N3C Domain Team: OMOP to OBO

Background

Electronic health record (EHR) data alone are insufficient to address many important questions about the causes of disease. EHR data characterize populations, care, and outcomes, but are divorced from our accumulated knowledge of the biological mechanisms that produce those outcomes. Linking the observations in EHRs with related biomedical knowledge will greatly expand the scope of EHR-based research. This requires that both EHR data and biomedical knowledge be rendered and linked to one another in a standardized and computable form. Significant progress in this linking has been achieved in the OMOP2OBO mapping effort led by Tiffany Callahan. These mappings relate OMOP standard concepts for representing EHR data to OBO ontologies for representing biomedical knowledge.

Objective 1:

The goal of this working group is to demonstrate the use of these mappings in support of important new investigations of COVID-19. As the mappings provide a means for introducing domain knowledge expertise, they also have the potential to benefit observational analyses by reducing the inclusion of noisy variables.

Objective 2:

Phenopackets

Meeting time: Team meetings are held bi-weekly on Fridays at 10:00am PT / 1:00pm ET starting 01/07/22.

Meeting invitation: OMOP to OBO meeting