/ctakes-standalone

ctakes standalone

Primary LanguageShell

cTakes Standalone

This is a maven project that builds an application integrated with cTAKES. One can use it to run text through cTAKES on the command line.

Software

  • cTakes
  • Maven
  • Java
  • git & git-lfs

How to Run

  • Ensure Java, Maven, Git and Git Large File Store is installed
  • Git clone project
git clone https://github.com/tenthdoctor/ctakes-standalone
  • Build code
cd ctakes-standalone
mvn -Dmaven.test.skip=true clean package assembly:single
  • Run excutable
cd target/ctakes-standalone-*-bin/ctakes-standalone-*/

For Unix

sh startup.sh  --text "diabetes"

For Windows

startup.bat  --text "diabetes"

Command line options:

  • --help: displays the help text
  • --inputfile file: file containing text to annotate
  • --outputfile file: file to write the results to
  • --text text: text to annotate
  • --pipeline ["default", "fast"]
  • --outputformat ["sentence", "text", "json"]: 'sentence' will display the results along side of the original sentence(s). 'text' will display the results for one entity on a single line. 'json' will display the results in a json array.

If using the "default" pipeline you need to supply a username and password to use the UMLS dictionary. Modify the start script with those values.