NWICU-MEDS 0.0.11

An ETL pipeline to extract NWICU data into the MEDS format.

NWICU MEDS Extraction ETL

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

we provide an ETL for the following resource: Moukheiber, D., Temps, W., Molgi, B., Li, Y., Lu, A., Nannapaneni, P., Chahin, A., Hao, S., Torres Fabregas, F., Celi, L. A., Wong, A., Lloyd, M., Borrat Frigola, X., Lee, H., Schneider, D., Pollard, T., Luo, Y., Kho, A., & Mark, R. (2024). Northwestern ICU (NWICU) database (version 0.1.0). PhysioNet. https://doi.org/10.13026/s84w-1829.