Enhancing Semantic Interoperability in Precision Medicine: Converting OMOP CDM to Beacon v2 in the Spanish IMPaCT-Data Project

This repository provides resources and a tutorial notebook for converting OMOP CDM data to Beacon v2 format, as described in our study.

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Google Colab Tutorial

Access the interactive tutorial on Google Colab via the link below:

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Local Copy of the Tutorial

If you prefer running the tutorial locally, the notebook is available here:

Local Copy

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Convert-Pheno Tool

The Convert-Pheno tool is a key resource for transforming OMOP CDM datasets into Beacon v2 format. Below are relevant resources for using the tool:

• CLI Source Code: GitHub Repository
• CPAN Distribution: Perl Module Documentation
• Docker Image: Docker Hub Tags

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How to Cite

If you use this tutorial or tools in your work, please consider citing our paper:

Rueda et al. Enhancing Semantic Interoperability in Precision Medicine: Converting OMOP CDM to Beacon v2 in the Spanish IMPaCT-Data Project.

DOI (Pre-print; medRxiv): https://doi.org/10.1101/2024.12.25.24319606