Install

• Download CTakes (e.g., follow ctakes user installation) to CTAKES_HOME.
• Clone this repository, cd into it and run 'mvn package'.
• To set up necessary resources, run the following:

ln -s $CTAKES_HOME/resources resources
ln -s $CTAKES_HOME/desc desc

Running Server

You can also start a simple REST Server with the following command (assuming you are in root dir):

java -Dctakes.umlsuser=<YOUR_UMLS_ID_HERE> -Dctakes.umlspw=<YOUR_UMLS_PASSSWORD_HERE> -Xmx5g -cp target/ctakes-server-0.1.jar:resources/ de.dfki.lt.ctakes.Server host(e.g. localhost) port(e.g. 9999) desc/path/to/desc.xml

You can then use the REST service via GET requests with parameters "text". E.g., in browser:

http://localhost:9999/ctakes?text=Pain in the left leg.

Running from Docker

1. Clone this repository

https://github.com/choyiny/ctakes-server.git

2. Create an .env file with the following information

HOST=0.0.0.0
PORT=9999
UMLSUSER=<YOUR UMLS USERNAME>
UMLSPW=<YOUR UMLS PASSWORD>

3. Run docker compose on daemon mode

docker-compose up -d

YTex Install Notes

• Follow YTex installation on ctakes website
  • you do not need to care about optional installation steps
• requires Java-7

Recommendations

• use desc/ctakes-ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml
• comment assertion-node, because it requires a different scala version and is therefore not supported:

<!--node>AssertionAnnotator</node-->

• exchange DictionaryLookupAnnotatorDB location to the following (because it works better):

<delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
    <!--import location="./DictionaryLookupAnnotator.xml" /-->
    <import location="../../../ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml"/>
</delegateAnalysisEngine>