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

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turbomam merged 1 commit into from
Jun 2, 2026
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Finalize w3id IRI scheme: collapse version-IRI doubling (#436), declare w3id canonical (#435) #462

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10 changes: 10 additions & 0 deletions README.md
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Expand Up @@ -26,6 +26,16 @@ METPO releases are available from multiple sources:

Editors of this ontology should use the edit version, [src/ontology/metpo-edit.owl](src/ontology/metpo-edit.owl)

## Identifiers and resolution

The canonical IRI for every METPO term is under the `https://w3id.org/metpo/` namespace, with a bare 7-digit local identifier:

- Term IRI: `https://w3id.org/metpo/<id>` (e.g. `https://w3id.org/metpo/1000482`)
- 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.)

@turbomam turbomam Jun 2, 2026

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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/).


## Contact

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.
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4 changes: 2 additions & 2 deletions metpo-base.json
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@@ -1,6 +1,6 @@
{
"graphs" : [ {
"id" : "https://w3id.org/metpo/metpo/metpo-base.json",
"id" : "https://w3id.org/metpo/metpo-base.json",
"meta" : {
"basicPropertyValues" : [ {
Comment on lines 1 to 5

@turbomam turbomam Jun 2, 2026

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

"pred" : "http://purl.org/dc/elements/1.1/type",
Expand Down Expand Up @@ -39,7 +39,7 @@
"pred" : "http://www.w3.org/2002/07/owl#versionInfo",
"val" : "2026-06-02"
} ],
"version" : "https://w3id.org/metpo/metpo/releases/2026-06-02/metpo-base.json"
"version" : "https://w3id.org/metpo/releases/2026-06-02/metpo-base.json"
},
"nodes" : [ {
"id" : "http://purl.org/dc/elements/1.1/type",
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4 changes: 2 additions & 2 deletions metpo-base.obo
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@@ -1,8 +1,8 @@
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
Comment on lines 1 to +5

@turbomam turbomam Jun 2, 2026

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

property_value: dce:type IAO:8000001
property_value: dcterms:contributor https://orcid.org/0000-0001-9076-6066
property_value: dcterms:creator "METPO Development Team" xsd:string
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8 changes: 4 additions & 4 deletions metpo-base.owl
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@@ -1,6 +1,6 @@
<?xml version="1.0"?>
<rdf:RDF xmlns="https://w3id.org/metpo/metpo/metpo-base.owl#"
xml:base="https://w3id.org/metpo/metpo/metpo-base.owl"
<rdf:RDF xmlns="https://w3id.org/metpo/metpo-base.owl#"
xml:base="https://w3id.org/metpo/metpo-base.owl"
xmlns:IAO="http://purl.obolibrary.org/obo/IAO_"
xmlns:dce="http://purl.org/dc/elements/1.1/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
Expand All @@ -9,8 +9,8 @@
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:dcterms="http://purl.org/dc/terms/">
<owl:Ontology rdf:about="https://w3id.org/metpo/metpo/metpo-base.owl">
<owl:versionIRI rdf:resource="https://w3id.org/metpo/metpo/releases/2026-06-02/metpo-base.owl"/>
<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>
Comment on lines +12 to 16

@turbomam turbomam Jun 2, 2026

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

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4 changes: 2 additions & 2 deletions metpo-full.json
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{
"graphs" : [ {
"id" : "https://w3id.org/metpo/metpo/metpo-full.json",
"id" : "https://w3id.org/metpo/metpo-full.json",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.org/dc/terms/contributor",
Expand Down Expand Up @@ -36,7 +36,7 @@
"pred" : "http://www.w3.org/2002/07/owl#versionInfo",
"val" : "2026-06-02"
} ],
"version" : "https://w3id.org/metpo/metpo/releases/2026-06-02/metpo-full.json"
"version" : "https://w3id.org/metpo/releases/2026-06-02/metpo-full.json"
},
"nodes" : [ {
"id" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass",
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4 changes: 2 additions & 2 deletions metpo-full.obo
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@@ -1,12 +1,12 @@
format-version: 1.2
data-version: https://w3id.org/metpo/metpo/releases/2026-06-02/metpo-full.owl
data-version: https://w3id.org/metpo/releases/2026-06-02/metpo-full.owl
idspace: dce http://purl.org/dc/elements/1.1/
idspace: dcterms http://purl.org/dc/terms/
idspace: metpo https://w3id.org/metpo/
idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl#
idspace: qudt http://qudt.org/schema/qudt/
idspace: skos http://www.w3.org/2004/02/skos/core#
ontology: https://w3id.org/metpo/metpo/metpo-full.owl
ontology: https://w3id.org/metpo/metpo-full.owl
property_value: dcterms:contributor https://orcid.org/0000-0001-9076-6066
property_value: dcterms:creator "METPO Development Team" xsd:string
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
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8 changes: 4 additions & 4 deletions metpo-full.owl
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@@ -1,6 +1,6 @@
<?xml version="1.0"?>
<rdf:RDF xmlns="https://w3id.org/metpo/metpo/metpo-full.owl#"
xml:base="https://w3id.org/metpo/metpo/metpo-full.owl"
<rdf:RDF xmlns="https://w3id.org/metpo/metpo-full.owl#"
xml:base="https://w3id.org/metpo/metpo-full.owl"
xmlns:IAO="http://purl.obolibrary.org/obo/IAO_"
xmlns:dce="http://purl.org/dc/elements/1.1/"
xmlns:obo="http://purl.obolibrary.org/obo/"
Expand All @@ -14,8 +14,8 @@
xmlns:metpo="https://w3id.org/metpo/"
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="https://w3id.org/metpo/metpo/metpo-full.owl">
<owl:versionIRI rdf:resource="https://w3id.org/metpo/metpo/releases/2026-06-02/metpo-full.owl"/>
<owl:Ontology rdf:about="https://w3id.org/metpo/metpo-full.owl">
<owl:versionIRI rdf:resource="https://w3id.org/metpo/releases/2026-06-02/metpo-full.owl"/>
<dcterms:contributor rdf:resource="https://orcid.org/0000-0001-9076-6066"/>
<dcterms:creator>METPO Development Team</dcterms:creator>
<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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4 changes: 2 additions & 2 deletions metpo.json
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{
"graphs" : [ {
"id" : "https://w3id.org/metpo/metpo.json",
"id" : "https://w3id.org/metpo.json",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.org/dc/terms/contributor",
Expand Down Expand Up @@ -36,7 +36,7 @@
"pred" : "http://www.w3.org/2002/07/owl#versionInfo",
"val" : "2026-06-02"
} ],
"version" : "https://w3id.org/metpo/metpo/releases/2026-06-02/metpo.json"
"version" : "https://w3id.org/metpo/releases/2026-06-02/metpo.json"
},
"nodes" : [ {
"id" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass",
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4 changes: 2 additions & 2 deletions metpo.obo
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@@ -1,12 +1,12 @@
format-version: 1.2
data-version: https://w3id.org/metpo/metpo/releases/2026-06-02/metpo.owl
data-version: https://w3id.org/metpo/releases/2026-06-02/metpo.owl
idspace: dce http://purl.org/dc/elements/1.1/
idspace: dcterms http://purl.org/dc/terms/
idspace: metpo https://w3id.org/metpo/
idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl#
idspace: qudt http://qudt.org/schema/qudt/
idspace: skos http://www.w3.org/2004/02/skos/core#
ontology: https://w3id.org/metpo/metpo.owl
ontology: https://w3id.org/metpo.owl
property_value: dcterms:contributor https://orcid.org/0000-0001-9076-6066
property_value: dcterms:creator "METPO Development Team" xsd:string
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
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8 changes: 4 additions & 4 deletions metpo.owl
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@@ -1,6 +1,6 @@
<?xml version="1.0"?>
<rdf:RDF xmlns="https://w3id.org/metpo/metpo.owl#"
xml:base="https://w3id.org/metpo/metpo.owl"
<rdf:RDF xmlns="https://w3id.org/metpo.owl#"
xml:base="https://w3id.org/metpo.owl"
xmlns:IAO="http://purl.obolibrary.org/obo/IAO_"
xmlns:dce="http://purl.org/dc/elements/1.1/"
xmlns:obo="http://purl.obolibrary.org/obo/"
Expand All @@ -14,8 +14,8 @@
xmlns:metpo="https://w3id.org/metpo/"
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="https://w3id.org/metpo/metpo.owl">
<owl:versionIRI rdf:resource="https://w3id.org/metpo/metpo/releases/2026-06-02/metpo.owl"/>
<owl:Ontology rdf:about="https://w3id.org/metpo.owl">
<owl:versionIRI rdf:resource="https://w3id.org/metpo/releases/2026-06-02/metpo.owl"/>
<dcterms:contributor rdf:resource="https://orcid.org/0000-0001-9076-6066"/>
<dcterms:creator>METPO Development Team</dcterms:creator>
<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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4 changes: 2 additions & 2 deletions src/ontology/Makefile
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Expand Up @@ -19,9 +19,9 @@ CONFIG_HASH= b36e24392153d51eead1fd6d833e68e831bdb46877e7485056d8
# these can be overwritten on the command line

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
Comment on lines 21 to +24

@turbomam turbomam Jun 2, 2026

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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.)

EDIT_FORMAT= owl
SRC = $(ONT)-edit.$(EDIT_FORMAT)
MAKE_FAST= $(MAKE) IMP=false PAT=false COMP=false MIR=false
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6 changes: 3 additions & 3 deletions src/ontology/components/metpo_sheet.owl
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@@ -1,13 +1,13 @@
Prefix(:=<https://w3id.org/metpo/metpo/components/metpo_sheet.owl#>)
Prefix(:=<https://w3id.org/metpo/components/metpo_sheet.owl#>)
Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<https://w3id.org/metpo/metpo/components/metpo_sheet.owl>
<https://w3id.org/metpo/metpo/releases/2026-06-02/components/metpo_sheet.owl>
Ontology(<https://w3id.org/metpo/components/metpo_sheet.owl>
<https://w3id.org/metpo/releases/2026-06-02/components/metpo_sheet.owl>
Annotation(owl:versionInfo "2026-06-02")

Declaration(Class(<http://www.geneontology.org/formats/oboInOwl#ObsoleteClass>))
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