INSPIRE-MEDS 0.0.13

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

INSPIRE-MEDS

The INSPIRE dataset is a publicly available research dataset in perioperative medicine, which includes approximately 130,000 cases (50% of all surgical cases) who underwent anesthesia for surgery at an academic institution in South Korea between 2011 and 2020. This comprehensive dataset includes patient characteristics such as age, sex, American Society of Anesthesiologists physical status classification, diagnosis, surgical procedure code, department, and type of anesthesia. It also includes vital signs in the operating theatre, general wards, and intensive care units (ICUs), laboratory results from six months before admission to six months after discharge, and medication during hospitalization. Complications include total hospital and ICU length of stay and in-hospital death. This pipeline extracts the INSPIRE dataset (from physionet, https://physionet.org/content/inspire/) into the MEDS format.

Usage:

pip install INSPIRE_MEDS
export DATASET_DOWNLOAD_USERNAME=$PHYSIONET_USERNAME
export DATASET_DOWNLOAD_PASSWORD=$PHYSIONET_PASSWORD
MEDS_extract-INSPIRE root_output_dir=$ROOT_OUTPUT_DIR

When you run this, the program will:

1. Download the needed raw INSPIRE files for the currently supported version into $ROOT_OUTPUT_DIR/raw_input.
2. Perform initial, pre-MEDS processing on the raw INSPIRE 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-INSPIRE 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-INSPIRE --help for more information on the arguments and options. You can also run

MEDS_extract-INSPIRE root_output_dir=$ROOT_OUTPUT_DIR

to run the entire pipeline.

MEDS-transforms settings

If you want to convert a large dataset, you can use parallelization with MEDS-transforms (the MEDS-transformation step that takes the longest).

Using local parallelization with the hydra-joblib-launcher package, you can set the number of workers:

pip install hydra-joblib-launcher --upgrade

Then, you can set the number of workers as environment variable:

export N_WORKERS=8

Moreover, you can set the number of subjects per shard to balance the parallelization overhead based on how many subjects you have in your dataset:

export N_SUBJECTS_PER_SHARD=100000

The MIMIC-IV OMOP Dataset

We use the demo dataset for MIMIC-IV in the OMOP format, which is a subset of the MIMIC-IV dataset. This dataset downloaded from Physionet does not include the standard dictionary linking definitions but should otherwise be functional

Particularities

• Care site is added to the visit as text
• Add support for care_site table (visit_detail)