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Machine-Learning-for-Medical-Language / ctakes-rest-package

Quick repo to get setup running cTAKES REST server and making calls
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Instructions for running cTAKES rest server to get CUIs for documents.

  1. Install Docker (and make sure it's running correctly)

  2. Create a UMLS account: https://uts.nlm.nih.gov/license.html

  3. Run the command to create the docker container using the Dockerfile in this directory:

    docker build -t ctakes-web-rest .

  4. Create environment variables for your UMLS account:

    export umls_api_key=<your umls api key>

  5. Start the docker container:

    ./start_rest.sh

    This will take quite a while to start up. If you get the docker container id with docker ps you can check the progress of this container startup with docker logs <container id>. You only need to specify the first few characters of the container id. The container is ready when the final line of the log has the following: org.apache.catalina.startup.Catalina.start Server startup in [25,329] milliseconds.

  6. Run the script sample_extract_cuis.py, which demonstrates how to use the functions in ctakes_rest.py to extract CUIs using the REST server. Take a look at output.txt to make sure it ran correctly -- on each line it should print out a filename followed by a space-delimited list of CUIs.

python sample_extract_cuis.py fake_notes/ output.txt
  1. Modify the code in sample_extract_cuis.py to iterate and extract text from your documents. Modify the file writing code so that the first part of each line is some unique identifier for that document/patient.