Transforming French Electronic Health Records into the Observational Medical Outcome Partnership's Common Data Model: A Feasibility Study

Abstract

Background: Common data models (CDMs) enable data to be standardized, and facilitate data exchange, sharing, and storage, particularly when the data have been collected via distinct, heterogeneous systems. Moreover, CDMs provide tools for data quality assessment, integration into models, visualization, and analysis. The observational medical outcome partnership (OMOP) provides a CDM for organizing and standardizing databases. Common data models not only facilitate data integration but also (and especially for the OMOP model) extends the range of available statistical analyses.

Objective: This study aimed to evaluate the feasibility of implementing French national electronic health records in the OMOP CDM.

Methods: The OMOP's specifications were used to audit the source data, specify the transformation into the OMOP CDM, implement an extract-transform-load process to feed data from the French health care system into the OMOP CDM, and evaluate the final database.

Results: Seventeen vocabularies corresponding to the French context were added to the OMOP CDM's concepts. Three French terminologies were automatically mapped to standardized vocabularies. We loaded nine tables from the OMOP CDM's "standardized clinical data" section, and three tables from the "standardized health system data" section. Outpatient and inpatient data from 38,730 individuals were integrated. The median (interquartile range) number of outpatient and inpatient stays per patient was 160 (19-364).

Conclusion: Our results demonstrated that data from the French national health care system can be integrated into the OMOP CDM. One of the main challenges was the use of international OMOP concepts to annotate data recorded in a French context. The use of local terminologies was an obstacle to conceptual mapping; with the exception of an adaptation of the International Classification of Diseases 10th Revision, the French health care system does not use international terminologies. It would be interesting to extend our present findings to the 65 million people registered in the French health care system.

Fig. 1

A summary of the integration process. CDM, common data model; ETL, extract–transform–load; OHDSI, observational health data sciences and informatics; OMOP, observational medical outcome partnership; SNDS, Système National des Données de Santé.

Fig. 2

A schematic diagram of the structural mapping between our extraction of the SNDS data and the OMOP CDM. Hospital-sourced data are shown in red, outpatient data are shown in green, and the final OMOP tables are shown in blue. PMSI, Program de Médicalisation du Système d'Information; SNIIRAM.

Fig. 3

Dashboard summary generated by Achilles. CDM, common data model; PAERPA, Personnes Agées en Risque de Perte d'Autonomie.

Fig. 4

Concept type per person computed by Achilles.

Fig. 5

Time to the next hospital admission according to the rank of the hospital admission (also see Appendix C , available in the online version).