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Objective <p>To 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.</p> Materials and methods <p>We 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.</p> Results <p>We 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).</p> Discussion and conclusion <p>This 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.</p>

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Enhancing semantic interoperability in precision medicine: converting OMOP CDM to Beacon v2 in the Spanish IMPaCT-Data project

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年7月8日

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  • Manuel Rueda,
  • Juan Manuel Ramírez-Anguita,
  • Victoria López-Sánchez,
  • Sergi Aguiló-Castillo,
  • Maria Eugenia Gas López,
  • Alberto Labarga,
  • Miguel-Ángel Mayer,
  • Javier Ripoll Esteve,
  • Ivo G. Gut

摘要

Objective

To 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 methods

We 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.

Results

We 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 conclusion

This 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.