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. 2024 Aug 13:12:e49542.
doi: 10.2196/49542.

Transforming Primary Care Data Into the Observational Medical Outcomes Partnership Common Data Model: Development and Usability Study

Mathilde Fruchart  1 , Paul Quindroit  1 , Chloé Jacquemont  2 , Jean-Baptiste Beuscart  1 , Matthieu Calafiore  1   2 , Antoine Lamer  1   3
Affiliations

Transforming Primary Care Data Into the Observational Medical Outcomes Partnership Common Data Model: Development and Usability Study

Mathilde Fruchart et al. JMIR Med Inform. .

Abstract

Background: Patient-monitoring software generates a large amount of data that can be reused for clinical audits and scientific research. The Observational Health Data Sciences and Informatics (OHDSI) consortium developed the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) to standardize electronic health record data and promote large-scale observational and longitudinal research.

Objective: This study aimed to transform primary care data into the OMOP CDM format.

Methods: We extracted primary care data from electronic health records at a multidisciplinary health center in Wattrelos, France. We performed structural mapping between the design of our local primary care database and the OMOP CDM tables and fields. Local French vocabularies concepts were mapped to OHDSI standard vocabularies. To validate the implementation of primary care data into the OMOP CDM format, we applied a set of queries. A practical application was achieved through the development of a dashboard.

Results: Data from 18,395 patients were implemented into the OMOP CDM, corresponding to 592,226 consultations over a period of 20 years. A total of 18 OMOP CDM tables were implemented. A total of 17 local vocabularies were identified as being related to primary care and corresponded to patient characteristics (sex, location, year of birth, and race), units of measurement, biometric measures, laboratory test results, medical histories, and drug prescriptions. During semantic mapping, 10,221 primary care concepts were mapped to standard OHDSI concepts. Five queries were used to validate the OMOP CDM by comparing the results obtained after the completion of the transformations with the results obtained in the source software. Lastly, a prototype dashboard was developed to visualize the activity of the health center, the laboratory test results, and the drug prescription data.

Conclusions: Primary care data from a French health care facility have been implemented into the OMOP CDM format. Data concerning demographics, units, measurements, and primary care consultation steps were already available in OHDSI vocabularies. Laboratory test results and drug prescription data were mapped to available vocabularies and structured in the final model. A dashboard application provided health care professionals with feedback on their practice.

Keywords: EHR; Observational Medical Outcomes Partnership; common data model; dashboard; data reuse; data warehouse; electronic health record; patient monitoring; patient tracking system; primary care; primary care data; reproducible research.

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Conflict of interest statement

Conflicts of Interest: None declared.

Figures

Figure 1.
Figure 1.. Pipeline of the primary care data transformation into the OMOP CDM. CDM: Common Data Model; ETL: extract-transform-load; OMOP: Observational Medical Outcomes Partnership.
Figure 2.
Figure 2.. Structural mapping of each source variable to the OMOP CDM format. Common Data Model; OMOP: Observational Medical Outcomes Partnership.
Figure 3.
Figure 3.. The data quality assessment dashboard. NA: not available.
Figure 4.
Figure 4.. The prototype primary care dashboard. PriCaDa: Primary Care Data Warehouse.
See this image and copyright information in PMC

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