Development of a COVID-19 Application Ontology for the ACT Network

medRxiv. 2021 Apr 14;2021.03.15.21253596. doi: 10.1101/2021.03.15.21253596. Preprint


Clinical data networks that leverage large volumes of data in electronic health records (EHRs) are significant resources for research on coronavirus disease 2019 (COVID-19). Data harmonization is a key challenge in seamless use of multisite EHRs for COVID-19 research. We developed a COVID-19 application ontology in the national Accrual to Clinical Trials (ACT) network that enables harmonization of data elements that that are critical to COVID-19 research. The ontology contains over 50,000 concepts in the domains of diagnosis, procedures, medications, and laboratory tests. In particular, it has computational phenotypes to characterize the course of illness and outcomes, derived terms, and harmonized value sets for SARS-CoV-2 laboratory tests. The ontology was deployed and validated on the ACT COVID-19 network that consists of nine academic health centers with data on 14.5M patients. This ontology, which is freely available to the entire research community on GitHub at, will be useful for harmonizing EHRs for COVID-19 research beyond the ACT network.

Keywords: COVID-19; clinical data network; electronic health records; ontology.

Publication types

  • Preprint