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callahantiff / OMOP2OBO

OMOP2OBO: A Python Library for mapping OMOP standardized clinical terminologies to Open Biomedical Ontologies
http://tiffanycallahan.com/OMOP2OBO_Dashboard
MIT License
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Generate OMOP2OBO Mappings to OHDSI Cohort Definitions #55

Open callahantiff opened 3 years ago

callahantiff commented 3 years ago

TASK

Create a Jupyter Notebook (or other tool) that takes in an OHDSI Cohort Definition (from here) and returns the OMOP2OBO mappings.

@jmbanda - What do you think about this? If we had a small tool that could take in the code set(s) for a given OHDSI cohort and return the OMOP2OBO mappings for each concept.

jmbanda commented 3 years ago

I think this is a great idea. We should start with basic Cohort definitions, before we move into the Phenotype Library stuff. I think there are some structural changes that I am not very familiar with.

callahantiff commented 3 years ago

Excellent. That makes sense. This wouldn't be something we formally implemented for a while, but I am wondering if it would be useful to have an example for one that we can include in the initial OMOP2OBO paper. Maybe we can talk through this a bit more in a few weeks.

chrisroederucdenver commented 2 years ago

FWIW, the cohort definition link is having issues. It comes up with "! Problem while computing ..1 = !database == "CPRD"."