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fix(iri): collapse doubled version IRI (#436); declare w3id canonical (#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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‎README.md‎

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Editors of this ontology should use the edit version, [src/ontology/metpo-edit.owl](src/ontology/metpo-edit.owl)
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## Identifiers and resolution
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The canonical IRI for every METPO term is under the `https://w3id.org/metpo/` namespace, with a bare 7-digit local identifier:
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- Term IRI: `https://w3id.org/metpo/<id>` (e.g. `https://w3id.org/metpo/1000482`)
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- The ontology prefix `METPO:` expands to `https://w3id.org/metpo/`
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- 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`)
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**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.)
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## Contact
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Please use this GitHub repository's [Issue tracker](https://github.com/berkeleybop/metpo/issues) to request new terms/classes or report errors or specific concerns related to the ontology.

‎metpo-base.json‎

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{
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"graphs" : [ {
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"id" : "https://w3id.org/metpo/metpo/metpo-base.json",
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"id" : "https://w3id.org/metpo/metpo-base.json",
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"meta" : {
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"basicPropertyValues" : [ {
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"pred" : "http://purl.org/dc/elements/1.1/type",
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"pred" : "http://www.w3.org/2002/07/owl#versionInfo",
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"val" : "2026-06-02"
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} ],
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"version" : "https://w3id.org/metpo/metpo/releases/2026-06-02/metpo-base.json"
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"version" : "https://w3id.org/metpo/releases/2026-06-02/metpo-base.json"
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},
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"nodes" : [ {
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"id" : "http://purl.org/dc/elements/1.1/type",

‎metpo-base.obo‎

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format-version: 1.2
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data-version: https://w3id.org/metpo/metpo/releases/2026-06-02/metpo-base.owl
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data-version: https://w3id.org/metpo/releases/2026-06-02/metpo-base.owl
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idspace: dce http://purl.org/dc/elements/1.1/
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idspace: dcterms http://purl.org/dc/terms/
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ontology: https://w3id.org/metpo/metpo/metpo-base.owl
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ontology: https://w3id.org/metpo/metpo-base.owl
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property_value: dce:type IAO:8000001
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property_value: dcterms:contributor https://orcid.org/0000-0001-9076-6066
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property_value: dcterms:creator "METPO Development Team" xsd:string

‎metpo-base.owl‎

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<?xml version="1.0"?>
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<rdf:RDF xmlns="https://w3id.org/metpo/metpo/metpo-base.owl#"
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xml:base="https://w3id.org/metpo/metpo/metpo-base.owl"
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<rdf:RDF xmlns="https://w3id.org/metpo/metpo-base.owl#"
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xml:base="https://w3id.org/metpo/metpo-base.owl"
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xmlns:IAO="http://purl.obolibrary.org/obo/IAO_"
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xmlns:dce="http://purl.org/dc/elements/1.1/"
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xmlns:owl="http://www.w3.org/2002/07/owl#"
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xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
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xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
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xmlns:dcterms="http://purl.org/dc/terms/">
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<owl:Ontology rdf:about="https://w3id.org/metpo/metpo/metpo-base.owl">
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<owl:versionIRI rdf:resource="https://w3id.org/metpo/metpo/releases/2026-06-02/metpo-base.owl"/>
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<owl:Ontology rdf:about="https://w3id.org/metpo/metpo-base.owl">
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<owl:versionIRI rdf:resource="https://w3id.org/metpo/releases/2026-06-02/metpo-base.owl"/>
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<dce:type rdf:resource="http://purl.obolibrary.org/obo/IAO_8000001"/>
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<dcterms:contributor rdf:resource="https://orcid.org/0000-0001-9076-6066"/>
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<dcterms:creator>METPO Development Team</dcterms:creator>

‎metpo-full.json‎

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{
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"graphs" : [ {
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"id" : "https://w3id.org/metpo/metpo/metpo-full.json",
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"id" : "https://w3id.org/metpo/metpo-full.json",
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"meta" : {
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"basicPropertyValues" : [ {
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"pred" : "http://purl.org/dc/terms/contributor",
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"pred" : "http://www.w3.org/2002/07/owl#versionInfo",
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"val" : "2026-06-02"
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} ],
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"version" : "https://w3id.org/metpo/metpo/releases/2026-06-02/metpo-full.json"
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"version" : "https://w3id.org/metpo/releases/2026-06-02/metpo-full.json"
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},
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"nodes" : [ {
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"id" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass",

‎metpo-full.obo‎

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format-version: 1.2
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data-version: https://w3id.org/metpo/metpo/releases/2026-06-02/metpo-full.owl
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data-version: https://w3id.org/metpo/releases/2026-06-02/metpo-full.owl
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idspace: dce http://purl.org/dc/elements/1.1/
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idspace: dcterms http://purl.org/dc/terms/
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idspace: metpo https://w3id.org/metpo/
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idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl#
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idspace: qudt http://qudt.org/schema/qudt/
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idspace: skos http://www.w3.org/2004/02/skos/core#
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ontology: https://w3id.org/metpo/metpo/metpo-full.owl
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ontology: https://w3id.org/metpo/metpo-full.owl
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property_value: dcterms:contributor https://orcid.org/0000-0001-9076-6066
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property_value: dcterms:creator "METPO Development Team" xsd:string
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property_value: dcterms:description "METPO provides standardized terms for the phenotypic traits, growth conditions, metabolic capabilities, and morphology of bacteria and archaea. It integrates heterogeneous microbial trait resources (BactoTraits, BacDive, Madin et al.) and supports knowledge-graph and literature-mining workflows in projects such as KG-Microbe. METPO follows OBO Foundry conventions and reuses terms from PATO, GO, CHEBI, NCBITaxon, and related ontologies where possible." xsd:string

‎metpo-full.owl‎

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<?xml version="1.0"?>
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<rdf:RDF xmlns="https://w3id.org/metpo/metpo/metpo-full.owl#"
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xml:base="https://w3id.org/metpo/metpo/metpo-full.owl"
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<rdf:RDF xmlns="https://w3id.org/metpo/metpo-full.owl#"
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xml:base="https://w3id.org/metpo/metpo-full.owl"
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xmlns:IAO="http://purl.obolibrary.org/obo/IAO_"
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xmlns:dce="http://purl.org/dc/elements/1.1/"
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xmlns:obo="http://purl.obolibrary.org/obo/"
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xmlns:metpo="https://w3id.org/metpo/"
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xmlns:dcterms="http://purl.org/dc/terms/"
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xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
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<owl:Ontology rdf:about="https://w3id.org/metpo/metpo/metpo-full.owl">
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<owl:versionIRI rdf:resource="https://w3id.org/metpo/metpo/releases/2026-06-02/metpo-full.owl"/>
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<owl:Ontology rdf:about="https://w3id.org/metpo/metpo-full.owl">
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<owl:versionIRI rdf:resource="https://w3id.org/metpo/releases/2026-06-02/metpo-full.owl"/>
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<dcterms:contributor rdf:resource="https://orcid.org/0000-0001-9076-6066"/>
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<dcterms:creator>METPO Development Team</dcterms:creator>
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<dcterms:description>METPO provides standardized terms for the phenotypic traits, growth conditions, metabolic capabilities, and morphology of bacteria and archaea. It integrates heterogeneous microbial trait resources (BactoTraits, BacDive, Madin et al.) and supports knowledge-graph and literature-mining workflows in projects such as KG-Microbe. METPO follows OBO Foundry conventions and reuses terms from PATO, GO, CHEBI, NCBITaxon, and related ontologies where possible.</dcterms:description>

‎metpo.json‎

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{
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"graphs" : [ {
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"id" : "https://w3id.org/metpo/metpo.json",
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"id" : "https://w3id.org/metpo.json",
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"meta" : {
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"basicPropertyValues" : [ {
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"pred" : "http://purl.org/dc/terms/contributor",
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"pred" : "http://www.w3.org/2002/07/owl#versionInfo",
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"val" : "2026-06-02"
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} ],
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"version" : "https://w3id.org/metpo/metpo/releases/2026-06-02/metpo.json"
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"version" : "https://w3id.org/metpo/releases/2026-06-02/metpo.json"
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},
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"nodes" : [ {
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"id" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass",

‎metpo.obo‎

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format-version: 1.2
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data-version: https://w3id.org/metpo/metpo/releases/2026-06-02/metpo.owl
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data-version: https://w3id.org/metpo/releases/2026-06-02/metpo.owl
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idspace: dce http://purl.org/dc/elements/1.1/
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idspace: dcterms http://purl.org/dc/terms/
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idspace: metpo https://w3id.org/metpo/
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idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl#
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idspace: qudt http://qudt.org/schema/qudt/
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idspace: skos http://www.w3.org/2004/02/skos/core#
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ontology: https://w3id.org/metpo/metpo.owl
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ontology: https://w3id.org/metpo.owl
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property_value: dcterms:contributor https://orcid.org/0000-0001-9076-6066
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property_value: dcterms:creator "METPO Development Team" xsd:string
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property_value: dcterms:description "METPO provides standardized terms for the phenotypic traits, growth conditions, metabolic capabilities, and morphology of bacteria and archaea. It integrates heterogeneous microbial trait resources (BactoTraits, BacDive, Madin et al.) and supports knowledge-graph and literature-mining workflows in projects such as KG-Microbe. METPO follows OBO Foundry conventions and reuses terms from PATO, GO, CHEBI, NCBITaxon, and related ontologies where possible." xsd:string

‎metpo.owl‎

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<?xml version="1.0"?>
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<rdf:RDF xmlns="https://w3id.org/metpo/metpo.owl#"
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xml:base="https://w3id.org/metpo/metpo.owl"
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<rdf:RDF xmlns="https://w3id.org/metpo.owl#"
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xml:base="https://w3id.org/metpo.owl"
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xmlns:IAO="http://purl.obolibrary.org/obo/IAO_"
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xmlns:dce="http://purl.org/dc/elements/1.1/"
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xmlns:obo="http://purl.obolibrary.org/obo/"
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xmlns:metpo="https://w3id.org/metpo/"
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xmlns:dcterms="http://purl.org/dc/terms/"
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xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
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<owl:Ontology rdf:about="https://w3id.org/metpo/metpo.owl">
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<owl:versionIRI rdf:resource="https://w3id.org/metpo/metpo/releases/2026-06-02/metpo.owl"/>
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<owl:Ontology rdf:about="https://w3id.org/metpo.owl">
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<owl:versionIRI rdf:resource="https://w3id.org/metpo/releases/2026-06-02/metpo.owl"/>
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<dcterms:contributor rdf:resource="https://orcid.org/0000-0001-9076-6066"/>
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<dcterms:creator>METPO Development Team</dcterms:creator>
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<dcterms:description>METPO provides standardized terms for the phenotypic traits, growth conditions, metabolic capabilities, and morphology of bacteria and archaea. It integrates heterogeneous microbial trait resources (BactoTraits, BacDive, Madin et al.) and supports knowledge-graph and literature-mining workflows in projects such as KG-Microbe. METPO follows OBO Foundry conventions and reuses terms from PATO, GO, CHEBI, NCBITaxon, and related ontologies where possible.</dcterms:description>

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