Apache cTAKES
==================================
Detailed documentation can found at:
http://incubator.apache.org/ctakes

Requirements
---------------------------------------
Java 1.6 is required to run cTAKES
Maven 3.0.0 is required for building it
**cTAKES Resources is required to build with unit tests and running cTAKES.**
Download the cTAKES Resources zip file from:
http://sourceforge.net/projects/ctakesresources/files/
Unzip it to the resources directory (or local folder) and add the resources directory to your CLASSPATH

Running the default pipeline in the UIMA CAS Visual Debugger
or in the Collection Processing Engine
----------------------------------------------------------------
Run bin/runctakesCVD/CPE.sh.bat
Load AE (analysis engine)
Select desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextProcessor
Enter note or other text
Run analysis engine
NOTE: The included example dictionary is very small. Try a sentence such as: 
Patient took aspirin for knee pain

Using UMLS resources
----------------------------------------------------------------
If you plan to use the UMLS Resources:
Add the java args -Dctakes.umlsuser=[username] -Dctakes.umlspw=[password]
Alternatively, you can save it to the desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml