fix: emit uppercase METPO idspace in OBO release artifacts (#557)#560
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Declare Prefix(METPO:=<https://w3id.org/metpo/>) in metpo-edit.owl so the release pipeline assigns the uppercase METPO prefix to the term namespace instead of the lowercase 'metpo' ROBOT otherwise picks during the merge. The .obo artifacts now emit 'idspace: METPO' and 'id: METPO:...' (matching OBO Foundry uppercase-idspace convention and bioregistry preferred_prefix METPO), consistent with the uppercase METPO: CURIE prefix used elsewhere (#16). No Makefile change and no post-processing: the fix is one prefix declaration in the hand-edited source, which survives update_repo. Artifacts regenerated with obolibrary/odkfull:v1.6.1 prepare_release, TODAY pinned to the committed version date (2026-06-12), so the only change is the prefix case. Term count unchanged (1455). Closes #557. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Pull request overview
This PR fixes the METPO CURIE prefix casing in released OBO artifacts by declaring an explicit METPO prefix for the https://w3id.org/metpo/ namespace in the hand-edited ontology source, ensuring ROBOT emits idspace: METPO and id: METPO: rather than lowercase metpo.
Changes:
- Add
Prefix(METPO:=<https://w3id.org/metpo/>)tosrc/ontology/metpo-edit.owlso downstream ROBOT steps consistently use the uppercase prefix. - Regenerate release OWL artifacts (
metpo.owl,metpo-base.owl,metpo-full.owl) so the XML namespace prefix and affected QName usages useMETPO(semantic IRI unchanged).
Reviewed changes
Copilot reviewed 4 out of 7 changed files in this pull request and generated no comments.
| File | Description |
|---|---|
| src/ontology/metpo-edit.owl | Declares the METPO prefix for the term namespace so ROBOT/convert-to-OBO has an explicit uppercase idspace mapping. |
| metpo.owl | Regenerated artifact reflecting the uppercase METPO namespace prefix in serialization. |
| metpo-full.owl | Regenerated artifact reflecting the uppercase METPO namespace prefix in serialization. |
| metpo-base.owl | Regenerated artifact reflecting the uppercase METPO namespace prefix in serialization. |
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Closes #557.
The released
.oboartifacts shippedidspace: metpo+id: metpo:...(lowercase), which conflicts with the blessed uppercaseMETPO:prefix (#16) and with OBO Foundry's uppercase-idspace convention (GO, CHEBI, PATO).Root cause
Nothing in the source declared a prefix for the
https://w3id.org/metpo/namespace, so ROBOT assigned the lowercasemetpoduring the release merge/reason chain, androbot convert -f obofaithfully copied that case. Verified by reproducing the merge chain locally (details in #557).Fix
One line in
metpo-edit.owl:Prefix(METPO:=<https://w3id.org/metpo/>). Declaring the prefix upstream makes ROBOT useMETPO(no lowercase, no duplicate idspace). No change to the ODK-generated Makefile, and no post-processing. The fix lives in the hand-edited source, so it survivesupdate_repo.Artifacts
Regenerated with
obolibrary/odkfull:v1.6.1prepare_release, withTODAYpinned to the committed version date (2026-06-12) so the only change is the prefix case. All three.obonow emitidspace: METPOandid: METPO:(0 lowercase). Term count unchanged (1455). The.jsonartifacts use full IRIs and are unaffected.The
artifact-freshnesscheck should pass since a fresh build now reproduces these.