Group the eight flagellar arrangement values under their axis, keeping flagellated as a parent - #625
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…g flagellated as a parent
METPO:1007005 flagellar arrangement was adopted as the grouping class for the
flagellation-pattern values, but seven of the eight values stayed under
METPO:1000704 flagellated and only polytrichous sat under the axis. The axis
was near-empty and the values were split across two parents.
Each of the eight now has both parents: flagellar arrangement, so the axis
groups its values, and flagellated, so peritrichous still entails flagellated,
motile and motility as it does today and as its definition ("A motility
phenotype in which...") says. METPO already asserts two parents on nine rows
in the numeric-limits family; OMP models the same axis the same way
(OMP:0000078 flagellum arrangement phenotype).
Verified with the repo's own template rule (stubs + metpo_sheet + properties +
deprecated, ROBOT 1.9.10): robot diff against main shows exactly 8 axioms
added and 0 removed; both builds are consistent under ELK.
Closes #616
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FcR9NMbL1o3svKyBqsNKpA
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🟢 Approval recommended
The change is narrowly scoped to parent-field updates in the template TSV and aligns the hierarchy with the stated modeling intent without introducing inconsistencies in the edited rows.
Pull request overview
This PR fixes the ontology class hierarchy for the flagellar arrangement axis by ensuring all eight flagellar arrangement values are grouped under METPO:1007005 flagellar arrangement, while preserving METPO:1000704 flagellated as a parent where needed so existing entailments (e.g., motility-related ancestry) are not lost.
Changes:
- Re-parented
METPO:1005031–METPO:1005037to have two parents:flagellar arrangement|flagellated. - Added
flagellatedas an additional parent forMETPO:1007006 polytrichous flagellationso it aligns with the other arrangement values.
File summaries
| File | Description |
|---|---|
| src/templates/metpo_sheet.tsv | Updates the parent column for eight flagellar-arrangement classes to consistently group them under the flagellar arrangement axis while keeping flagellated as a parent. |
Review details
- Files reviewed: 1/1 changed files
- Comments generated: 0
- Review effort level: Lite
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Same command the artifact-freshness workflow runs, in obolibrary/odkfull:v1.6.1: make IMP=false PAT=false MIR=false TODAY=2026-06-12 prepare_release. robot diff of metpo.owl against main: 8 axioms added, 0 removed, the eight SubClassOf statements from the template change and nothing else. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FcR9NMbL1o3svKyBqsNKpA
This was referenced Sep 3, 2026
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Why
Closes #616.
METPO:1007005 flagellar arrangementwas adopted to group the flagellation-pattern values, but seven of the eight stayed underMETPO:1000704 flagellatedand onlypolytrichous flagellationsat under the axis. The axis had one child and the values were split across two parents, so anything enumerating the arrangement axis had to look in two places.What changed
Column 4 of
src/templates/metpo_sheet.tsvon eight rows:METPO:1005031to1005037gainflagellar arrangement;METPO:1007006 polytrichous flagellationgainsflagellated. Each of the eight now readsflagellar arrangement|flagellated.Two parents rather than one, so that
peritrichous flagellationstill entailsflagellated,motileandmotility, as it does today and as all seven definitions state ("A motility phenotype in which..."). Moving them under the axis alone would have silently dropped that entailment. METPO already asserts two parents on nine rows in the numeric-limits family (e.g.temperature optimum), and OMP models this axis the same way (OMP:0000078 flagellum arrangement phenotypewithperitrichous,lophotrichous,monotrichous,amphitrichousas children).Validation
Built with the repo's own component rule from
metpo.Makefile(stubs, metpo_sheet, metpo-properties and deprecated templates together), ROBOT 1.9.10, on this branch and onmain.8 added, 0 removed.
robot reason --reasoner ELKsucceeds on both.Documentation impact
None. Definitions are unchanged and remain true under the new placement.
Scope and complexity
One file, eight cells in one column.
🤖 Generated with Claude Code
https://claude.ai/code/session_01FcR9NMbL1o3svKyBqsNKpA