Prefixes, some notes by Nico

[matentzn]

@kevinschaper I looked at your prefix counts and was wondering about some typing that is potentially missing. Not sure if that is relevant at this stage!

   "biolink:OntologyClass": {
     "FBbt": 16858, # `biolink:AnatomicalEntity`
     "Orphanet": 5078,# `biolink:Disease`?
     "OBO": 31080,# Odd prefix, should check what this is.
     "UMLS": 8353,# `biolink:Disease`?
     "FMA": 6703, # `biolink:AnatomicalEntity`
     "DOID": 4368,# `biolink:Disease`
     "WBbt": 223,# `biolink:AnatomicalEntity`
     "ZFA": 3205,# `biolink:AnatomicalEntity`
     "CARO": 23,# `biolink:AnatomicalEntity`
     "UPHENO": 8,# `biolink:PhenotypicFeature`
     "WBPhenotype": 2695,# `biolink:PhenotypicFeature`
     "XAO": 1705,# `biolink:AnatomicalEntity`
     "MA": 3072,# `biolink:AnatomicalEntity`
     "EMAPA": 1,# `biolink:AnatomicalEntity`
     "DDANAT": 65,# `biolink:AnatomicalEntity`
     "DDPHENO": 1,# `biolink:PhenotypicFeature`
   },

[kevinschaper]

I think this might be getting assigned by kgx in the conversion of monarch.json. We could think about doing our own conversion to kgx format, or maybe improve kgx's ability to convert ontologies to biolink.

[sierra-moxon]

In the works for kgx at the moment, is an ontology walker to better assign ontology classes.

[monicacecilia]

Dear @sierra-moxon & @kevinschaper: could I kindly ask for a status update on this issue? Thanks! 🌷

[monicacecilia]

Is this still relevant? @matentzn @kevinschaper @sierra-moxon

[matentzn]

From my perspective this can be closed - this was meant as a "consider this" 2 years ago and a lot has changed since then - I am sure it This was still a problem, we would know by now. @kevinschaper if you feel better to have it open, reopen.