AUMCdb MEDS Extraction ETL

This pipeline extracts the AUMCdb dataset into MEDS format.

Usage:

git clone https://github.com/prockenschaub/AUMCdb_MEDS.git
cd AUMCdb_MEDS
pip install .
MEDS_extract-AUMCdb raw_input_dir=$RAW_INPUT_DIR pre_MEDS_dir=$PRE_MEDS_DIR MEDS_cohort_dir=$MEDS_COHORT_DIR

Note

To use this repository, you first need to download the AUMCdb database and unzip it. Please refer to the AUMCdb Github page for more information on how to get access to the data.

Examples:

There is currently no publically available demo dataset for AUMCdb. However, you can refer to the MIMIC_IV_MEDS respository for an example of how to run a MEDS ETL pipeline.