Thanks a lot for your replies. CPE did the job for me. I used it with the "test_plaintext.xml" CPE descriptor and "AggregatePlainTextUmlsProcessor" as the Analysis Engine. Gave the path to input directory and gave a custom output directory for writing CAS to XML file and that did it for me! Now I have the annotation for each input file stored in an XML file in the output directory. :)
On Wed, Jun 18, 2014 at 8:03 PM, Pei Chen <[email protected]> wrote: > Also check out the main class in: > > https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java > It uses uimaFIT style to programmatically wire up a pipeline and one can > also use uimaFIT to access the Annotations (TypeSystem). > > --Pei > > > On Wed, Jun 18, 2014 at 10:16 AM, vijay garla <[email protected]> wrote: > >> To Annotate: >> If you have a CPE, and all the components in your pipeline are threadsafe >> (i.e. drop LVG from your pipeline), you can increase the threads in the cpe >> config >> You can use this class: org.apache.ctakes.ytex.tools.RunCPE to run a cpe >> from the command line/script >> >> Alternatively, run multiple CPE's in parallel (they need to be processing >> different subsets of the corpus) >> >> To extract annotations: >> Add the YTEX DBConsumer to store the annotations in a database (see >> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1.2+-+YTEX+DBConsumer >> ) >> Make sure you configure 'types to ignore' - you don't want to store >> annotations for punctuation. >> >> You can add the DBConsumer to any pipeline/CPE - you don't need any other >> YTEX components (however, you do have to set up a database). >> >> >> >> >> On Wed, Jun 18, 2014 at 4:56 AM, Richard Eckart de Castilho < >> [email protected]> wrote: >> >>> A Groovy script has been mentioned on the developers list that >>> illustrates how to use uimaFIT to compose and run a cTAKES pipeline. [1] >>> >>> I do not know if these scripts are only in SVN or if they are (planned >>> to) be part of a release or of some documentation. >>> >>> Cheers, >>> >>> -- Richard >>> >>> [1] >>> http://mail-archives.apache.org/mod_mbox/ctakes-dev/201312.mbox/%3c996fc801c05df64a84246a106facacd021a...@msgpexcha08a.mfad.mfroot.org%3E >>> >>> On 18.06.2014, at 07:33, Abhishek Raj <[email protected]> wrote: >>> >>> > Hello. I have been looking for a way to run ctakes programatically to >>> annotate large number of documents and extract those annotations. I haven't >>> come across any docs so far which explains how to do that. If someone could >>> throw some light on this issue, it'd be great. Thanks! :) >>> >>> >> >
