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Citation for Convert-Pheno

Citation

Rueda M, et al. Convert-Pheno: A software toolkit for the interconversion of standard data models for phenotypic data. J Biomed Inform. 2023 Nov 28:104558. doi: 10.1016/j.jbi.2023.104558. PMID: 38035971.

Publication scope

The software paper describes the feature set available at publication time. This documentation follows the current release and therefore includes later formats, output routes, and multi-entity BFF support that are not covered in the original article.

  • Convert-Pheno software paper: the main citation for the tool is the Journal of Biomedical Informatics article listed above.
  • OMOP-CDM to Beacon v2 mapping work: Rueda M, et al. Enhancing semantic interoperability in precision medicine: converting OMOP CDM to Beacon v2 in the Spanish IMPaCT-Data project. BMC Medical Informatics and Decision Making. 2026. doi: 10.1186/s12911-026-03649-0. The accompanying tutorial repository documents the mapping workflow implemented in Convert-Pheno.
Funding agencies
  • This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 831434 (3TR). The JU receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA.
Convert-Pheno
Funding agencies
  • Institutional support was from the Spanish Instituto de Salud Carlos III, Fondo de Investigaciones Sanitarias and cofunded with ERDF funds (PI19/01772).
  • We acknowledge the institutional support of the Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III and the 2014–2020 Smart Growth Operating Program, to the EMBL partnership and institutional co-financing with the European Regional Development Fund (MINECO/FEDER, BIO2015-71792-P).
  • We also acknowledge the support from the Generalitat de Catalunya through the Departament de Salut, Departament d’Empresa i Coneixement.