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From digital paula <cybersat...@hotmail.com>
Subject RE: Question pertaining to HistoryOf and SegmentID features -HistoryOf Feature Resolved
Date Tue, 03 Dec 2013 03:34:00 GMT
Just closing out HistoryOf feature and will create another thread for the sectionizer.  
 
From: Pei.Chen@childrens.harvard.edu
To: user@ctakes.apache.org
Subject: RE: Question pertaining to HistoryOf and SegmentID features
Date: Wed, 27 Nov 2013 14:42:31 +0000









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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