Preliminary steps:

• Obtain access to the MIMIC III database (ask your PI).
• Obtain a UMLS account and API key
• Install Docker and docker-compose

Setup cTAKES containers:

• git clone [email protected]:Machine-Learning-for-Medical-Language/ctakes-rest-package.git
• cd ctakes-rest-package
• export umls_api_key=<api key from above>
• docker-compose up -d --scale ctakes=N # This starts N containers -- each requires around 4 GB RAM.

Run the python script to process the data -- run with -h to receive detailed documentation of the options:

• python process_mimic.py --input-path <path to NOTEEVENTS.csv file> --output-format <json|mongo|xmi|fhir> --output_dir <directory to write files if output format is file-based>

For MongoDB usage, setup a few indices for faster querying: a. TODO