omop-cdm is a Python package that contains SQLAlchemy declarative table definitions of several versions of the OHDSI OMOP CDM.
omop-cdm requires Python >= 3.9.
Install from PyPI:
pip install omop-cdmThe omop-cdm table definitions are tested to be compatible with PostgreSQL.
Though not officially supported, omop-cdm doesn't use postgres-specific features of SQLAlchemy, so it can likely be used for other database types as well.
omop-cdm contains table defintions for the following CDM versions:
- CDM 5.4
- CDM 5.3.1
- CDM 6.0.0 (not recommended)
- Make sure Poetry is installed.
- Install the project and dependencies via
poetry install. - Set up the pre-commit hook scripts via
poetry run pre-commit install.
Several developer actions (e.g. run tests, code format, lint) are available via nox sessions. For a complete list, run:
nox --listomop-cdm uses semantic versioning.
Releases should be made from the main branch. Before creating a release on GitHub, make sure the CHANGELOG has been updated and the version number in pyproject.toml is correct.
Once the GitHub release has been made, the package will be automatically uploaded to PyPI (via the publish.yml workflow).