Thanks, I tried using the AggregateTemplateFiller.xml from the template-filler module, and I specified the relation extractor pipeline that I was using before from the relation-extractor project (there is also a different one in the template-filler project called "RelationExtractorAggregateWithoutOrangeBook"). However, I don't see a difference, the severity is still null.
Just wondering - is there some reason that the TemplateFiller is not included by default? It seems confusing that there are getters for properties that aren't set in general ...even when one runs the default clinical pipeline instead of the RelationExtractorAggregate, these getters are there, but there are no relations. Thanks Chase On Wed, Mar 19, 2014 at 1:04 PM, Chen, Pei <pei.c...@childrens.harvard.edu>wrote: > If I remember correctly, I think those attributes were set in > IdentifiedAnnotation via: > ctakes-template-filler/desc/analysis_engine/TemplateFillerAnnotator.xml > One can look at the logic in: > org.apache.ctakes.template.filler.ae.TemplateFillerAnnotator [1] > > Have you tried added that to the pipeline? > > [1] > http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-template-filler/src/main/java/org/apache/ctakes/template/filler/ae/TemplateFillerAnnotator.java > > --Pei > > > -----Original Message----- > > From: Chase Master [mailto:chasemast...@gmail.com] > > Sent: Wednesday, March 19, 2014 1:56 PM > > To: dev@ctakes.apache.org > > Subject: getSeverity etc. for relation extractor > > > > Hi, > > > > I am trying to output the relations associated with > DiseaseDisorderMentions > > and other types. But I want to start by iterating over > > DiseaseDisorderMention, not BinaryTextRelations since I want to be sure > to > > find them all, even if they have no associated relation. > > > > I always get null when using any of the getters like "getSeverity()". I > am > > using the example text "He had a slight fracture in the proximal right > fibula". > > When I iterate over BinaryTextRelations, I see the following valid > values: > > BinaryTextRelation slightFracture = iterator.next(); > > slightFracture.getArg1().getArgument().getCoveredText() is "fracture" > > slightFracture.getArg2().getArgument().getCoveredText() is "slight". > > However, for the "fracture" DiseaseDisorderMention, getSeverity() is > null. > > If it wasn't, I would then grab > > disease.getSeverity().getArg1().getArgument().getCoveredText(), or for > > Arg2. > > > > Thanks, > > Chase >
