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eds-scikit is a tool to assist data scientists working on the AP-HP's Clinical Data Warehouse. It is specifically targeted for OMOP-standardized data. It main goals are to:
This library is developed and maintained by the core team of AP-HP’s Clinical Data Warehouse (EDS) with the strong support of Inria's SODA team.
Please check the online documentation for more informations. You will find
Detailed explanation of the project goal and working principles
A complete API documentation
Various Jupyter Notebooks describing how to use various functionnalities of eds-scikit
And more !
eds-scikit stands on the shoulders of Spark 2.4 which requires:
Python ~3.7.1
Java 8
You can install eds-scikit via pip
:
pip install "eds-scikit[aphp]"
:warning: If you get an an error during installation, please try downgrading pip via pip install -U "pip<23" before install
eds-scikit`
:warning: If you don't work in AP-HP's ecosystem (EDS), please install via:
pip install eds-scikit
You can now import the library via
import eds_scikit
Please check our contributing guidelines.
If you use eds-scikit
, please cite us as below.
@misc{eds-scikit,
author = {Petit-Jean, Thomas and Remaki, Adam and Maladière, Vincent and Varoquaux, Gaël and Bey, Romain},
doi = {10.5281/zenodo.7401549},
title = {eds-scikit: data analysis on OMOP databases},
url = {https://github.com/aphp/eds-scikit}
}
We would like to thank the following funders: