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Map to UMLS semantic types #14
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Thanks for pointing to this Chris. We should take the list of terms in
https://metamap.nlm.nih.gov/Docs/SemanticTypes_2013AA.txt
Place them in the appropriate OBO ontologies. And then do user testing, to
see how fast they find them if the first choice is the ontology vs. if they
browse in the core. The later better be better, or we failed.
(, and then use th
…On Thu, Mar 21, 2019 at 8:10 AM Chris Mungall ***@***.***> wrote:
I think it will be important for communicating obo-core to a wider
audience to map to UMLS semantic types
table here:
https://metamap.nlm.nih.gov/Docs/SemanticTypes_2013AA.txt
Hierarchy:
https://www.nlm.nih.gov/research/umls/META3_current_semantic_types.html
Yes, it is a bit odd, I don't know why "Bird" is in there, and "Fish" is
paraphyletic...
And note there is absolutely no point in trying to make equivalence axioms
or any kind of BFO interpretation of the UMLS types, yes, neoplastic
*process* is under *disease* is under pathologic *function*. The goal is
to compare *conceptual* coverage between OBO-Core and UMLS STs.
Note that these could be transferred across from the biolink model
mappings: biolink/biolink-model#7
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(b) external resources [sio,wikidata,biotop,mesh,...] See beckyjackson#1 beckyjackson#2 Still to do OBOFoundry#14 UMLS I also include an import in manual-core that brings in the matches; we indicate these as skos annotations to avoid 'polluting' core note a bug in the owlapi means we lose some axiom annotations on these.
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I think it will be important for communicating obo-core to a wider audience to map to UMLS semantic types
table here:
https://metamap.nlm.nih.gov/Docs/SemanticTypes_2013AA.txt
Hierarchy:
https://www.nlm.nih.gov/research/umls/META3_current_semantic_types.html
Yes, it is a bit odd, I don't know why "Bird" is in there, and "Fish" is paraphyletic...
And note there is absolutely no point in trying to make equivalence axioms or any kind of BFO interpretation of the UMLS types, yes, neoplastic process is under disease is under pathologic function. The goal is to compare conceptual coverage between OBO-Core and UMLS STs.
Note that these could be transferred across from the biolink model mappings: biolink/biolink-model#7
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