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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: Assertion module
Date Thu, 15 Aug 2013 15:51:00 GMT
> ATTR_SUBJECT_ in edu.mayo.bmi.uima.core.type.constants.CONST, is it
> possible to meaningfully change them?
Could you clarify a bit more about meaningfully changing them?  i.e. did you mean to write
another classifier to make the subject attribute more specific? Such as "sibling, biological
father/mother?"
I presume you mean ATTR_SUBJECT* in:
http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/type/constants/CONST.java

You may find the below links helpful:
ML: http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java
And additional Rules: http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/SubjectAttributeAnalysisEngine.java

> -----Original Message-----
> From: Wu, Stephen T., Ph.D. [mailto:Wu.Stephen@mayo.edu]
> Sent: Thursday, August 15, 2013 11:49 AM
> To: dev@ctakes.apache.org
> Subject: Re: Assertion module
> 
> Hi chase,
> 
> >pipeline, which calls the Assertion module.  I noticed that for
> >something like ³Anna¹s father has had knee pain for years², the subject
> >attribute gets set to family_member.  Is it possible to be more specific?
> See below.
> 
> >
> >does it assume that the subject of every statement is the patient
> >unless the phrase suggests otherwise?
> Yes.
> 
> >If the possible values are specified by the prefix ATTR_SUBJECT_ in
> >edu.mayo.bmi.uima.core.type.constants.CONST, is it possible to
> >meaningfully change them?
> CONST does indeed include all the possible values.  It is possible to rewrite
> the Subject annotator in the assertion module such that other values can be
> assigned.  However, you would be working without "meaningful" evaluation
> on its accuracy.  In other words, if you assign "family_member" we have
> human-annotated cases of what that looks like, but if we come up with a
> new method to assign "father" we have no way to figure out whether we're
> doing a good job or not.
> 
> >Also, the value of ³confidence² is set by the assertion module.  Is the
> >score referencing the assignment of subject, or whether it¹s generic,
> >or the polarity, or other attributes?
> I believe the "confidence" number was intended to be for the named entity
> recognition (ctakes-dictionary-lookup). The newer version of assertion (in
> trunk but not the default in ctakes-clinical-pipeline) does not assign this
> value.  Matt Coarr -- any comments on what the medfacts version does?
> 
> hth
> 
> stephen


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