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
