IMI-SOPHIA Maastricht Study OMOP converter

This repository holds the code to read the Maastricht Study dataset, and convert it into the correct columns in the configured OMOP database. The main file holding this conversion script is located in R_script_converted.ipynb.

Requirements

The following software requirements are needed to run this code:

• R (tested in version 4.3.1)
• on linux: libpq-dev (use sudo apt update && sudo apt install libpq-dev to install this package)
• Jupyter Lab with support for R (you can use the jupyter/datascience-notebook docker image for convenience, which requires Docker)
• A running OMOP database in PostgreSQL. This repository makes use of these instructions.

Data requirements

The data needs to be in a folder outside of this git repository, but next to your current folder in the hierarchy. The code will refer to data files in ../data.