Data fixes: alkaphilic label spelling (#470) + NaCl delta high range bound (#471)#477
Closed
turbomam wants to merge 1 commit into
Closed
Data fixes: alkaphilic label spelling (#470) + NaCl delta high range bound (#471)#477turbomam wants to merge 1 commit into
turbomam wants to merge 1 commit into
Conversation
… high range bound (#471) Two pure-data corrections, made in the Google Sheet (SoT) and rebuilt: - METPO:1003002/1003004/1003005 labels `alkaphilic` -> `alkaliphilic` (the exact synonyms already had the correct spelling). - METPO:1000482 NaCl delta high: moved `8` from range_max to range_min so it agrees with the `xsd:decimal[>= 8]` equivalent_class_formula (a lower bound). Fixes #470, #471. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Contributor
There was a problem hiding this comment.
Pull request overview
This PR applies two QC-driven, source-of-truth (Google Sheet) data corrections and propagates them through the template snapshots and generated release artifacts, keeping METPO term labels and numeric range metadata consistent with intended semantics.
Changes:
- Fixes the misspelled primary labels
alkaphilic→alkaliphilicfor METPO:1003002/1003004/1003005 (with downstream regeneration). - Corrects METPO:1000482 “NaCl delta high” by moving the boundary value
8fromrange_maxtorange_minto match the[>= 8]restriction.
Reviewed changes
Copilot reviewed 12 out of 12 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
src/templates/stubs.tsv |
Updates the stub labels for the three alkaliphily terms to the corrected spelling. |
src/templates/metpo_sheet.tsv |
Applies the label spelling fixes and corrects the NaCl delta high bin’s min/max range columns. |
src/ontology/components/metpo_sheet.owl |
Regenerates the sheet-derived OWL component reflecting the corrected labels and range_min annotation. |
metpo.owl |
Updates the released OWL with corrected labels and the range_min property for METPO:1000482. |
metpo.obo |
Updates the released OBO with corrected term names and range_min for METPO:1000482. |
metpo.json |
Updates the released JSON with corrected labels and swaps the range predicate to range_min for METPO:1000482. |
metpo-full.owl |
Propagates the same label/range fixes into the full OWL release. |
metpo-full.obo |
Propagates the same label/range fixes into the full OBO release. |
metpo-full.json |
Propagates the same label/range fixes into the full JSON release. |
metpo-base.owl |
Propagates the same label/range fixes into the base OWL release. |
metpo-base.obo |
Propagates the same label/range fixes into the base OBO release. |
metpo-base.json |
Propagates the same label/range fixes into the base JSON release. |
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
This was referenced Jun 2, 2026
Contributor
Author
turbomam
added a commit
that referenced
this pull request
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>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Two pure-data corrections from the QC review (#468), made via the Google Sheet (SoT) and rebuilt.
alkaphilic→alkaliphilic(exact synonyms were already correct).8moved fromrange_maxtorange_minto match the[>= 8]formula.Single batched PR because both edit the one Google Sheet; the granularity is in the issues (#470, #471).
stubs.tsvchange is the auto-propagated label fix. Leaving open for CI + Copilot. Fixes #470, #471.