Odysseus have been performing quite a few conversions of EHR and TA specific (for example FlatIron / Oncology, GI, etc…) data sets into OMOP CDM. One area that has constantly required a quite intense custom mapping is mapping lab tests, specifically around biomarker and gene data. Talking to a few folks on our vocabulary team and outside, I understand that there is no comprehensive biomarker and gene vocabularies are available in OMOP Standardized Vocabs. LOINC does have some but it is incomplete and insufficient. Performing custom mapping of such data - while it does enabling researchers to perform local research but does defeat the goal of query interoperability. And using biomarker data in OMOP CDM queries has become very common.
Reflecting on my days back in Pharma TI/TV area, I remember there were quite a few Gene and Biomarker ontologies back in those days, some open source and some commercial. However, I admit it’s been quite a few years and things have changed quite a bit. So, opening up this discussion here:
Is this an acute problem for others? Should one of our 2020 goals to bring a comprehensive Gene/BioMarker/Genomics vocab/ontology into OHDSI?
What curated ontologies exist in this space today that we can bring into OHDSI?