https://github.com/vemonet/omop-cdm-owl

🦉 An OWL ontology for the OMOP Common Data Model
https://github.com/vemonet/omop-cdm-owl

omop-cdm owl-ontology

Last synced: about 2 months ago
JSON representation

🦉 An OWL ontology for the OMOP Common Data Model

• Host: GitHub
• URL: https://github.com/vemonet/omop-cdm-owl
• Owner: vemonet
• License: other
• Created: 2023-12-08T10:21:31.000Z (about 1 year ago)
• Default Branch: main
• Last Pushed: 2023-12-08T15:04:51.000Z (about 1 year ago)
• Last Synced: 2024-04-17T04:59:20.458Z (9 months ago)
• Topics: omop-cdm, owl-ontology
• Language: Python
• Homepage: https://vemonet.github.io/omop-cdm-owl
• Size: 161 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

Awesome Lists containing this project

README

        
# 🦉OWL ontology for the OMOP CDM 🩺

[![Update documentation website](https://github.com/vemonet/omop-cdm-owl/actions/workflows/publish.yml/badge.svg)](https://github.com/vemonet/omop-cdm-owl/actions/workflows/publish.yml)

A repository to build an OWL ontology for the [Observational Medical Outcomes Partnership Common Data Model](https://www.ohdsi.org/data-standardization/) (OMOP CDM).

A documentation website is built and published at **[vemonet.github.io/omop-cdm-owl](https://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](https://bitbucket.org/jibalamy/owlready2/src/master/pymedtermino2/omop_cdm/import_omop_cdm.py). 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](https://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:

```bash

python -m venv .venv

```

Activate the virtual environment:

```bash

source .venv/bin/activate

```

```bash

./scripts/install.sh

```

## 🦉 Generate the OWL ontology

Run the script:

```bash

python generate_omop_owl.py

```

## 📖 Generate the docs locally

Generate ontology and build the docs website:

```bash

./scripts/build.sh

```

Start a web server to check the generated docs locally:

```bash

./scripts/start.sh

```