AUMCdb-MEDS 0.0.3

A template ETL pipeline to extract AUMCdb data into the MEDS format.

AUMCdb MEDS Extraction ETL

This pipeline extracts the AUMCdb dataset into MEDS format. The AUMCdb dataset is a publicly available dataset from the Amsterdam University Medical Centers (AUMC) that contains clinical data from the hospital. You first need to request access here.

Usage:

pip install AUMCdb_MEDS
MEDS_extract-AUMCdb input_dir=$RAW_DATA_DIR output_dir=$MEDS_DIR

If you want, you can also use the do_download flag to download the data directly from the AUMCdb repository. You need to set the AUMCDB_API_KEY environment variable to your API key. Please get it from here: AUMCdb API Key

export AUMCDB_API_KEY=your_api_key
MEDS_extract-AUMCdb input_dir=$RAW_DATA_DIR output_dir=$MEDS_DIR

This will download the dataset automatically for you.