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.
- cTakes
- Maven
- Java
- git & git-lfs
- 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.