OMOP-MEDS 0.0.6

An ETL to convert OMOP data to the MEDS format.

MEDS OMOP ETL with MEDS-Transforms

An ETL pipeline for transforming OMOP datasets into the MEDS format using the MEDS-Transforms library. Thanks to the developers of the first OMOP MEDS ETL, from which we took inspiration, which can be found here: https://github.com/Medical-Event-Data-Standard/meds_etl. We currently support OMOP 5.3 and 5.4 datasets.

pip install OMOP_MEDS
OMOP_MEDS root_output_dir=$ROOT_OUTPUT_DIR

To try with the MIMIC-IV OMOP demo dataset, you can run:

OMOP_MEDS root_output_dir=/path/to/your/output do_download=True ++do_demo=True

Example config for an OMOP dataset:

dataset_name: MIMIC_IV_OMOP
raw_dataset_version: 1.0
omop_version: 5.3

urls:
  dataset:
    - https://physionet.org/content/mimic-iv-demo-omop/0.9/
    - url: EXAMPLE_CONTROLLED_URL
      username: ${oc.env:DATASET_DOWNLOAD_USERNAME}
      password: ${oc.env:DATASET_DOWNLOAD_PASSWORD}
  demo:
    - https://physionet.org/content/mimic-iv-demo-omop/0.9/
  common:
    - EXAMPLE_SHARED_URL # Often used for shared metadata files

Citation

If you use this dataset, please use the citation link in Github.