🦉OWL ontology for the OMOP CDM 🩺

A repository to build an OWL ontology for the Observational Medical Outcomes Partnership Common Data Model (OMOP CDM).

A documentation website is built and published at vemonet.github.io/omop-cdm-owl

This project reuse and modify the script published in this publication: https://hal.science/hal-03479322/document. The original script can be found here. Special thanks to Jean-Baptiste Lamy who developed the original script.

The script to build the ontology has been modified to add:

• Labels for classes and properties
• Change the ontology URI to https://w3id.org/omop/ontology/
• Add metadata to the owl:Ontology (license, label, description, preferred prefix and namespace)

♻️ The documentation website hosted at vemonet.github.io/omop-cdm-owl is automatically updated by a GitHub Action at every change to the ontology file.

📥 Install dependencies

Make sure Java ~17 and python >=3.8 are installed. We recommend to enable a python virtual environment.

Create the virtual environment:

python -m venv .venv

Activate the virtual environment:

source .venv/bin/activate

./scripts/install.sh

🦉 Generate the OWL ontology

Run the script:

python generate_omop_owl.py

📖 Generate the docs locally

Generate ontology and build the docs website:

./scripts/build.sh

Start a web server to check the generated docs locally:

./scripts/start.sh