Return-Path: X-Original-To: apmail-ctakes-user-archive@www.apache.org Delivered-To: apmail-ctakes-user-archive@www.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id 93F0A10651 for ; Thu, 28 Nov 2013 05:34:09 +0000 (UTC) Received: (qmail 29651 invoked by uid 500); 28 Nov 2013 05:34:08 -0000 Delivered-To: apmail-ctakes-user-archive@ctakes.apache.org Received: (qmail 29552 invoked by uid 500); 28 Nov 2013 05:34:05 -0000 Mailing-List: contact user-help@ctakes.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: user@ctakes.apache.org Delivered-To: mailing list user@ctakes.apache.org Received: (qmail 29545 invoked by uid 99); 28 Nov 2013 05:34:05 -0000 Received: from nike.apache.org (HELO nike.apache.org) (192.87.106.230) by apache.org (qpsmtpd/0.29) with ESMTP; Thu, 28 Nov 2013 05:34:05 +0000 X-ASF-Spam-Status: No, hits=2.2 required=5.0 tests=HTML_MESSAGE,RCVD_IN_DNSWL_NONE,SPF_PASS X-Spam-Check-By: apache.org Received-SPF: pass (nike.apache.org: domain of cybersation@hotmail.com designates 65.54.51.92 as permitted sender) Received: from [65.54.51.92] (HELO snt0-omc4-s41.snt0.hotmail.com) (65.54.51.92) by apache.org (qpsmtpd/0.29) with ESMTP; Thu, 28 Nov 2013 05:33:57 +0000 Received: from SNT148-W14 ([65.55.90.201]) by snt0-omc4-s41.snt0.hotmail.com with Microsoft SMTPSVC(6.0.3790.4675); Wed, 27 Nov 2013 21:33:36 -0800 X-TMN: [i06hf5YWl8UyfO2wSF5NDUDE7bAtAiij] X-Originating-Email: [cybersation@hotmail.com] Message-ID: Content-Type: multipart/alternative; boundary="_731ba7df-3941-4e7c-8907-c99483d25156_" From: digital paula To: "user@ctakes.apache.org" Subject: RE: Question pertaining to HistoryOf and SegmentID features Date: Thu, 28 Nov 2013 00:33:35 -0500 Importance: Normal In-Reply-To: <52960848.60809@childrens.harvard.edu> References: ,,,,<5294AF14.3080706@childrens.harvard.edu>,,<924DE05C19409B438EB81DE683A942D910610327@CHEXMBX1A.CHBOSTON.ORG>,,, <924DE05C19409B438EB81DE683A942D910610756@CHEXMBX1A.CHBOSTON.ORG>,<52960848.60809@childrens.harvard.edu> MIME-Version: 1.0 X-OriginalArrivalTime: 28 Nov 2013 05:33:36.0222 (UTC) FILETIME=[628057E0:01CEEBFB] X-Virus-Checked: Checked by ClamAV on apache.org --_731ba7df-3941-4e7c-8907-c99483d25156_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Hi Tim=2C =20 I see that....Pei is pretty quick in getting things fixed! Yes=2C I'm go= ing to test the sectionizer next. =20 =20 As for now you have a wonderful Thanksgiving. Actually=2C I hope everyone = on this list has a wonderful Thanksgiving. =20 Regards=2C Paula =20 Date: Wed=2C 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 =0A= =0A= =0A= =0A= =0A= You've got to be pretty quick on the draw to beat Pei to a fix! :)=0A= Paula=2C if you're looking to contribute=2C I would recommend the=0A= sectionizer too -- it's something that at this point would be a big=0A= impact to me and probably a few others=2C and would also be the=0A= easiest for someone like yourself who is familiar with the basics=0A= and interested in learning more to get going on. I guess it only=0A= makes sense to spend your time on something if it will be useful to=0A= you=2C but just thought I'd let you know that testing/improving the=0A= sectionizer would be great bang for your buck for the community. =0A= Tim =0A= =20 =0A= =20 =0A= On 11/27/2013 09:42 AM=2C Chen=2C Pei=0A= wrote: =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= Paula=2C=0A= It=92s=0A= already fixed in trunk=0A= J=3B=0A= feel free to give it a test.=0A= =0A= https://issues.apache.org/jira/browse/CTAKES-274=0A= Thanks=0A= for pointing that out- would you like to try out the=0A= sectionizer? Just curious on the use case for the=0A= sections. Is it clinical research on top of plaintext=0A= notes?=0A= --Pei=0A= =0A= =0A= =0A= =0A= From:=0A= digital paula [mailto:cybersation@hotmail.com]=0A= =20 =0A= Sent: Wednesday=2C November 27=2C 2013 12:46 AM =0A= To: user@ctakes.apache.org =0A= Subject: RE: Question pertaining to HistoryOf=0A= and SegmentID features=0A= =0A= =0A= =0A= =0A= Pei=2C =0A= =20 =0A= Thanks so much for the super prompt response. A good=0A= reminder to us all. When it's not working as=0A= expected then try a clean/rebuild to fix it. After the=0A= clean/rebuild it's working as expected. =0A= =20 =0A= By the way=2C as for your side note on whether it's worth= =0A= updating the StatusAnnotator to populate historyOf. =0A= If the Assertion module is going to be released soon=0A= with historyOf feature then I don't think it matters=0A= with updating Status Annotator historyOf feature since=0A= the Assertion component really is a replacement for the=0A= Status Annotator. However=2C if it's a minor effort to=0A= make the Status Annotator populate historyOf=2C why=0A= not. I'd like to fix it as my first code contribution=0A= to the open source community. :-) =0A= =20 =0A= Regards=2C =0A= Paula=0A= =0A= =0A= =0A= =0A= Date:=0A= Tue=2C 26 Nov 2013 23:04:05 -0500 =0A= Subject: Re: Question pertaining to HistoryOf and=0A= SegmentID features =0A= From: chenpei@apache.org =0A= To: user@ctakes.apache.org=0A= =0A= Paula=2C=0A= =0A= Could=0A= you attach the desc xml and the output xml? Also=2C= =0A= are you using trunk?=0A= =0A= =0A= Strange=2C=0A= i'm seeing uncertainty being set to 1/history: =0A= =0A= =0A= <..DiseaseDisorderMention=0A= _indexed=3D"1" _id=3D"299" _ref_sofa=3D"6" begin=3D"1= 1"=0A= end=3D"19" id=3D"5" _ref_ontologyConceptArr=3D"293"= =0A= typeID=3D"2" segmentID=3D"SIMPLE_SEGMENT"=0A= discoveryTechnique=3D"1" confidence=3D"0.0"=0A= polarity=3D"0" uncertainty=3D"1"=0A= conditional=3D"false" generic=3D"false" historyOf=3D"= 0"=0A= _ref_Segment=3D"20"/>=0A= =0A= =0A= =0A= =0A= =0A= Side=0A= note- Not sure if its worth updating the=0A= StatusAnnotator to populate the hisoryOf attribute=0A= now (obviously those types were not avail=0A= previously.)=0A= =0A= =0A= =0A= =0A= =0A= On=0A= Tue=2C Nov 26=2C 2013 at 10:37 PM=2C Pei Chen =0A= wrote:=0A= =0A= That=0A= annotator will set the=0A= IdentifiedAnnotation.*uncertainty()* with one of=0A= the following values:=0A= =0A= HISTORY_STATUS =3D=0A= 1=3B=0A= FAMILY_HISTORY_STATUS =3D=0A= 2=3B=0A= PROBABLE_STATUS =3D=0A= 3=3B=0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= On=0A= Tue=2C Nov 26=2C 2013 at 10:32 PM=2C digital= =0A= paula =0A= wrote:=0A= =0A= =0A= Hi=0A= Pei=2C =0A= =20 =0A= Thanks for the prompt response. =0A= Okay=2C I uncommented out=0A= StatusAnnotator in the=0A= AggregatePlaintextPipeline=0A= config/descriptor and tried again with=0A= this text. =0A= =20 =0A= "history of diabetes. hx diabetes.=0A= prior diabetes. " =0A= =20 =0A= Uncertainty and HistoryOf features=0A= remained 0.....doesn't look like=0A= anything happened. Note that I'm=0A= validating using the CVD debugger=0A= tool. =0A= =20 =0A= =20 =0A= I did read something on that the=0A= Status and Assertion have overlapping=0A= functionality so I commented out=0A= Assertion and still the same thing. =0A= I looked at the=0A= StatusIndicatorFSM.java file=2C text=0A= with history "hx" and "history" should=0A= be annotated so I'm not sure why it's=0A= not working. =0A= =20 =0A= Am I missing some config? =20 =0A= =20 =0A= Regards=2C =0A= Paula =0A= =0A= =0A= =0A= =0A= =0A= From:=0A= =0A= Pei.Chen@childrens.harvard.edu=0A= =0A= =20 =0A= To: user@ctakes.apache.org =0A= Subject: RE: Question pertaining=0A= to HistoryOf and SegmentID=0A= features=0A= =0A= Date:=0A= Tue=2C 26 Nov 2013 20:46:12 +0000=0A= =0A= =0A= =0A= =0A= Paula=2C =0A= If=0A= you would like to use the old=0A= status annotator for history=0A= in the interim while the new=0A= assertion module models are=0A= added. =0A= One=0A= can just uncomment the below=0A= from your=0A= AggregatePlaintextPipeline=0A= config/descriptor: =0A= =0A= =0A= =0A= That=0A= annotator will set the=0A= IdentifiedAnnotation.uncertainty(= )=0A= with one of the following=0A= values: =0A= HISTORY_STATUS =3D 1=3B =0A= FAMILY_HISTORY_STATUS =3D 2=3B =0A= PROBABLE_STATUS =3D 3=3B =0A= =20 =0A= --Pei =0A= =0A= =0A= =0A= =0A= From:=0A= digital paula [mailto:cyber= sation@hotmail.com]=0A= =20 =0A= Sent: Tuesday=2C=0A= November 26=2C 2013 10:00= =0A= AM =0A= To: user@ctakes.apache.org =0A= Subject: RE:=0A= Question pertaining to=0A= HistoryOf and SegmentID=0A= features=0A= =0A= =0A= =0A= =0A= Hi=0A= Tim=2C =0A= =20 =0A= I remember you=2C you helped= =0A= me out a while back! I=0A= can't tell you how much=0A= that BagOfAnnotations.java=0A= file has been a=0A= Godsend! Thanks again=0A= for posting it last month. =0A= =20 =0A= As for historyOf=0A= feature=2C I don't so much= =0A= mind performance so if you=0A= have something that=0A= works for the historyOf=0A= with just only=0A= a performance issue=2C I'll= =0A= still take it. I do=0A= appreciate your prompt=0A= response on the historyOf=0A= feature which saved me=0A= from stepping through the=0A= code which I've done a few=0A= times....the time spent=0A= stepping through is=0A= equivalent to watching a=0A= feature film and there's a=0A= lot going on in the=0A= code that I don't=0A= understand yet. =0A= =20 =0A= =20 =0A= As for sementID's with the=0A= rule-based sectionizer/segmen= ter=2C=0A= I'd like to help out with=0A= testing. It appears=0A= that the first step is=0A= manual configuration per=0A= your email. Pei=2C when=0A= you have a moment I'd like=0A= to start with explanation=0A= of how it works then we=0A= can move forward from=0A= there. =20 =0A= =20 =0A= Thanks. =0A= =20 =0A= Regards=2C =0A= Paula=0A= =0A= =0A= =0A= =0A= Date:=0A= Tue=2C 26 Nov 2013=0A= 09:24:20 -0500 =0A= From: timothy.miller@childr= ens.harvard.edu =0A= To: user@ctakes.apache.org =0A= Subject: Re: Question=0A= pertaining to HistoryOf=0A= and SegmentID features =0A= =20 =0A= Hi Paula=2C =0A= The historyOf module is=0A= currently under=0A= development=2C that=0A= explains those files=0A= you're seeing. As of=0A= right now we are not=0A= satisfied enough with=0A= the performance to=0A= release it publicly. It=0A= is marked 0 because it=0A= is defined as an integer=0A= field I believe=2C so it=0A= can't be assigned null.=0A= =20 =0A= =20 =0A= As for the segment IDs=0A= in your other question=2C= =0A= the default segmenter=0A= just makes the whole=0A= document one segment=0A= because we don't yet=0A= have a module robust=0A= enough to run on notes=0A= from any institution. We=0A= have been hoping to get=0A= one developed but=0A= nothing has materialized=0A= so far. There is a=0A= rule-based=0A= sectionizer/segmenter in=0A= the cTAKES distribution=0A= but it requires some=0A= manual configuration and=0A= is not very widely=0A= tested. If you are=0A= interested in helping=0A= test it out that would=0A= be great. Pei would be=0A= the best person to=0A= explain to you how it=0A= works=2C we'll see if he's= =0A= able to chime in. =0A= (Ah=2C I just checked and= =0A= saw he already pointed=0A= you to it. If you want=0A= to try it we can help=0A= you get it working.) =0A= =20 =0A= Thanks =0A= Tim =0A= =20 =0A= =0A= =0A= On=0A= 11/25/2013 11:13 PM=2C=0A= digital paula wrote:=0A= =0A= =0A= =0A= Matt=2C=0A= sorry but I sent the=0A= email by accident=0A= and didn't finish my=0A= thought. Since=0A= there's this file=0A= (historyOf.psv) in=0A= the Assertion folder=0A= it gives the=0A= impression that=0A= Assertion can be=0A= configured to=0A= account for=0A= historyOf. Though=0A= I tried some of the=0A= words such as "had=0A= diabetes" or "prior=0A= diabetes" and value=0A= still 0 for=0A= historyOf=0A= feature. I think it=0A= is configurable=0A= because of the fact=0A= the default value=0A= for historyOf=0A= is 0 as opposed to=0A= . =0A= Maybe I should step=0A= through the code and=0A= see where and when=0A= it's assigning 0. =0A= =20 =0A= =20 =0A= Regards=2C =0A= Paula =0A= =0A= =0A= =0A= =0A= =0A= From: =0A= cybersation@hotmail.com =0A= To: user@ctakes.apach= e.org =0A= Subject: RE:=0A= Question=0A= pertaining to=0A= HistoryOf and=0A= SegmentID features =0A= Date: Mon=2C 25 Nov= =0A= 2013 23:09:33=0A= -0500=0A= =0A= Hi Matt=2C =0A= =20 =0A= it's me again. =0A= Are you sure=0A= that=0A= historyOf feature= =0A= can't be=0A= configured using=0A= Assertion. I=0A= was looking=0A= around the=0A= Assertion folder=0A= and came=0A= across a file=0A= called=0A= historyOf.psv. =0A= What is this? =0A= =20 =0A= =20 =0A= It contains the=0A= following: =0A= =20 =0A= has=0A= been|historyOf|hist= oryOf =0A= =20 =0A= had|historyOf|historyOf =0A= =20 =0A= hx of=0A= recent|historyOf|hi= storyOf =0A= =20 =0A= hx=0A= of|historyOf|histor= yOf =0A= =20 =0A= hx|historyOf|historyOf =0A= =20 =0A= recent|historyOf|historyOf =0A= =20 =0A= s/p|historyOf|historyOf =0A= =20 =0A= status=0A= post|historyOf|hist= oryOf =0A= =20 =0A= post|historyOf|historyOf =0A= =20 =0A= previous|historyOf|historyOf =0A= =20 =0A= prior|historyOf|historyOf =0A= =20 =0A= =0A= =0A= =0A= =0A= =0A= From: =0A= mcoarr@mitre.org =0A= To: user@ctakes.a= pache.org =0A= Subject: Re:=0A= Question=0A= pertaining to=0A= HistoryOf and=0A= SegmentID=0A= features =0A= Date: Tue=2C 26= =0A= Nov 2013=0A= 02:50:59 +0000=0A= =0A= The=0A= ctakes=0A= assertion=0A= module does=0A= not have an=0A= option to set=0A= the historyOf=0A= attribute.=0A= The assertion=0A= module only=0A= sets subject=2C= =0A= polarity=2C=0A= uncertainty=2C=0A= conditional=2C=0A= and generic.=0A= =0A= =0A= =0A= =0A= =0A= Matt=0A= =0A= =0A= =0A= =0A= =0A= From:=0A= digital=0A= paula =0A= Reply-To: "user@c= takes.apache.org"=0A= =0A= Date: Monday=2C= =0A= 2013-11-25=0A= 15:13 =0A= To: "user@ctakes.= apache.org"=0A= =0A= Subject: RE:=0A= Question=0A= pertaining to=0A= HistoryOf and=0A= SegmentID=0A= features=0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =0A= =20 = --_731ba7df-3941-4e7c-8907-c99483d25156_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable
Hi Tim=2C
 =3B
I see t= hat....Pei =3Bis pretty =3Bquick in getting things fixed! =3B&n= bsp=3B =3B Yes=2C I'm going to =3Btest the sectionizer next. = =3B =3B
 =3B
As for now you have a wonderful Thanksgiving.&nb= sp=3B Actually=2C I hope everyone on this list has a wonderful Thanksgiving= .
 =3B
Regards=2C
Paula
 =3B
Date: Wed=2C 27 Nov 2013 09:57:12 -0500
From: timothy.miller@child= rens.harvard.edu
To: user@ctakes.apache.org
Subject: Re: Question per= taining to HistoryOf and SegmentID features

=0A= =0A= =0A= =0A= =0A= You've got to be pretty quick on the draw to beat Pei to a fix! :)=0A= Paula=2C if you're looking to contribute=2C I would recommend the=0A= sectionizer too -- it's something that at this point would be a big=0A= impact to me and probably a few others=2C and would also be the=0A= easiest for someone like yourself who is familiar with the basics=0A= and interested in learning more to get going on. I guess it only=0A= makes sense to spend your time on something if it will be useful to=0A= you=2C but just thought I'd let you know that testing/improving the=0A= sectionizer would be great bang for your buck for the community.
=0A= Tim
=0A=
=0A=
=0A=
On 11/27/2013 09:42 AM=2C Chen=2C Pei= =0A= wrote:
=0A=
=0A=
=0A= =0A= =0A= =0A= =0A=
=0A=

Paula=2C<= /span>

=0A=

It=92s=0A= already fixed in trunk=0A= J= =3B=0A= feel free to give it a test.=0A=

=0A=

https://issues.apache.org/jira/browse= /CTAKES-274

=0A=

Thanks=0A= for pointing that out- would you like to try out the=0A= sectionizer? =3B Just curious on the use case for the=0A= sections. =3B Is it clinical research on top of plaintext= =0A= notes?

=0A=

--Pei

=0A=

 =3B<= /span>

=0A=
=0A=
=0A=
=0A=

From:=0A= digital paula [mailto:cybersation@hotmail.com]=0A=
=0A= Sent: Wednesday=2C November 27=2C 2013 12:46 AM=0A= To: user@ctakes.apache.org
=0A= Subject: RE: Question pertaining to HistoryOf=0A= and SegmentID features

=0A=
=0A=
=0A=

 =3B

=0A=
=0A=

Pei=2C
=0A=  =3B
=0A= Thanks so much for the super =3Bprompt response. = =3B =3B =3BA good=0A= reminder to us all. =3B =3B When =3Bit's not wo= rking as=0A= expected =3Bthen try a clean/rebuild to fix it. =3B=  =3B After the=0A= clean/rebuild it's working as expected.
=0A=  =3B
=0A= By the way=2C =3B =3Bas for your side note on wheth= er it's worth=0A= updating the StatusAnnotator to populate historyOf. =3B=  =3B =3B=0A= If the Assertion module is going to be released soon=0A= with historyOf feature then I don't think it matters=0A= with updating Status Annotator historyOf feature since=0A= the Assertion component really is a replacement for the=0A= Status Annotator. =3B =3B However=2C if it's a = =3Bminor effort to=0A= make the Status Annotator populate historyOf=2C why=0A= not. =3B =3B =3B I'd like to fix it as my first= code contribution=0A= to the open source community. =3B =3B:-)
=0A=  =3B
=0A= Regards=2C
=0A= Paula

=0A=
=0A=
= =0A=
=0A=
=0A=

Date:=0A= Tue=2C 26 Nov 2013 23:04:05 -0500
=0A= Subject: Re: Question pertaining to HistoryOf and=0A= SegmentID features
=0A= From: chenpei@apach= e.org
=0A= To: user@ctakes= .apache.org

=0A=
=0A=

Paula=2C

=0A=
=0A=

Could=0A= you attach the desc xml and the output xml? Also=2C= =0A= are  =3Byou using trunk?

=0A=
=0A=
=0A=

Strange=2C=0A= i'm seeing uncertainty being set to 1/history: = =3B

=0A=
=0A=
=0A=

<=3B..DiseaseDisorderMention=0A= _indexed=3D"1" _id=3D"299" _ref_sofa=3D"6" begin=3D"1= 1"=0A= end=3D"19" id=3D"5" _ref_ontologyConceptArr=3D"293"= =0A= typeID=3D"2" segmentID=3D"SIMPLE_SEGMENT"=0A= discoveryTechnique=3D"1" confidence=3D"0.0"=0A= polarity=3D"0" uncertainty=3D"1"=0A= conditional=3D"false" generic=3D"false" historyOf=3D"= 0"=0A= _ref_Segment=3D"20"/>=3B

=0A=
=0A=
=0A=

 =3B

=0A=
=0A=
=0A=

Side=0A= note- Not sure if its worth updating the=0A= StatusAnnotator to populate the hisoryOf attribute=0A= now (obviously those types were not avail=0A= previously.)

=0A=
=0A=
=0A=
=0A=

 =3B

=0A=
=0A=

On=0A= Tue=2C Nov 26=2C 2013 at 10:37 PM=2C Pei Chen <=3B<= a href=3D"mailto:chenpei@apache.org" target=3D"_blank">chenpei@apache.org>=3B=0A= wrote:

=0A=
=0A=

That=0A= annotator will set the=0A= IdentifiedAnnotation.*uncertainty()* with one of=0A= the following values:

=0A=
=0A=

HISTORY_ST= ATUS=  =3B=3D=0A= 1=3B

=0A=

FAMILY_HIS= TORY_STATUS =3B=3D=0A= 2=3B

=0A=

PROBABLE_S= TATUS =3B=3D=0A= 3=3B

=0A=
=0A=
=0A=
=0A=
=0A=
=0A=

 =3B

=0A=
=0A=

On=0A= Tue=2C Nov 26=2C 2013 at 10:32 PM=2C digital= =0A= paula <=3Bcybersation@hotmail.com>=3B=0A= wrote:

=0A=
=0A=
=0A=

Hi=0A= Pei=2C
=0A=  =3B
=0A= Thanks for the prompt response. =3B&n= bsp=3B =3B=0A= Okay=2C I uncommented out=0A= StatusAnnotator in the=0A= AggregatePlaintextPipeline=0A= config/descriptor and tried again with=0A= this text.
=0A=  =3B
=0A= "history of diabetes. hx diabetes.=0A= prior diabetes. =3B"
=0A=  =3B
=0A= Uncertainty and HistoryOf features=0A= remained 0.....doesn't look like=0A= anything happened. =3B =3B = =3B Note that I'm=0A= validating using the CVD debugger=0A= tool. =3B=0A=
=0A=  =3B
=0A= I did =3Bread something =3Bon tha= t the=0A= Status and Assertion have overlapping=0A= functionality so I commented out=0A= Assertion and still the same thing. = =3B =3B =3B=0A= I looked at the=0A= StatusIndicatorFSM.java file=2C text=0A= with history "hx" and "history" should=0A= be annotated so I'm not sure why it's=0A= not working.
=0A=  =3B
=0A= Am I missing some config? =3B =3B=
=0A=  =3B
=0A= Regards=2C
=0A= Paula
=0A=  =3B

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From:=0A= =0A= Pei.Chen@childrens.harvard.edu

=0A=
=0A=


=0A= To: user@ctakes.apache.org
=0A= Subject: RE: Question pertaining=0A= to HistoryOf and SegmentID=0A= features

=0A=
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Date:=0A= Tue=2C 26 Nov 2013 20:46:12 +0000

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 =3B

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Paula=2C
=0A= If=0A= you would like to use the old=0A= status annotator for history=0A= in the interim while the new=0A= assertion module models are=0A= added.
=0A= One=0A= can just uncomment the below=0A= from your=0A= AggregatePlaintextPipeline=0A= config/descriptor:
=0A=  =3B =3B =3B =3B =3B&nb= sp=3B =3B=0A= =0A= <=3B!--
=0A=  =3B&nbs= p=3B =3B =3B =3B =3B =3B =3B =3B =3B = =3B =3B =3B=0A= <=3Bnode>=3BStatusAnnotator<=3B/node>=3B
=0A=  =3B&nbs= p=3B =3B =3B =3B =3B =3B =3B=0A= -->=3B
=0A= That=0A= annotator will set the=0A= IdentifiedAnnotation.uncertainty(= )=0A= with one of the following=0A= values:
=0A= HISTORY_STA= TUS = =3D 1=3B=0A= FAMILY_HIST= ORY_STATUS =3D 2=3B
=0A= PROBABLE_ST= ATUS= =3D 3=3B=0A=  =3B
=0A= --Pei<= br>=0A=  =3B

=0A=
= =0A=
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Fr= om:=0A= digital paula [mailto:cybersation@hotmail= .com]=0A=
=0A= Sent: Tuesday=2C=0A= November 26=2C 2013 10:00= =0A= AM
=0A= To: user@ctakes.apache.org
= =0A= Subject: RE:=0A= Question pertaining to=0A= HistoryOf and SegmentID=0A= features

=0A=
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 =3B

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Hi=0A= Tim=2C
=0A=  =3B
=0A= I remember you=2C you helped= =0A= me out a while back! =3B&= nbsp=3B I=0A= can't tell you how much=0A= that BagOfAnnotations.java=0A= file has been =3B a=0A= Godsend! =3B =3B Than= ks again=0A= for posting it =3Blast mo= nth.
=0A=  =3B
=0A= As for historyOf=0A= feature=2C =3B =3B&nb= sp=3BI don't so much=0A= mind performance so if you=0A= have something that=0A= works =3Bfor the historyO= f=0A= with just =3Bonly=0A= a =3Bperformance issue=2C= I'll=0A= still take it. =3BI do=0A= appreciate your prompt=0A= response on the historyOf=0A= feature which saved me=0A= from stepping through the=0A= code which I've done a few=0A= times....the time spent=0A=  =3Bstepping through = =3Bis=0A= equivalent to watching a=0A= feature film and there's a=0A= lot going on in the=0A= code =3Bthat I don't=0A= understand yet. =3B = =3B=0A=
=0A=  =3B
=0A= As for sementID's with the=0A= rule-based =3Bsectionizer= /segmenter=2C=0A=  =3BI'd like to =3Bhe= lp out with=0A= testing. =3B =3B = =3B =3B It appears=0A= that the first step is=0A= manual configuration per=0A= your email. =3B =3B P= ei=2C when=0A= you have a moment I'd like=0A= to =3B start with explana= tion=0A= of how it works then we=0A= can move forward from=0A= there. =3B =3B
=0A=  =3B
=0A= Thanks.
=0A=  =3B
=0A= Regards=2C
=0A= Paula

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Date:=0A= Tue=2C 26 Nov 2013=0A= 09:24:20 -0500
=0A= From: timothy.miller@childre= ns.harvard.edu
=0A= To: user@ctakes.apache.org
=0A= Subject: Re: Question=0A= pertaining to HistoryOf=0A= and SegmentID features
= =0A=
=0A= Hi Paula=2C
=0A= The historyOf module is=0A= currently under=0A= development=2C that=0A= explains those files=0A= you're seeing. As of=0A= right now we are not=0A= satisfied enough with=0A= the performance to=0A= release it publicly. It=0A= is marked 0 because it=0A= is defined as an integer=0A= field I believe=2C so it=0A= can't be assigned null.=0A=
=0A=
=0A= As for the segment IDs=0A= in your other question=2C= =0A= the default segmenter=0A= just makes the whole=0A= document one segment=0A= because we don't yet=0A= have a module robust=0A= enough to run on notes=0A= from any institution. We=0A= have been hoping to get=0A= one developed but=0A= nothing has materialized=0A= so far. There is a=0A= rule-based=0A= sectionizer/segmenter in=0A= the cTAKES distribution=0A= but it requires some=0A= manual configuration and=0A= is not very widely=0A= tested. If you are=0A= interested in helping=0A= test it out that would=0A= be great. Pei would be=0A= the best person to=0A= explain to you how it=0A= works=2C we'll see if he's= =0A= able to chime in.
=0A= (Ah=2C I just checked and= =0A= saw he already pointed=0A= you to it. If you want=0A= to try it we can help=0A= you get it working.)
=0A=
=0A= Thanks
=0A= Tim
=0A=
=0A=

=0A=
=0A=

On=0A= 11/25/2013 11:13 PM=2C=0A= digital paula wrote:

=0A=
=0A=
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=0A=

<= span style=3D'font-family: "Calibri"=2C"sans-serif"=3B'>Matt=2C=0A= sorry =3Bbut I sent= the=0A= email by accident=0A= and didn't finish my=0A= thought. =3B = =3BSince=0A= there's this file=0A= (historyOf.psv) in=0A= the Assertion folder=0A= it gives the=0A= impression that=0A= Assertion can be=0A= configured to=0A= account for=0A= historyOf. =3B = =3B Though=0A= I tried some of the=0A= words such as "had=0A= diabetes" or "prior=0A= diabetes" =3Band va= lue=0A= still 0 for=0A= historyOf=0A= feature. =3B = =3BI think it=0A= is configurable=0A= because of the =3Bf= act=0A= the =3Bdefault valu= e=0A= for historyOf=0A= is =3B0 =3Bas o= pposed to=0A= <=3BNULL>=3B = =3B. =3B=0A= Maybe I should step=0A= through the code and=0A= see where and when=0A= it's assigning 0. = =3B =3B=0A=
=0A=  =3B
=0A= Regards=2C
=0A= Paula
=0A=  =3B

=0A=
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From: =0A= cybersation@hotmail.com
=0A= To: user@ctakes.apache.org
= =0A= Subject: RE:=0A= Question=0A= pertaining to=0A= HistoryOf and=0A= SegmentID features=0A= Date: Mon=2C 25 Nov= =0A= 2013 23:09:33=0A= -0500

=0A=
=0A=

Hi Matt=2C
= =0A=  =3B
=0A= it's me again. = =3B=0A= Are you sure=0A= that=0A= historyOf =3Bfe= ature=0A= can't be=0A= configured using=0A= Assertion. =3B&= nbsp=3B I=0A= was looking=0A= around the=0A= Assertion folder=0A= and came=0A= across =3Ba&nbs= p=3Bfile=0A= called=0A= historyOf.psv. = =3B=0A= What is this? = =3B =3B=0A=
=0A=  =3B
=0A= It contains the=0A= following:
=0A=  =3B
=0A= has=0A= been|historyOf|hist= oryOf
=0A=
=0A= had|historyOf|historyOf
=0A=
=0A= hx of=0A= recent|historyOf|hi= storyOf
=0A=
=0A= hx=0A= of|historyOf|histor= yOf
=0A=
=0A= hx|historyOf|historyOf
=0A=
=0A= recent|historyOf|historyOf
=0A=
=0A= s/p|historyOf|historyOf
=0A=
=0A= status=0A= post|historyOf|hist= oryOf
=0A=
=0A= post|historyOf|historyOf
=0A=
=0A= previous|historyOf|historyOf
=0A=
=0A= prior|historyOf|historyOf
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From: =0A= mcoarr@mitre.org
=0A= To: user@ctakes.apache.org=0A= Subject: Re:=0A= Question=0A= pertaining to=0A= HistoryOf and=0A= SegmentID=0A= features
=0A= Date: Tue=2C 26= =0A= Nov 2013=0A= 02:50:59 +0000

=0A=
=0A=

The=0A= ctakes=0A= assertion=0A= module does=0A= not have an=0A= option to set=0A= the historyOf=0A= attribute.=0A=  =3BThe asser= tion=0A= module only=0A= sets subject=2C= =0A= polarity=2C=0A= uncertainty=2C=0A= conditional=2C=0A= and generic.

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Matt=

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 =3B

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From:=0A= digit= al=0A= paula <=3Bcybersation@hotmail= .com>=3B
=0A= Reply-To: = "user@ctakes.ap= ache.org"=0A= <=3Buser@ctakes.apache.org= >=3B
=0A= Date: Mond= ay=2C=0A= 2013-11-25=0A= 15:13
=0A= To: "user@ctakes.apache.o= rg"=0A= <=3Buser@ctakes.apache.org= >=3B
=0A= Subject: R= E:=0A= Question=0A= pertaining to=0A= HistoryOf and=0A= SegmentID=0A= features

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