Fix typos in uberon-edit.obo via codespell (follow-up to #3759) - #3762
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Fix typos in uberon-edit.obo via codespell (follow-up to #3759)#3762yarikoptic wants to merge 2 commits into
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Remove uberon-edit.obo from the codespell skip list. The previous PR (obophenotype#3759) deferred this file pending curator review of false positives. That review has now been done: 40+ domain-specific terms added to ignore-words-list, each with an inline comment in .codespellrc explaining why it is protected (Latin TA synonyms, anatomical abbreviations, intentional misspellings in RELATED synonyms, non-English words in citations, proper names). Co-Authored-By: Claude Code 2.1.251 / Claude Sonnet 4.6 <noreply@anthropic.com>
~100 genuine typos corrected via `codespell -w` (auto) and manual
editing. Domain-specific false positives are protected by the updated
.codespellrc (see previous commit); only plain spelling errors are
changed here.
Highlights of manually reviewed fixes:
- "auxillery nerve" RELATED syn left intact (intentional misspelling)
- "collumn dentis" EXACT syn left intact (from ncithesaurus:Collum_Dentis)
- "Formen" → "Foramen" (codespell suggested wrong "Foremen")
- "palatte" → "palate" (codespell suggested wrong "palette")
- "develop- ment" → "development" (broken word in comment)
- "con- sists" → "consists" (broken word in taxon_notes)
- "deep dorsal bein" → "deep dorsal vein" (typo of "vein")
- "trough the stylopodiam" → "through the stylopodiam" (trough is
correct in another context, so protected in ignore-words-list)
- "foor" / "fot" → "foot" (multi-suggestion, manual fix)
- Various multi-suggestion fixes: eigth→eighth, partion→portion,
identiy→identity, inernal→internal, extermal→external,
tranverse→transverse, retricts→restricts, throught→through,
tha→that, fo→of
Also reserialised via `robot convert -i uberon-edit.obo -f obo -o
uberon-edit.obo` to normalise synonym ordering.
Co-Authored-By: Claude Code 2.1.251 / Claude Sonnet 4.6 <noreply@anthropic.com>
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The continuation to the
Fix typos in
src/ontology/uberon-edit.obodetected by codespell, and expandcodespell coverage to include this file going forward.
#3759 explicitly skipped
uberon-edit.obopending a curator-reviewedpass of domain-specific false positives. AI did its review, now it is
for an HI (Human Intelligence) curator to contribute.
Summary
Commit 1 —
.codespellrc: removesuberon-edit.obofrom the skiplist and adds 40+ words to
ignore-words-listso that domain-specificterms (Latin TA synonyms, anatomical abbreviations, intentional misspellings
in RELATED synonyms, non-English words in citations, proper names) are not
touched by codespell.
Commit 2 —
uberon-edit.obo: ~100 genuine typo fixes, applied viacodespell -w(auto-fix for single-suggestion cases) plus manual fixesfor domain-sensitive, multi-suggestion, and broken-word cases.
Notable manual decisions:
Formen → Foramen(codespell suggested wrong "Foremen")palatte → palate(codespell suggested wrong "palette")bein → veinin a comment about dorsal penile veindevelop- ment,con- sists— broken words across line breaks joinedtrough the stylopodiam → through the stylopodiam(manual, sincetroughis protected globally)Rationale (by Claude) for scope
All changes are in non-logical content (definitions, comments,
taxon_notes, editor_notes, external_definitions, synonyms) — no
is_a,intersection_of, orrelationshiplines were touched. Changesto EXACT synonyms sourced from external databases were treated conservatively
(e.g.
auxilleryandcollumnleft intact as RELATED/EXACT from theirsource).
The codespell CI check (added in #3759) now covers
uberon-edit.oboandwill flag any new typos on future PRs.
Test plan
codespell .passes with zero errors on this branchrobot convertreserialisation applied to normalise synonym orderingNotes for reviewers
The expanded
ignore-words-listin.codespellrctuned up to bringcomments to the words. Potentially such skips could be set up via an external
file but I think there is no point to breed those files, as
.codespellrcisalready tool specific.
Follow-up from #3759 (infrastructure PR). The
docs/odk-workflows/follow-up (odkcore PR) is tracked separately.
🤖 Generated with Claude Code 2.1.251 / Claude Sonnet 4.6 in an interactive session.
Reviewed and submitted by @yarikoptic (
as yarikoptic-gitmatewas intended but didn't happen ;) ).