ArticleBMC medical informatics and decision making2026
Enhancing semantic interoperability in precision medicine: converting OMOP CDM to Beacon v2 in the Spanish IMPaCT-Data project.
Article in BMC medical informatics and decision making, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
objectiveTo evaluate a file-based approach for converting OMOP CDM data into GA4GH Beacon v2 format and outline an alternative on-the-fly architecture for real-time access, with the aim of enhancing semantic interoperability within Spain's IMPaCT-Data program for personalized medicine. MATERIALS AND
methodsWe used the Convert-Pheno tool to transform OMOP CDM exports into Beacon v2 format using a file-based approach. In addition, we describe an architecture that connects PostgreSQL-based OMOP CDM instances directly to the Beacon v2 API, enabling real-time data access without intermediary text files.
resultsWe successfully converted OMOP CDM datasets from three research centers (CNAG, IIS La Fe, and HMar) to Beacon v2 format with high data completeness (≥ 99.9% across most domains). DISCUSSION AND
conclusionThis study evaluates a file-based approach and describes an alternative on-the-fly architecture for integrating OMOP CDM data with Beacon v2. These approaches provide practical options for integrating OMOP CDM data with Beacon v2 in different deployment settings.
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