Objective: To introduce novel methods to convert OMOP CDM data into GA4GH Beacon v2 format, enhancing semantic interoperability within Spain-s IMPaCT-Data program for personalized medicine. Materials and Methods: We utilized a file-based approach with the Convert-Pheno tool to transform OMOP CDM exports into Beacon v2 format. Additionally, we developed a direct connection from PostgreSQL OMOP CDM 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 nearly 100% data completeness. The direct connection approach improved data freshness and adaptability for dynamic environments. Discussion and Conclusion: This study introduces two methodologies for integrating OMOP CDM data with Beacon v2, offering performance optimization or real-time access. These methodologies can be adopted by other centers to enhance interoperability and collaboration in health data sharing.

The authors have declared no competing interest.

Institutional support was from the Spanish Instituto de Salud Carlos III (ISCIII), Fondo de Investigaciones Sanitarias and co-funded with ERDF funds (PI19/01772). We acknowledge the institutional support of the Spanish Ministry of Science and Innovation through the ISCIII and the 2014-2020 Smart Growth Operating Program and institutional co-financing with the European Regional Development Fund (MINECO/FEDER, BIO2015-71792-P). We also acknowledge the support of the Centro de Excelencia Severo Ochoa, and the Generalitat de Catalunya through the Departament de Salut, Departament d_Empresa i Coneixement and the CERCA Programme to the institute. This work was partially funded through the IMPaCT-Data Project (Exp. IMP/00019) by ISCIII, co-funded by European Union, FEDER "A way to do Europe" and in the case of Hospital del Mar by the European Health Data Evidence Network (EHDEN) from the Innovative Medicines Agency 2 Undertaking (JU), under grant agreement No 806968 of the European Union_s Horizon 2020 and EFPIA

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Yes

The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

Health Research Institute Hospital La Fe: All data extraction methods adhered to relevant guidelines and regulations, with the study receiving approval on May 29, 2024 from the Ethics Committee for Biomedical Research with Medicines of the University and Polytechnic La Fe Hospital of Valencia, under registration number 2024-0484-1. IMASIS-2 was used with permission of the Ethics Committee of the Hospital del Mar, under registration number 2023/11262.

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Yes

I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).

Yes

I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.

Yes

All data produced in the present study are available upon reasonable request to the authors.