Open matentzn opened 2 years ago
cc @dosumis @cmungall
Agreed.
Also agreed that the master mapping file can lives on the OMO repo.
An alternative approach might be to include the prefix declarations in machine-readable form (but "reified") within the ontology rather than linking out, using the SHACL vocabulary. We're using this here: https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/registry/obo_prefixes.ttl
@balhoff totally, good idea. Would you say, just importing this with owl:imports?
@balhoff totally, good idea. Would you say, just importing this with owl:imports?
Yeah that sounds great.
Here is the current bioregistry shacl prefixmap: https://github.com/biopragmatics/bioregistry/blob/main/exports/contexts/obo_synonyms.context.ttl
This brings us only half-way. What remains is how we can connect this information with other validation information, such as ID regex patterns?
Does shacl have a way of representing the regex? Or can we introduce a new property to go along with shacl where we can add regexes into this bioregistry export?
Update: indeed it does! See https://github.com/biopragmatics/bioregistry/blob/main/exports/contexts/bioregistry.context.ttl for an example of the Bioregistry output in shacl that includes sh:pattern
for many resources.
Update, SHACL does have a way to represent patterns. See https://github.com/biopragmatics/bioregistry/blob/main/exports/contexts/bioregistry.context.ttl for an example.
I am trying to make a dent into the non-interpretability of the prefixes used in hasDbXref expressions. As discussed in great detail elsewhere, hasDbXref will continue to be a CURIE string (not an entity) that lives outside of the normal RDF world. In order to standardise uses of prefixes, I want to propose at least an AP that we can use to link to a context we can use to disambiguate the prefixes used in the hasDbXref properties of some ontology. So I envision an annotation like:
This could then tell the user that
refers to and HPO term.
Or better yet, linking it to a formal context.
Anyone opposed to such a property?