/cTAKES-Python-API

cTAKES Python API interface for the Default Clinical Pipeline

Primary LanguagePython

What you'll be able to do

  1. Interact with cTAKES Default Clinical Pipeline through a Python RESTful API doing:
    • Annotations for;
      • Anatomical sites,
      • Signs/Symptoms,
      • Procedures,
      • Diseases/Disorders and
      • Medications.

Input: Plain Text File Output: XMI File

Orginal wiki page: https://cwiki.apache.org/confluence/display/CTAKES/Default+Clinical+Pipeline

cTAKES Install Instructions

  1. Execute ./ctakes-install/ctakes-install.sh, which will:
    • Download a copy of cTAKES into ./ctakes-install/tmp
    • Extract cTAKES then copy into ctakes-install (cTAKES_HOME) directory
    • Download ctakes-resources-4.0-bin.zip into ./ctakes-install/tmp
    • Unzip ctakes-resources-4.0-bin.zip and copy into apache-ctakes-4.0.0/resources
    • Remove/clean /tmp directory from ctakes-install
    • Set your UMLS credentials in umls.sh

Note: If you don't have a UMLS username & password you'll need to request one at https://uts.nlm.nih.gov/license.html

Setting up Python RESTful API Instructions

COMING SOON!