OMOP2OBO (Beta-Release)

Precision medicine requires timely synthesis of clinical and genomic data. Despite large-scale biobanking efforts, most electronic health records (EHRs) do not systematically integrate nor have the infrastructure to incorporate genomic data. Common data models (CDMs) have solved many of the challenges of utilizing EHR data, yet they do not include resources needed to integrate or interpret clinical and genomic data. Biomedical ontologies provide accurate and semantically computable representations of biological knowledge. Aligning patient data to open biomedical ontologies (OBO) requires manual and/or semi-automated curation and domain expertise, limiting existing efforts to specific diseases and clinical data. We introduce OMOP2OBO - the first health system-wide, disease-agnostic mappings between standardized clinical terminologies in the Observational Medical Outcomes Partnership (OMOP) CDM and several OBO foundry ontologies. These mappings were validated by domain experts and their coverage was examined in several health systems. The mappings are openly available at  https://github.com/callahantiff/OMOP2OBO/wiki.