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.
Access the interactive tutorial on Google Colab via the link below:
If you prefer running the tutorial locally, the notebook is available here:
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
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