The bdi-kit is a library that assist users in performing data harmonization. It provides state-of-the-art tools to streamline the process of integrating and transforming disparate datasets (with a focus on biomedical data), and includes APIs for performing tasks such as:
- Schema matching
- Value matching
- Data transformation to a target schema/standard
Warning: bdi-kit is currently in alpha stage and under heavy development. Expect APIs to change.
Documentation is available at https://bdi-kit.readthedocs.io/.
You can install the latest stable version of this library from PyPI:
pip install bdi-kit
To install the latest development version:
pip install git+https://github.com/VIDA-NYU/bdi-kit@devel
We format code using the black code formatter. The CI runs for every pull request and will fail if code is not properly formatted. To make sure formatting is correct, you can do the following steps.
Make sure you have black installed:
pip install black
To format the code, anyone can use the command before committing your changes:
make format
Or you can use the black command directly:
black ./bdikit/