search

OBOFoundry / COB

An experimental ontology containing key terms from Open Biological and Biomedical Ontologies (OBO)
https://obofoundry.github.io/COB
Creative Commons Zero v1.0 Universal
39 stars 8 forks source link

Map to UMLS semantic types #14

Open cmungall opened 5 years ago

cmungall commented 5 years ago

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: https://github.com/biolink/biolink-model/issues/7

bpeters42 commented 5 years ago

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 notifications@github.com 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 https://github.com/biolink/biolink-model/issues/7

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/Experimental-OBO-Core/issues/14, or mute the thread https://github.com/notifications/unsubscribe-auth/ANN9Ivhb0Ihr-xZp9pCA2drkGPH6x3zlks5vY6DMgaJpZM4cBqa- .

-- Bjoern Peters Professor La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters