Automated production of research data marts from a canonical fast healthcare interoperability resource data repository: applications to COVID-19 research

• Published in: Journal of the American Medical Informatics Association : JAMIA 2021-08, Vol.28 (8), p.1605-1611
• Main Authors: Lenert, Leslie A, Ilatovskiy, Andrey V, Agnew, James, Rudisill, Patricia, Jacobs, Jeff, Weatherston, Duncan, Deans Jr, Kenneth R
• Format: Article
• Language: English
• Subjects: Research and Applications
• ISSN: 1527-974X; 1067-5027; 1527-974X
• DOI: 10.1093/jamia/ocab108

Abstract Objective The rapidly evolving COVID-19 pandemic has created a need for timely data from the healthcare systems for research. To meet this need, several large new data consortia have been developed that require frequent updating and sharing of electronic health record (EHR) data in different common data models (CDMs) to create multi-institutional databases for research. Traditionally, each CDM has had a custom pipeline for extract, transform, and load operations for production and incremental updates of data feeds to the networks from raw EHR data. However, the demands of COVID-19 research for timely data are far higher, and the requirements for updating faster than previous collaborative research using national data networks have increased. New approaches need to be developed to address these demands. Methods In this article, we describe the use of the Fast Healthcare Interoperability Resource (FHIR) data model as a canonical data model and the automated transformation of clinical data to the Patient-Centered Outcomes Research Network (PCORnet) and Observational Medical Outcomes Partnership (OMOP) CDMs for data sharing and research collaboration on COVID-19. Results FHIR data resources could be transformed to operational PCORnet and OMOP CDMs with minimal production delays through a combination of real-time and postprocessing steps, leveraging the FHIR data subscription feature. Conclusions The approach leverages evolving standards for the availability of EHR data developed to facilitate data exchange under the 21st Century Cures Act and could greatly enhance the availability of standardized datasets for research.