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.
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.