This is the home of the Related Project - NLP cTAKES Project space.
News: cTAKES is now incubating as an Apache Software Foundation Project!

There is a wealth of information within the plain text clinical narrative.  The purpose of this cell is to harness the unstructured information by allowing i2b2 users to query and join that information with existing i2b2 concepts.  Currently, the entire note is commonly stored as a single row in the observation_blob field in the observation_fact table in i2b2.  One of NLP cTAKES' features is its capability to 'read' through and extract concepts from plain text notes and transform them into structured and normalized information.  The purpose of this cell is to incorporate cTAKES and i2b2 by formatting the output of cTAKES into the i2b2 observation_fact table format (facts, concepts, modifiers, and values) which can then be easily queried by existing i2b2 interfaces.
There will be 2 main components:


Quick Start Guide:

In addition to deploying the cTAKES GUI as a war file to a managed servlet container such as JBoss or Tomcat, cTAKES provides a standalone web server version running Jetty out of the box.

  1. Java JDK (not JRE) 1.6+ is required.  Feel free to download and install the Java JDK from:
  2. Download the cTAKES GUI code (currently in beta) from
  3. Unzip the contents to a local directory
  4. If required, modify the startup.bat or with the path to your JAVA_HOME environment variable.  Also available as an environment variable is the JETTY_PORT (defaults to 9998).
  5. Open a command line window/terminal and execute or startup.bat
  6. Wait for the message "Jetty running on http://localhost:9998/index.jsp"
  7. Open your favorite web browser and point the url to: http://localhost:9998/index.jsp
  8. cTAKES GUI Quick Reference Guide.pdf

*Design and Architecture
*Installation Guide

Contact Information

Pei J Chen
Children's Hospital Boston


Guergana K Savova, PhD
Children's Hospital Boston


Jonathan Bickel, MD
Children's Hospital Boston


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