bdi-kit

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 and visualizations for peforming 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

Documentation is available at https://bdi-kit.readthedocs.io/.

Installation

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

Contributing

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/