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From digital paula <cybersat...@hotmail.com>
Subject RE: Question pertaining to HistoryOf and SegmentID features
Date Thu, 28 Nov 2013 05:33:35 GMT
Hi Tim,
 
I see that....Pei is pretty quick in getting things fixed!    Yes, I'm going to test the sectionizer
next.  
 
As for now you have a wonderful Thanksgiving.  Actually, I hope everyone on this list has
a wonderful Thanksgiving.
 
Regards,
Paula
 
Date: Wed, 27 Nov 2013 09:57:12 -0500
From: timothy.miller@childrens.harvard.edu
To: user@ctakes.apache.org
Subject: Re: Question pertaining to HistoryOf and SegmentID features


  
    
  
  
    You've got to be pretty quick on the draw to beat Pei to a fix! :)
    Paula, if you're looking to contribute, I would recommend the
    sectionizer too -- it's something that at this point would be a big
    impact to me and probably a few others, and would also be the
    easiest for someone like yourself who is familiar with the basics
    and interested in learning more to get going on. I guess it only
    makes sense to spend your time on something if it will be useful to
    you, but just thought I'd let you know that testing/improving the
    sectionizer would be great bang for your buck for the community.

    Tim

    

    

    On 11/27/2013 09:42 AM, Chen, Pei
      wrote:

    
    
      
      
      
      
      
        Paula,
        It’s
            already fixed in trunk
          J;
            feel free to give it a test.
            
        https://issues.apache.org/jira/browse/CTAKES-274
        Thanks
            for pointing that out- would you like to try out the
            sectionizer?  Just curious on the use case for the
            sections.  Is it clinical research on top of plaintext
            notes?
        --Pei
         
        
          
            
              From:
                  digital paula [mailto:cybersation@hotmail.com]
                  

                  Sent: Wednesday, November 27, 2013 12:46 AM

                  To: user@ctakes.apache.org

                  Subject: RE: Question pertaining to HistoryOf
                  and SegmentID features
            
          
           
          
            Pei,

                 

                Thanks so much for the super prompt response.   A good
                reminder to us all.   When it's not working as
                expected then try a clean/rebuild to fix it.   After the
                clean/rebuild it's working as expected.

                 

                By the way,  as for your side note on whether it's worth
                updating the StatusAnnotator to populate historyOf.   
                If the Assertion module is going to be released soon
                with historyOf feature then I don't think it matters
                with updating Status Annotator historyOf feature since
                the Assertion component really is a replacement for the
                Status Annotator.   However, if it's a minor effort to
                make the Status Annotator populate historyOf, why
                not.    I'd like to fix it as my first code contribution
                to the open source community.  :-)

                 

                Regards,

                Paula
            
              
                  
                
              Date:
                  Tue, 26 Nov 2013 23:04:05 -0500

                  Subject: Re: Question pertaining to HistoryOf and
                  SegmentID features

                  From: chenpei@apache.org

                  To: user@ctakes.apache.org
              
                Paula,
                
                  Could
                      you attach the desc xml and the output xml? Also,
                      are  you using trunk?
                
                
                  Strange,
                      i'm seeing uncertainty being set to 1/history: 
                
                
                  <..DiseaseDisorderMention
                      _indexed="1" _id="299" _ref_sofa="6" begin="11"
                      end="19" id="5" _ref_ontologyConceptArr="293"
                      typeID="2" segmentID="SIMPLE_SEGMENT"
                      discoveryTechnique="1" confidence="0.0"
                      polarity="0" uncertainty="1"
                      conditional="false" generic="false" historyOf="0"
                      _ref_Segment="20"/>
                
                
                   
                
                
                  Side
                      note- Not sure if its worth updating the
                      StatusAnnotator to populate the hisoryOf attribute
                      now (obviously those types were not avail
                      previously.)
                
              
              
                 
                
                  On
                      Tue, Nov 26, 2013 at 10:37 PM, Pei Chen <chenpei@apache.org>
                      wrote:
                  
                    That
                        annotator will set the
                        IdentifiedAnnotation.*uncertainty()* with one of
                        the following values:
                    
                      HISTORY_STATUS =
                          1;
                      FAMILY_HISTORY_STATUS =
                          2;
                      PROBABLE_STATUS =
                          3;
                    
                  
                  
                    
                      
                         
                        
                          On
                              Tue, Nov 26, 2013 at 10:32 PM, digital
                              paula <cybersation@hotmail.com>
                              wrote:
                          
                            
                              Hi
                                  Pei,

                                   

                                  Thanks for the prompt response.   
                                  Okay, I uncommented out
                                  StatusAnnotator in the
                                  AggregatePlaintextPipeline
                                  config/descriptor and tried again with
                                  this text.

                                   

                                  "history of diabetes. hx diabetes.
                                  prior diabetes. "

                                   

                                  Uncertainty and HistoryOf features
                                  remained 0.....doesn't look like
                                  anything happened.    Note that I'm
                                  validating using the CVD debugger
                                  tool. 
                                  

                                   

                                  I did read something on that the
                                  Status and Assertion have overlapping
                                  functionality so I commented out
                                  Assertion and still the same thing.   
                                  I looked at the
                                  StatusIndicatorFSM.java file, text
                                  with history "hx" and "history" should
                                  be annotated so I'm not sure why it's
                                  not working.

                                   

                                  Am I missing some config?   

                                   

                                  Regards,

                                  Paula

                                   
                              
                                
                                    
                                  
                                From:
                                    
                                      Pei.Chen@childrens.harvard.edu
                                
                                  

                                      To: user@ctakes.apache.org

                                      Subject: RE: Question pertaining
                                      to HistoryOf and SegmentID
                                      features
                                
                                Date:
                                    Tue, 26 Nov 2013 20:46:12 +0000
                                
                                  
                                     
                                    
                                      Paula,

                                        If
                                          you would like to use the old
                                          status annotator for history
                                          in the interim while the new
                                          assertion module models are
                                          added.

                                        One
                                          can just uncomment the below
                                          from your
                                          AggregatePlaintextPipeline
                                          config/descriptor:

                                               
                                          
                                            <!-- 

                                                     
<node>StatusAnnotator</node>

                                                
                                          -->

                                        That
                                          annotator will set the
                                          IdentifiedAnnotation.uncertainty()
                                          with one of the following
                                          values:

                                        HISTORY_STATUS = 1;

                                        FAMILY_HISTORY_STATUS = 2;

                                        PROBABLE_STATUS = 3;

                                         

                                        --Pei

                                         
                                      
                                        
                                          
                                            From:
                                                digital paula [mailto:cybersation@hotmail.com]
                                                

                                                Sent: Tuesday,
                                                November 26, 2013 10:00
                                                AM

                                                To: user@ctakes.apache.org

                                                Subject: RE:
                                                Question pertaining to
                                                HistoryOf and SegmentID
                                                features
                                          
                                        
                                         
                                        
                                          Hi
                                              Tim,

                                               

                                              I remember you, you helped
                                              me out a while back!   I
                                              can't tell you how much
                                              that BagOfAnnotations.java
                                              file has been  a
                                              Godsend!   Thanks again
                                              for posting it last month.

                                               

                                              As for historyOf
                                              feature,   I don't so much
                                              mind performance so if you
                                              have something that
                                              works for the historyOf
                                              with just only
                                              a performance issue, I'll
                                              still take it. I do
                                              appreciate your prompt
                                              response on the historyOf
                                              feature which saved me
                                              from stepping through the
                                              code which I've done a few
                                              times....the time spent
                                               stepping through is
                                              equivalent to watching a
                                              feature film and there's a
                                              lot going on in the
                                              code that I don't
                                              understand yet.  
                                              

                                               

                                              As for sementID's with the
                                              rule-based sectionizer/segmenter,
                                               I'd like to help out with
                                              testing.     It appears
                                              that the first step is
                                              manual configuration per
                                              your email.   Pei, when
                                              you have a moment I'd like
                                              to  start with explanation
                                              of how it works then we
                                              can move forward from
                                              there.  

                                               

                                              Thanks.

                                               

                                              Regards,

                                              Paula
                                          
                                            
                                                
                                              
                                            Date:
                                                Tue, 26 Nov 2013
                                                09:24:20 -0500

                                                From: timothy.miller@childrens.harvard.edu

                                                To: user@ctakes.apache.org

                                                Subject: Re: Question
                                                pertaining to HistoryOf
                                                and SegmentID features

                                                

                                                Hi Paula,

                                                The historyOf module is
                                                currently under
                                                development, that
                                                explains those files
                                                you're seeing. As of
                                                right now we are not
                                                satisfied enough with
                                                the performance to
                                                release it publicly. It
                                                is marked 0 because it
                                                is defined as an integer
                                                field I believe, so it
                                                can't be assigned null.
                                                

                                                

                                                As for the segment IDs
                                                in your other question,
                                                the default segmenter
                                                just makes the whole
                                                document one segment
                                                because we don't yet
                                                have a module robust
                                                enough to run on notes
                                                from any institution. We
                                                have been hoping to get
                                                one developed but
                                                nothing has materialized
                                                so far. There is a
                                                rule-based
                                                sectionizer/segmenter in
                                                the cTAKES distribution
                                                but it requires some
                                                manual configuration and
                                                is not very widely
                                                tested. If you are
                                                interested in helping
                                                test it out that would
                                                be great. Pei would be
                                                the best person to
                                                explain to you how it
                                                works, we'll see if he's
                                                able to chime in.

                                                (Ah, I just checked and
                                                saw he already pointed
                                                you to it. If you want
                                                to try it we can help
                                                you get it working.)

                                                

                                                Thanks

                                                Tim

                                                

                                                
                                            
                                              On
                                                  11/25/2013 11:13 PM,
                                                  digital paula wrote:
                                            
                                            
                                              
                                                Matt,
                                                    sorry but I sent the
                                                    email by accident
                                                    and didn't finish my
                                                    thought.  Since
                                                    there's this file
                                                    (historyOf.psv) in
                                                    the Assertion folder
                                                    it gives the
                                                    impression that
                                                    Assertion can be
                                                    configured to
                                                    account for
                                                    historyOf.   Though
                                                    I tried some of the
                                                    words such as "had
                                                    diabetes" or "prior
                                                    diabetes" and value
                                                    still 0 for
                                                    historyOf
                                                    feature.  I think it
                                                    is configurable
                                                    because of the fact
                                                    the default value
                                                    for historyOf
                                                    is 0 as opposed to
                                                    <NULL> . 
                                                    Maybe I should step
                                                    through the code and
                                                    see where and when
                                                    it's assigning 0.  
                                                    

                                                     

                                                    Regards,

                                                    Paula

                                                     
                                                
                                                  
                                                      
                                                    
                                                  From: 
cybersation@hotmail.com

                                                      To: user@ctakes.apache.org

                                                      Subject: RE:
                                                      Question
                                                      pertaining to
                                                      HistoryOf and
                                                      SegmentID features

                                                      Date: Mon, 25 Nov
                                                      2013 23:09:33
                                                      -0500
                                                  
                                                    Hi Matt,

                                                         

                                                        it's me again. 
                                                        Are you sure
                                                        that
                                                        historyOf feature
                                                        can't be
                                                        configured using
                                                        Assertion.   I
                                                        was looking
                                                        around the
                                                        Assertion folder
                                                        and came
                                                        across a file
                                                        called
                                                        historyOf.psv. 
                                                        What is this?  
                                                        

                                                         

                                                        It contains the
                                                        following:

                                                       

                                                        has
                                                        been|historyOf|historyOf

                                                        

had|historyOf|historyOf

                                                        

                                                        hx of
                                                        recent|historyOf|historyOf

                                                        

                                                        hx
                                                        of|historyOf|historyOf

                                                        

hx|historyOf|historyOf

                                                        

recent|historyOf|historyOf

                                                        

s/p|historyOf|historyOf

                                                        

                                                        status
                                                        post|historyOf|historyOf

                                                        

post|historyOf|historyOf

                                                        

previous|historyOf|historyOf

                                                        

prior|historyOf|historyOf

                                                      

                                                         
                                                    
                                                      
                                                          
                                                        
                                                      From: 
mcoarr@mitre.org

                                                          To: user@ctakes.apache.org

                                                          Subject: Re:
                                                          Question
                                                          pertaining to
                                                          HistoryOf and
                                                          SegmentID
                                                          features

                                                          Date: Tue, 26
                                                          Nov 2013
                                                          02:50:59 +0000
                                                      
                                                        The
                                                          ctakes
                                                          assertion
                                                          module does
                                                          not have an
                                                          option to set
                                                          the historyOf
                                                          attribute.
                                                           The assertion
                                                          module only
                                                          sets subject,
                                                          polarity,
                                                          uncertainty,
                                                          conditional,
                                                          and generic.
                                                      
                                                      
                                                         
                                                      
                                                      
                                                        Matt
                                                      
                                                      
                                                         
                                                      
                                                      
                                                        From:
                                                          digital
                                                          paula <cybersation@hotmail.com>

                                                          Reply-To: "user@ctakes.apache.org"
                                                          <user@ctakes.apache.org>

                                                          Date: Monday,
                                                          2013-11-25
                                                          15:13

                                                          To: "user@ctakes.apache.org"
                                                          <user@ctakes.apache.org>

                                                          Subject: RE:
                                                          Question
                                                          pertaining to
                                                          HistoryOf and
                                                          SegmentID
                                                          features
                                                      
                                                      
                                                         
                                                      
                                                    
                                                  
                                                
                                              
                                            
                                             
                                          
                                        
                                      
                                    
                                  
                                
                              
                            
                          
                        
                         
                      
                    
                  
                
                 
              
            
          
        
      
    
    
 		 	   		  
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