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From Tim Miller <timothy.mil...@childrens.harvard.edu>
Subject Re: Question pertaining to HistoryOf and SegmentID features
Date Wed, 27 Nov 2013 14:57:12 GMT
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 <mailto:chenpei@apache.org>
> To: user@ctakes.apache.org <mailto: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 
> <mailto: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 <mailto: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 
> <mailto:Pei.Chen@childrens.harvard.edu>
>
>
> To: user@ctakes.apache.org <mailto: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 
> <mailto:cybersation@hotmail.com>]
> *Sent:* Tuesday, November 26, 2013 10:00 AM
> *To:* user@ctakes.apache.org <mailto: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 
> <mailto:timothy.miller@childrens.harvard.edu>
> To: user@ctakes.apache.org <mailto: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 <mailto:cybersation@hotmail.com>
>     To: user@ctakes.apache.org <mailto: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 <mailto:mcoarr@mitre.org>
>     To: user@ctakes.apache.org <mailto: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
>     <mailto:cybersation@hotmail.com>>
>     *Reply-To: *"user@ctakes.apache.org
>     <mailto:user@ctakes.apache.org>" <user@ctakes.apache.org
>     <mailto:user@ctakes.apache.org>>
>     *Date: *Monday, 2013-11-25 15:13
>     *To: *"user@ctakes.apache.org <mailto:user@ctakes.apache.org>"
>     <user@ctakes.apache.org <mailto:user@ctakes.apache.org>>
>     *Subject: *RE: Question pertaining to HistoryOf and SegmentID features
>


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