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Published 20 hours ago • verified publisher icon biolink

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

Open cmungall opened this issue 4 years ago • 6 comments

cmungall avatar Mar 18 '20 19:03 cmungall

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

mellybelly avatar Mar 21 '20 16:03 mellybelly

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

nlharris avatar Jan 28 '21 19:01 nlharris

@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

cmungall avatar Jan 29 '21 01:01 cmungall

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

sierra-moxon avatar Sep 07 '21 21:09 sierra-moxon

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)

cmungall avatar Sep 07 '21 23:09 cmungall

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

sierra-moxon avatar Jan 05 '22 19:01 sierra-moxon