Add an association type connecting (infectious) diseases to their infectious agent

biolink / biolink-model

Schema and generated objects for biolink data model and upper ontology

https://biolink.github.io/biolink-model/

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Add an association type connecting (infectious) diseases to their infectious agent #325

Open cmungall opened 4 years ago

mellybelly commented 4 years ago

Consider having a union class to associate with, eg. as in http://purl.obolibrary.org/obo/CARO_0001010 (organism or virus or viroid)

nlharris commented 3 years ago

is this still needed? can someone other than chris do it?

cmungall commented 3 years ago

@mellybelly's q is answered by the existing classes

https://w3id.org/biolink/vocab/OrganismTaxon - instances are NCBITaxon IDs
https://w3id.org/biolink/vocab/IndividualOrganism - instances are Chris, Melissa, a particular SARS-CoV-2 instance, etc

the association class can easily be added by anyone in the SRI DM team

We really want this for other projects too. It is the pattern @matentz is using to link MONDO classes to taxa, it is what @hrshdhg is using in KG-Microbe

sierra-moxon commented 3 years ago

@kevinschaper - can you let me know the priority of this in terms of monarch ingest? :) thx!

cmungall commented 3 years ago

As an exemplar of what associations would look like, here is a query for all disease to taxon associations from @balhoff's awesome Ubergraph: https://api.triplydb.com/s/ebmZZHZiL

(which in this case is coming from Mondo - would be great to get provenance into the inferred triples)

sierra-moxon commented 2 years ago

per clinical WG meeting: exposures provider would be good to consult, but don't have this yet.