> 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:chasemast...@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.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.
> > > 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: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
> > >
