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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: getSeverity etc. for relation extractor
Date Thu, 20 Mar 2014 15:25:41 GMT
 > 1) Should we populate IdentifiedAnnotation.severity() and bodylocationof() Directly in
RelationExtractorAnnotator instead of the template filler?  
  One minor issue might be the fact that multiple relations of the same type can (and most
likely will be) created for a single Identified Annotation.  Somehow a "best of" would need
to be arrived upon for storage in the IA.

> 2)Chase brought up a good point, should we add some of the commonly used components to
the defaultpipeline?  (DrugNER, RelationExtractor, TemplateFiller)? 
  One minor issue might be speed.  The longer a new user has to wait for results the less
they will enjoy their first cTakes experience.  If a user doesn't know what they are getting
and how to use it then the fruits of that additional runtime are wasted upon them.

I dislike clutter, but until it is easier to pick and choose components perhaps we could have
an "ExpertPipeline" with a fully fleshed-out workflow.  It would be great if (instead of cut
and paste) it referenced the default desc and then added the -more advanced- items to the
end.  It is just a thought.

Sean

> -----Original Message-----
> From: Chen, Pei
> Sent: Wednesday, March 19, 2014 5:58 PM
> To: dev@ctakes.apache.org
> Subject: RE: getSeverity etc. for relation extractor
> 
> Chase,
> I am not sure why or the reasoning behind this, but it might explain 
> why Severity is null for your DiseaseDisorderMention example:
> Line 319 in TemplateFillerAnnotator.java:
> 
> If I'm reading this logic correctly, it will only populate severity for
> SignSymptomMention....   Can't think of why not to populate it if it exists in
> the BinaryTextRelations-
> have you tried adding: ddm.setSeverity(degreeOfTextRelation); instead 
> of logging the error ???
> 
> 	    			if (eventMention instanceof
> DiseaseDisorderMention) {
> 	    				DiseaseDisorderMention ddm =
> (DiseaseDisorderMention) eventMention;
> 	    				logger.error("Need to implement attr for " + relation + " for 
> DiseaseDisorderMention");
> 	    			} else if (eventMention instanceof
> SignSymptomMention) {
> 	    				SignSymptomMention ssm =
> (SignSymptomMention) eventMention;
> 
> 	ssm.setSeverity(degreeOfTextRelation);
> 
> Would you mind opening a Jira attach a patch/test if it works for you?
> -Pei
> 
> > -----Original Message-----
> > From: Chase Master [mailto:chasemaster9@gmail.com]
> > Sent: Wednesday, March 19, 2014 4:09 PM
> > To: dev@ctakes.apache.org
> > Subject: Re: getSeverity etc. for relation extractor
> >
> > 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.Chen@childrens.harvard.edu>wrote:
> >
> > > If I remember correctly, I think those attributes were set in 
> > > IdentifiedAnnotation via:
> > > ctakes-template-filler/desc/analysis_engine/TemplateFillerAnnotator.
> > > xm
> > > l
> > > 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-fille
> > > r/
> > > sr
> > > c/main/java/org/apache/ctakes/template/filler/ae/TemplateFillerAnn
> > > ot
> > > at
> > > or.java
> > >
> > > --Pei
> > >
> > > > -----Original Message-----
> > > > From: Chase Master [mailto:chasemaster9@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
> > >

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