Purpose of class_uri and slot_uri in RDF version of biolink-model?

[balhoff]

We are using the RDF rendering of biolink-model to enable bridging from Biolink into our RDF database for the Translator CAM KP. In previous builds of our database, we used class_uri and slot_uri to navigate from Biolink terms to OBO ontology terms. In recent versions of Biolink, these seem no longer to be useful for this purpose. What are these for? In all the examples I looked at, they just seem to be the URI for the the Biolink term itself. For example:

<https://w3id.org/biolink/vocab/Cell> a meta:ClassDefinition ;
    skos:inScheme <https://w3id.org/biolink/biolink-model> ;
    meta:class_uri <https://w3id.org/biolink/vocab/Cell>

It seems odd for every Biolink term to link to itself.

cc @rajshruti18

[nlharris]

@balhoff are you still awaiting an answer to this?

[balhoff]

@balhoff are you still awaiting an answer to this?

Yes. Also in some cases the terms don't link to themselves, but to a parent (maybe that is part of the answer?):

<https://w3id.org/biolink/vocab/agent_id> a linkml:SlotDefinition ;
    skos:inScheme <https://w3id.org/biolink/biolink-model> ;
    linkml:alias "id" ;
    linkml:domain <https://w3id.org/biolink/vocab/Agent> ;
    linkml:domain_of <https://w3id.org/biolink/vocab/Agent> ;
    linkml:identifier true ;
    linkml:is_a <https://w3id.org/biolink/vocab/id> ;
    linkml:is_usage_slot true ;
    linkml:owner <https://w3id.org/biolink/vocab/Agent> ;
    linkml:range <https://w3id.org/biolink/vocab/string> ;
    linkml:required true ;
    linkml:slot_uri <https://w3id.org/biolink/vocab/id> ;

[sierra-moxon]

Hi @balhoff - we use very few slot and class uris in Biolink now, and the ones we have seem useful to me (mapping biolink:type -> rdf:type with no self-references to biolink.

I am going to close this as "done" but I can see potentially adding more class and slot uri annotations to biolink based on exact_mappings? please reopen if I got this wrong.