated component OWL and all release artifacts (
.owl,.obo,.jsonvariants).
Reviewed changes
Copilot reviewed 11 out of 11 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| src/templates/metpo_sheet.tsv | Reparents Fermentation to metabolism and updates the genus in the definition. |
| src/ontology/components/metpo_sheet.owl | Regenerated template component reflecting updated subclass + definition annotation. |
| metpo.owl | Release artifact updated for Fermentation parent + definition. |
| metpo.obo | Release artifact updated for Fermentation parent + definition. |
| metpo.json | Release artifact updated for Fermentation parent + definition + is_a edge. |
| metpo-full.owl | Full release artifact updated for Fermentation parent + definition. |
| metpo-full.obo | Full release artifact updated for Fermentation parent + definition. |
| metpo-full.json | Full release artifact updated for Fermentation parent + definition + is_a edge. |
| metpo-base.owl | Base release artifact updated for Fermentation parent + definition. |
| metpo-base.obo | Base release artifact updated for Fermentation parent + definition. |
| metpo-base.json | Base release artifact updated for Fermentation parent + definition + is_a edge. |
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Jun 2, 2026
#473, #479) (#480) * QC content fixes + nest extreme/restrictive preference phenotypes (#470 #471 #472 #473 #479) Consolidates all the Sheet-content QC fixes into one rebuild on top of the typed owl:deprecated fix (#467), because they all regenerate the same artifacts from the single Google Sheet and cannot be independent PRs. Supersedes #477 and #478. Content (all via the Sheet, SoT): - #470 labels alkaphilic -> alkaliphilic (METPO:1003002/1003004/1003005) - #471 NaCl delta high: range_min=8 (matches the >= 8 formula) - #472 Fermentation reparented respiration -> metabolism + def reworded - #473 + #479 nest genuine subset phenotypes under their base class (truth over flat-partition), genus reworded to "a <base> phenotype in which ...": extreme hyperthermophilic -> hyperthermophilic extremely/moderately/slightly halophilic -> halophilic obligately acidophilic -> acidophilic; obligately alkaliphilic -> alkaliphilic obligately anaerobic -> anaerobic; obligately aerobic -> aerobic The nested defs use genus "a <base> phenotype" (e.g. "a halophilic phenotype"), which the DEF-FORM check flags (genus != exact parent label) — intentional debt. Halophily threshold numbers (#474) are a separate decision and unchanged here. Fixes #470, #471, #472, #473, #479. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * lint: DEF-FORM accepts '<parent> phenotype' genus (the endorsed nesting form) The nested phenotypes (#473/#479) use genus 'a <base> phenotype in which ...' (e.g. 'a halophilic phenotype', parent 'halophilic'). That is hierarchy/label/ definition compatible but tripped DEF-FORM (genus != exact parent label). Accept '<parent>', '<parent> phenotype', '<parent> preference', '<parent> quality' as valid genus forms for adjectival parents. Regenerated baselines accordingly. The test/assay genus mismatches (#461) and other true mismatches still fire. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * style: ruff format the lint test/check edits Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * fix(content): use O₂ subscript in obligately anaerobic/aerobic defs (Copilot #480) Consistency with the other oxygen-preference definitions. Addresses the Copilot review comment on #480. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * style(content): normalize all definitions/synonyms to plain ASCII (consistency + simplicity) Replaces special Unicode in ontology content with ASCII for searchability and robustness: O2 (was O₂), >= (was ≥), 'C' (was °C), '-' (was en/em dash), and the em dash in METPO:2000068's def -> ';'. Covers 14 class defs, one literature-mining synonym, and one property def. All edits made in the Google Sheet (SoT) via gog; both TSVs are now 0 non-ASCII. Resolves Copilot's O2/O₂ consistency note (#480) in the ASCII direction. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
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Fixes #472 (from the QC review #468).
METPO:1002005
Fermentationwas parented underrespirationwith a self-contradictory definition. Fermentation is canonically not a form of respiration. Reparented tometabolism(= respiration's own parent, so Fermentation becomes a sibling of respiration) and reworded the genus toA metabolism in which ….Stacked on #477 (base =
qc-data-fixes-470-471) because both edit the single Google Sheet; this PR's diff is only the Fermentation row. GitHub will retarget tomainwhen #477 merges. Leaving open for CI + Copilot.Fixes #472.