Finalize w3id IRI scheme: collapse version-IRI doubling (#436), declare w3id canonical (#435) by turbomam · Pull Request #462 · berkeleybop/metpo

turbomam · 2026-06-02T01:49:28Z

Finishes the IRI-scheme work from #458 so the BioPortal release is clean.

#436 (version-IRI doubling). metpo-odk.yaml already set uribase: https://w3id.org, but the committed generated src/ontology/Makefile was never refreshed and still carried URIBASE=https://w3id.org/metpo plus a hardcoded ONTBASE=https://w3id.org/metpo/metpo. That produced …/metpo/metpo/releases/… version IRIs. Aligned the Makefile to the odk.yaml value and rebuilt. Now: version IRI https://w3id.org/metpo/releases/2026-06-02/metpo.owl, products https://w3id.org/metpo/metpo-{base,full}.owl, main ontology IRI https://w3id.org/metpo.owl (standard registry-root layout). No metpo/metpo/ left.

#435 (obolibrary PURL 404). Adopts option 2: README now declares https://w3id.org/metpo/ the only canonical resolution base and explicitly tells users not to use purl.obolibrary.org/obo/METPO_<id> (those 404 because METPO isn't OBO-registered). OBO registration (option 1) is out of scope.

Why a direct Makefile edit rather than make update_repo: URIBASE/ONTBASE are the documented "can be overwritten" config values, odk.yaml is already correct, and this keeps the PR a reviewable 2-line config change plus the rebuild instead of a full ODK scaffold regeneration. A future update_repo regenerates the same values.

Does not touch #437 (a BioPortal submission-form setting) or #450 (external w3id.org .htaccess). Term IRIs unchanged.

…#435) #436: the generated src/ontology/Makefile still had the pre-#458 URIBASE (https://w3id.org/metpo) and a hardcoded doubled ONTBASE (https://w3id.org/metpo/metpo), so version and product IRIs came out as https://w3id.org/metpo/metpo/releases/... even though metpo-odk.yaml already set uribase: https://w3id.org. Aligned the generated Makefile to odk.yaml (URIBASE=https://w3id.org, ONTBASE=https://w3id.org/metpo) and rebuilt. Version IRIs are now single-metpo (https://w3id.org/metpo/releases/2026-06-02/metpo.owl), products at https://w3id.org/metpo/metpo-{base,full}.owl, main ontology IRI https://w3id.org/metpo.owl. Zero metpo/metpo/ doubling remains. #435: documented https://w3id.org/metpo/ as the only canonical resolution base in the README and explicitly steered users away from http://purl.obolibrary.org/obo/METPO_<id> PURLs, which 404 because METPO is not registered in the OBO Foundry. (Adopts option 2 from #435; option 1, OBO registration, is out of scope.) Rebuilds all release artifacts. Term IRIs unchanged (https://w3id.org/metpo/<id>). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

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Pull request overview

This PR finalizes the METPO IRI scheme to consistently use w3id.org, removing the previous .../metpo/metpo/... path doubling in version IRIs and documenting w3id.org as the canonical resolution approach (vs. non-working OBO Library PURLs).

Changes:

Update ODK-generated src/ontology/Makefile URIBASE/ONTBASE so ontology IRIs and version IRIs are built under the intended w3id.org layout.
Regenerate release artefacts (metpo.owl / metpo-full.* / metpo-base.* / JSON/OBO) so ontology + version IRIs match the updated scheme.
Add README guidance on canonical term IRIs under https://w3id.org/metpo/ and warn against purl.obolibrary.org PURLs.

Reviewed changes

Copilot reviewed 12 out of 12 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
src/ontology/Makefile	Switches `URIBASE`/`ONTBASE` to align generated IRIs with `w3id.org` scheme (impacts release IRI construction).
src/ontology/components/metpo_sheet.owl	Updates component ontology IRI/versionIRI to remove `metpo/metpo` doubling.
README.md	Documents canonical METPO term IRIs and discourages obolibrary PURLs.
metpo.owl	Updates ontology IRI + versionIRI to new `w3id.org` layout (no doubled path).
metpo.obo	Updates `ontology:` and `data-version:` IRIs to match updated release IRIs.
metpo.json	Updates graph `id` and `version` IRIs to match updated release IRIs.
metpo-full.owl	Updates ontology IRI + versionIRI to remove `metpo/metpo` doubling.
metpo-full.obo	Updates `ontology:` and `data-version:` IRIs to match updated release IRIs.
metpo-full.json	Updates graph `id` and `version` IRIs to match updated release IRIs.
metpo-base.owl	Updates ontology IRI + versionIRI to remove `metpo/metpo` doubling.
metpo-base.obo	Updates `ontology:` and `data-version:` IRIs to match updated release IRIs.
metpo-base.json	Updates graph `id` and `version` IRIs to match updated release IRIs.

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turbomam · 2026-06-02T17:34:13Z

+- The ontology prefix `METPO:` expands to `https://w3id.org/metpo/`
+- Ontology document IRI: `https://w3id.org/metpo.owl` (release products and version IRIs live under `https://w3id.org/metpo/`, e.g. `https://w3id.org/metpo/releases/<date>/metpo.owl`)
+
+**Do not use `http://purl.obolibrary.org/obo/METPO_<id>`.** METPO is not registered in the OBO Foundry, so those PURLs do not resolve (HTTP 404) and are not METPO identifiers. `https://w3id.org/` is the only canonical resolution base for METPO. (Term-IRI resolution behavior is still being finalized; see issues #450 and #435.)


Addressed in #464 (and refined in #469): the README now distinguishes the resolver host (w3id.org) from the canonical identifier namespace (https://w3id.org/metpo/).

turbomam · 2026-06-02T17:34:15Z

 OBOBASE=                    http://purl.obolibrary.org/obo
-URIBASE=                    https://w3id.org/metpo
+URIBASE=                    https://w3id.org
 ONT=                        metpo
-ONTBASE=                    https://w3id.org/metpo/metpo
+ONTBASE=                    https://w3id.org/metpo


Correct, and this was the root cause. Fixed in #464: the base pipeline now uses --base-iri $(URIBASE)/metpo so it matches the term IRIs. (The broader URIBASE/IRI-scheme reconciliation is tracked in #465.)

turbomam · 2026-06-02T17:34:16Z

+    <owl:Ontology rdf:about="https://w3id.org/metpo/metpo-base.owl">
+        <owl:versionIRI rdf:resource="https://w3id.org/metpo/releases/2026-06-02/metpo-base.owl"/>
        <dce:type rdf:resource="http://purl.obolibrary.org/obo/IAO_8000001"/>
        <dcterms:contributor rdf:resource="https://orcid.org/0000-0001-9076-6066"/>
        <dcterms:creator>METPO Development Team</dcterms:creator>


Confirmed and fixed in #464: metpo-base.owl now carries all 1454 METPO classes (the base-IRI filter no longer strips them).

turbomam · 2026-06-02T17:34:18Z

 format-version: 1.2
-data-version: https://w3id.org/metpo/metpo/releases/2026-06-02/metpo-base.owl
+data-version: https://w3id.org/metpo/releases/2026-06-02/metpo-base.owl
 idspace: dce http://purl.org/dc/elements/1.1/ 
 idspace: dcterms http://purl.org/dc/terms/ 
-ontology: https://w3id.org/metpo/metpo/metpo-base.owl
+ontology: https://w3id.org/metpo/metpo-base.owl


Fixed in #464: metpo-base.obo now contains the METPO [Term] frames after the base-IRI filter fix + rebuild.

turbomam · 2026-06-02T17:34:19Z

 {
  "graphs" : [ {
-    "id" : "https://w3id.org/metpo/metpo/metpo-base.json",
+    "id" : "https://w3id.org/metpo/metpo-base.json",
    "meta" : {
      "basicPropertyValues" : [ {


Fixed in #464: metpo-base.json now contains the METPO class/property nodes after the base-IRI fix + rebuild.

…#463) (#464) The -base release products shipped with zero METPO terms (verified empty in the 2026-05-19 release and pre-#462 main; full artifacts unaffected). Root cause: the base pipeline used `remove --base-iri $(URIBASE)/METPO --axioms external`, but METPO term IRIs are https://w3id.org/metpo/<id> (lowercase, slash), so the filter never matched and every METPO axiom was stripped. The QC report rules already use the correct $(URIBASE)/metpo. Changed line 542 to match; metpo-base.* now carries all 1454 METPO classes (imported externals still excluded). Also reworded the README IRI paragraph (Copilot review on #462) to distinguish the resolver host (w3id.org) from the canonical identifier namespace (https://w3id.org/metpo/). Pre-existing defect, not introduced by #462. Fixes #463. Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>

Copilot AI review requested due to automatic review settings June 2, 2026 01:49

Copilot started reviewing on behalf of turbomam June 2, 2026 01:49 View session

turbomam merged commit 7002094 into main Jun 2, 2026
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turbomam deleted the iri-finalize-435-436 branch June 2, 2026 01:51

This was referenced Jun 2, 2026

Version IRI has duplicated metpo/ path segment #436

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purl.obolibrary.org PURLs for METPO terms dead-end at HTTP 404 #435

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Copilot AI reviewed Jun 2, 2026

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turbomam mentioned this pull request Jun 3, 2026

Prepare METPO for EBI OLS submission #213

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Finalize w3id IRI scheme: collapse version-IRI doubling (#436), declare w3id canonical (#435)#462

Finalize w3id IRI scheme: collapse version-IRI doubling (#436), declare w3id canonical (#435)#462
turbomam merged 1 commit into
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