Thanks, Sean! Erin
________________________________________ From: Finan, Sean <[email protected]> Sent: Thursday, May 11, 2017 1:08 PM To: [email protected] Subject: RE: Temporal module dictionary Hi Erin, Ok, thanks. I think that you are getting non-dictionary events from the temporal module. You could try to filter them out with an "if ( OntologyConceptUtil.getCuis( annotation ).isEmpty() ) {} or something like that. Sean -----Original Message----- From: Erin Gustafson [mailto:[email protected]] Sent: Thursday, May 11, 2017 2:04 PM To: [email protected] Subject: Re: Temporal module dictionary Hi Sean, The cuis are all within my dictionary. Erin ________________________________________ From: Finan, Sean <[email protected]> Sent: Thursday, May 11, 2017 12:39 PM To: [email protected] Subject: RE: Temporal module dictionary Hi Erin, Can you make a call to OntologyConceptUtil.getCuis( jcas ).forEach( System.out::println ) at the end of your pipeline? If any of the cuis are outside your dictionary then it is using some other source to get them. If not then you are getting non-dictionary events marked. Alternatively you could use the EntityCollector and/or CuiCollector singletons. If you don't want to write extra code then add one of the following cas consumers from core to the end of your pipeline: CuiCountFileWriter pretty.plaintext.PrettyTextWriterFit pretty.html.HtmlTextWriter Sean -----Original Message----- From: Erin Gustafson [mailto:[email protected]] Sent: Thursday, May 11, 2017 12:59 PM To: [email protected] Subject: RE: Temporal module dictionary Correct! -----Original Message----- From: Finan, Sean [mailto:[email protected]] Sent: Thursday, May 11, 2017 11:57 AM To: [email protected] Subject: RE: Temporal module dictionary Hi Erin, So, just to be clear, you changed line #110 in TemporalExtractionPipeline_ImplBase, the getFastPipeline() method from: builder.add( DefaultJCasTermAnnotator.createAnnotatorDescription() ); to: builder.add( DefaultJCasTermAnnotator.createAnnotatorDescription( path/to/my/config.xml ) ); Is that correct? Thanks, Sean -----Original Message----- From: Erin Gustafson [mailto:[email protected]] Sent: Thursday, May 11, 2017 12:44 PM To: [email protected] Subject: Temporal module dictionary Hi all, I would like to use the temporal module to detect temporal relations involving events specific to a phenotype. I've created a custom .bsv dictionary with a limited set of concepts relevant to that phenotype, which I have used in the past as input to the dictionary look-up algorithm. Now I'd like to try to use the same dictionary with the temporal module to limit the extracted relations to those involving events of interest. Is it possible to do this? I've plugged my dictionary in to FullTemporalExtractionPipeline, but the detected events still include concepts that fall outside my dictionary. Thanks, Erin
