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Principle #3 IDs - automated validation #1017
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Should ontologies be allowed to annotate external terms with In cases where the namespace annotation isn't used, we can just check that classes use numeric format if the IRI contains |
All IRIs must be unique. If an IRI is duplicated, the annotations will be merged in OWL. Duplicate labels and definitions may be a sign of two different terms with the same IRI. Labels and definitions may be duplicated for other reasons, though. Some ontologies do not use numeric identifiers for everything (e.g. PR). In the future, we are aiming to have base artefacts for each ontology. The base only contains the terms in that ontology's namespace. Revised check: |
I don't like relying on oio:hasOBONamespace
…On Thu, Aug 15, 2019 at 2:10 PM Becky Jackson ***@***.***> wrote:
Should ontologies be allowed to annotate external terms with
hasOBONamespace in their namespace? For example, ARO has some external
terms (e.g. from DOID) with the namespace value 'antibiotic_resistance'.
In cases where the namespace annotation isn't used, we can just check that
classes use numeric format if the IRI contains /obo/NS_ (where NS is the
actual namespace)
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On the call on Thursday, we revised this to my comment above so that |
For historical reasons, annotation properties may uses hashes (e.g. subset definitions). Object and data properties should not. This check will ignore annotation properties and apply only to classes, object, and data properties. The IRI must start with |
Update. AFAIK: this principle is to apply to OBO Foundry ontologies. Question: At present we don't allow numbers in the namespace. I think we should consider it. For example, should OBO:COVID-19_ be allowed? cc @bpeters42 |
This issue is only for automatic validation. Please move other discussion of the principle to issue #954, which I am about to update with the latest text. |
Question: At present we don't allow numbers in the namespace. I think we should consider it. For example, should OBO:COVID-19_ be allowed? |
FP 3 - URI/Identifier Space
Automated checks:
NAMESPACE_NUMID
formatMechanism:
Any IRI that starts with
http://purl.obolibrary.org/obo/IDSPACE
must end with_NUMID
. theIDSPACE
comes from the registry. All things that start withhttp://purl.obolibrary.org/obo/
must be a valid registry ID.There may be external classes that we can't predict. But, if the ontology usesoboInOwl:hasOBONamespace
on terms, we can check those entities. The value of that annotation should matchNAMESPACE
(ignoring case).If any class annotated withoboInOwl:hasOBONamespace
in the core namespace does not followNAMESPACE_NUMID
format (e.g. 'doid' namespace followsDOID_0000001
etc.), throw a warning.I know some ontologies may use text in the identifier of properties, so maybe that can be an info message? It is currently an error
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