Tools to Support Semantic Interoperability between Biomedical Ontologies and Clinical Terminologies

omop2obo is a semantic alignment algorithm and a collection of health system-wide, disease-agnostic mappings between clinical terminologies, like those available in the Observational Medical Outcomes Partnership (OMOP) Common Data Model, and Open Biomedical Foundry Ontologies (OBOs)

https://github.com/callahantiff/OMOP2OBO

omop2obo is a semantic alignment algorithm and a collection of health system-wide, disease-agnostic mappings between clinical terminologies, like those available in the Observational Medical Outcomes Partnership (OMOP) Common Data Model, and Open Biomedical Foundry Ontologies (OBOs).

Motivation

Common data models have solved many challenges of utilizing electronic health records, but have not yet meaningfully integrated clinical and molecular data. Aligning clinical data to open biological ontologies (OBOs), which provide semantically computable representations of biological knowledge, requires extensive manual curation and expertise.

Objective

To address these limitations, we have developed OMOP2OBO, the first health system-wide integration and alignment between the Observational Health Data Sciences and Informatics' Observational Medical Outcomes Partnership (OMOP) standardized clinical terminologies and eight OBO biomedical ontologies spanning diseases, phenotypes, anatomical entities, cell types, organisms, chemicals, metabolites, hormones, vaccines, and proteins. To verify that the mappings are both clinically and biologically meaningful, we have performed extensive experiments to verify the accuracy, generalizability, and logical consistency of each released mapping set.