Thanks everyone, and sorry for the delayed response. I tried adding
ddm.setSeverity(degreeOfTextRelation); as Pei suggested, but I found that
setAttributesFromOriginal is not even being called, but rather, just
mapToMentions. (It says that "with 3.1 don't need to map to proper mention
type, already creating as proper type"). I am working from the 3.1 tag.
Should I check out the trunk and see if James' changes help?
Thanks
Chase
On Mon, Mar 24, 2014 at 3:30 PM, Dligach, Dmitriy <
dmitriy.dlig...@childrens.harvard.edu> wrote:
> Hi Everybody,
>
> I wanted to clarify something in connection with this thread of emails:
>
> The relation extractor is a machine learning system. Thus, it is going to
> be pretty hard to reverse engineer it to determine why a specific mistake
> has been made... However, if there is a certain pattern, say, of location_of
> that it cannot seem to handle, it should be fixable by adding more training
> examples that annotate this pattern.
>
> Dima
>
>
>
>
> On Mar 24, 2014, at 15:21, Masanz, James J. wrote:
>
> > For the text "aneurysm in the middle cerebral artery"
> > 3.1 creates 3 location of relations
> > aneurysm : middle cerebral artery
> > aneurysm : cerebral artery
> > aneurysm : artery
> >
> > trunk also creates 3 location of relations
> > aneurysm : middle cerebral artery
> > aneurysm : cerebral artery
> > aneurysm : artery
> >
> > bodyLocation is not set for the IdentifiedAnnotation for "aneurysm" in
> either case.
> >
> > I've created CTAKES-290
> >
> > That jira issue will not address the fact the relation extractor does
> not create annotations for location of relations in "Rash on arm and leg".
> > I'll leave that determination to someone more familiar with the relation
> extractor
> >
> > -- James
> >
> > -Original Message-
> > From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
> > Sent: Monday, March 24, 2014 12:52 PM
> > To: dev@ctakes.apache.org
> > Subject: RE: getSeverity etc. for relation extractor
> >
> > Hi James, I don't have an exact phrase to use. We used the location_of
> with a brain aneurysm project, but the corpus is elsewhere now. However,
> it would tag things such as [aneurysm] : [middle cerebral artery] and
> [aneurysm] : [cerebral artery] - which is different from arm/leg, but an
> example of 2 locations for one entity.
> >
> > From: Masanz, James J. [masanz.ja...@mayo.edu]
> > Sent: Monday, March 24, 2014 11:05 AM
> > To: 'dev@ctakes.apache.org'
> > Subject: RE: getSeverity etc. for relation extractor
> >
> > I ran 3.1 against "pain in arm and leg" and I get just one location_of
> relation.
> > And again no location_of relations for "rash on arm and leg"
> >
> > Sean, what was the exact phrase you used with the incubator version?
> (or was that a while ago and lost)
> >
> > -Original Message-
> > From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
> > Sent: Friday, March 21, 2014 3:59 PM
> > To: dev@ctakes.apache.org
> > Subject: RE: getSeverity etc. for relation extractor
> >
> > Hi James,
> >
> > It is starting to resemble a row of falling dominoes ...
> >
> > I ran with an incubator version of the "location of" extractor and it
> did seem to find multiple locations for a single d/d. Functionality may
> have changed since then.
> >
> > Thanks for all of your attention to this topic.
> >
> > Sean
> >
> > -Original Message-
> > From: Masanz, James J. [mailto:masanz.ja...@mayo.edu]
> > Sent: Friday, March 21, 2014 4:34 PM
> > To: 'dev@ctakes.apache.org'
> > Subject: RE: getSeverity etc. for relation extractor
> >
> > Running from trunk, I don't get any relations for "Rash on arm and leg"
> :(
> >
> > If I change the text to "pain in arm and leg" I get one
> LocationOfTextRelation annotation with arg1=SignSymptomMention (pain) and
> arg2=AnatomicalSiteMention (arm)
> >
> > Does the relation extractor support creating a 2nd relation involving
> pain - the one between pain and leg (is this just an unfortunate choice of
> example) or does the relation extractor need enhancement before it would
> create mutiple location_of for a single SignSymptomMention or
> DiseaseDisorderMention
> >
> > BTW, I will have to debug the setting of bodyLocation in the code
> because even for "pain in arm", when running from trunk, the
> LocationOfTextRelation annotation is being created, but the bodyLocation
> within the SignSymptomMention is not being set because the code in
> TemplateFillerAnnotator expects arg1 and arg2 to be swapped from what they
> currently are. I'll take a look at what it was in cTAKES 3.1 and find out
> if this is a bug in TemplateFillerAnnotator or something else.
> >
> > -- James
> >
> > -Original Message-
> > From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
> > Sent: Friday, March 21, 2014 12:30 PM
> > To: dev@ctakes.apache.org
> > Subject: RE: getSeverity etc. for relation extractor
> >
> >> until we have a definite, well-defined nee
