NWICU MEDS Extraction ETL

PyPI - Version codecov tests code-quality Python Version license PRs contributors DOI MEDS v0.3.3

This pipeline extracts the NWICU dataset (from physionet, https://physionet.org/content/nwicu-northwestern-icu/0.1.0/) into the MEDS format.

Usage:

pip install NWICU_MEDS
export DATASET_DOWNLOAD_USERNAME=$PHYSIONET_USERNAME
export DATASET_DOWNLOAD_PASSWORD=$PHYSIONET_PASSWORD
MEDS_extract-NWICU root_output_dir=$ROOT_OUTPUT_DIR

When you run this, the program will:

  1. Download the needed raw NWICU files for the currently supported version into $ROOT_OUTPUT_DIR/raw_input.
  2. Perform initial, pre-MEDS processing on the raw NWICU files, saving the results in $ROOT_OUTPUT_DIR/pre_MEDS.
  3. Construct the final MEDS cohort, and save it to $ROOT_OUTPUT_DIR/MEDS_cohort.

You can also specify the target directories more directly, with

export DATASET_DOWNLOAD_USERNAME=$PHYSIONET_USERNAME
export DATASET_DOWNLOAD_PASSWORD=$PHYSIONET_PASSWORD
MEDS_extract-NWICU raw_input_dir=$RAW_INPUT_DIR pre_MEDS_dir=$PRE_MEDS_DIR MEDS_cohort_dir=$MEDS_COHORT_DIR

Examples and More Info:

You can run MEDS_extract-NWICU --help for more information on the arguments and options. You can also run

MEDS_extract-NWICU root_output_dir=$ROOT_OUTPUT_DIR

to run the entire pipeline.

Citation

If you find our work useful, please cite the resource through the github repository (or the bibtex entry below), and cite the original dataset through PhysioNet. The following is the recommended citation for this package:

@software{van_de_Water_NWICU_MEDS_ETL_2025,
author = {van de Water, Robin Philippus},
doi = {10.5281/zenodo.14892134},
license = {MIT},
month = feb,
title = {{NWICU\_MEDS ETL}},
url = {https://github.com/rvandewater/NWICU_MEDS},
year = {2025}
}

This is the original dataset citation from PhysioNet:

@article{PhysioNet-nwicu-northwestern-icu-0.1.0,
  author = {Moukheiber, Dana and Temps, William and Molgi, Bhadrappa and Li, Yikuan and Lu, Alice and Nannapaneni, Prasanth and Chahin, Abdulrahman and Hao, Sicheng and {Torres Fabregas}, Felipe and Celi, Leo Anthony and Wong, Adrian and Lloyd, Maxwell and {Borrat Frigola}, Xavier and Lee, Hyung-Chul and Schneider, Daniel and Pollard, Tom and Luo, Yuan and Kho, Abel and Mark, Roger},
  title = {{Northwestern ICU (NWICU) database}},
  journal = {{PhysioNet}},
  year = {2024},
  month = nov,
  note = {Version 0.1.0},
  doi = {10.13026/s84w-1829},
  url = {https://doi.org/10.13026/s84w-1829}
}
```
.

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Credits

Author: Robin van de Water

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MIT License

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