Hi Sean, Thank you so much for your very helpful and comprehensive response. I was able to generate the xmi results in the output directory and used UIMA Cas Visual Debugger (CVD) as suggested to view the information. I have two questions: 1. What is the best reference for me to study and understand the annotations. 2. Is there a CLI equivalent to CVD? I need the annotated outputs in a readable format without the help of CVD.
Thanks, Maral On Thu, Jul 18, 2019 at 12:52 PM Finan, Sean < [email protected]> wrote: > Hi Maral, > > This might be what you are talking about with respect to the Default > Clinical Pipeline > > https://cwiki.apache.org/confluence/display/CTAKES/Default+Clinical+Pipeline > > That lists a command line method for running a set of files and getting > xml output. > > The default clinical pipeline configuration is actually contained in the > plain text (piper) file > resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper > > If you are looking at source code then the file is > ctakes-clinical-pipeline-res/src/main/resources/ ... > > You can also select and run a piper file with a gui > https://cwiki.apache.org/confluence/display/CTAKES/Piper+File+Submitter+GUI > > Both methods are mentioned near the bottom of one of the pages detailing > pipeline configuration > https://cwiki.apache.org/confluence/display/CTAKES/Piper+Files > > There are several example pipelines constructed with code and/or plain > text files in the ctakes-examples and ctakes-examples-res modules. You can > look at the different "Hello World" examples. > > Since you are playing with maven, you can run the profile "runPiperGui". > mvn clean compile -DskipTests -PrunPiperGui > > Sean > > > ________________________________________ > From: Maral Amir <[email protected]> > Sent: Thursday, July 18, 2019 2:29 PM > To: [email protected] > Subject: cTAKES Pipeline [EXTERNAL] > > Hi, > > I just build my developer version of cTAKES with the help of wonderful > cTAKES developers. > > For my next step, I would appreciate if somebody direct me to a right path. > I am planning to process text clinical documents through the entire > pipeline to generate xml output. I see the website suggest walking through > the Default Clinical Pipeline. I understand there are also multiple git > repositories on developed command line tool based Apache cTAKES. > My final goal is to integrate cTAKES with some Python packages( OCR, etc.) > into one pipeline and have some form of web service at the end. I would > deeply appreciate any suggestions. > > Thanks, > Maral >
