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 BAE4B10600 for ; Wed, 25 Sep 2013 13:59:50 +0000 (UTC) Received: (qmail 7595 invoked by uid 500); 25 Sep 2013 13:59:50 -0000 Delivered-To: apmail-ctakes-user-archive@ctakes.apache.org Received: (qmail 7414 invoked by uid 500); 25 Sep 2013 13:59:45 -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 7292 invoked by uid 99); 25 Sep 2013 13:59:43 -0000 Received: from athena.apache.org (HELO athena.apache.org) (140.211.11.136) by apache.org (qpsmtpd/0.29) with ESMTP; Wed, 25 Sep 2013 13:59:43 +0000 X-ASF-Spam-Status: No, hits=2.2 required=5.0 tests=HTML_MESSAGE,RCVD_IN_DNSWL_NONE,SPF_PASS,T_FRT_BELOW2 X-Spam-Check-By: apache.org Received-SPF: pass (athena.apache.org: local policy) Received: from [98.138.120.48] (HELO nm41.bullet.mail.ne1.yahoo.com) (98.138.120.48) by apache.org (qpsmtpd/0.29) with ESMTP; Wed, 25 Sep 2013 13:59:36 +0000 Received: from [127.0.0.1] by nm41.bullet.mail.ne1.yahoo.com with NNFMP; 25 Sep 2013 13:59:14 -0000 Received: from [98.138.90.56] by nm41.bullet.mail.ne1.yahoo.com with NNFMP; 25 Sep 2013 13:56:34 -0000 Received: from [98.139.212.149] by tm9.bullet.mail.ne1.yahoo.com with NNFMP; 25 Sep 2013 13:56:34 -0000 Received: from [98.139.212.196] by tm6.bullet.mail.bf1.yahoo.com with NNFMP; 25 Sep 2013 13:56:34 -0000 Received: from [127.0.0.1] by omp1005.mail.bf1.yahoo.com with NNFMP; 25 Sep 2013 13:56:34 -0000 X-Yahoo-Newman-Property: ymail-4 X-Yahoo-Newman-Id: 192200.56797.bm@omp1005.mail.bf1.yahoo.com Received: (qmail 63043 invoked by uid 60001); 25 Sep 2013 13:56:34 -0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=yahoo.com; s=s1024; t=1380117394; bh=1j6TqKkfTCmpQMX7XqoKQQ3ylmpI1X/384NvspyXP5E=; h=X-YMail-OSG:Received:X-Rocket-MIMEInfo:X-Mailer:References:Message-ID:Date:From:Reply-To:Subject:To:In-Reply-To:MIME-Version:Content-Type; b=6RCS39Zp+hXezDF69YFR0nVRjJZug4F/NrFc+ikczwV5fBsH3aomklW1/7bgJEeHIawNnk9uYrm0PEbZDFzHxfrFGGdcGMD3yPnhjxMLZx7GZ+omuul6wtN5B/v6GA43xHh/R3y4sGPkJhLkzXOYgRCBNfB49gZuetJCTRAyIxE= DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=X-YMail-OSG:Received:X-Rocket-MIMEInfo:X-Mailer:References:Message-ID:Date:From:Reply-To:Subject:To:In-Reply-To:MIME-Version:Content-Type; b=ZJofjW42bpqrQGgbpJq/w/GM8YEeDkuwUy1+fEZePoXs5ILKgQseg7ptyOerJIjv44E7DpTZrZnMNbY0eUsCQVdV9GJkTBUHwKCshTClW+9WSucJmXOWbVExM/A//KmTIHyjKiqUTRfBmJZ1BvtDNQWX5bjnbXUbDoABI0oWIcc=; X-YMail-OSG: UKuj3noVM1loBFGcSjTH57Ets2ntg1SutRuPbZu5wluxYfu dvPON87X5bWHl3IBqB5..ftDGNysuv7ZsWeLu8VWFioHLdFharZ07quNO4ow LPUUKyY6kD02.rBlcZxHmXePrzzpopyIZwS89NM5VB3dWRUfCbISknqkquJU lkXWL57Ox.LxGbwoZ4M9ZdlaDIO4pfyc96Xf0cfy9pOE9lbNux6_7Y0edwUC 3pbdjrTRTxad.c6yrRP04ebRAzeIjkmINa5lPBpPYyFMnGmLwvO7dVSjUzF9 UAhU2d7oZnWD24GwuLNAVK4Xn4p6iAQQHI9_mlBM.yVRQ2re9AU4WgQWXFi9 xuHRGvIbNzrxLSHYkqMmwRY4sdeXdIaU20OubIRWf9TOObxJoX.nKZqO0P.w jijqV9TvBCS7f5VHs_VzTrhVU_VtIi1ZOLKbZQtTqIEnXqMIioHc4tOzFDgo KQF7KBakVCf4pBrqbnFrMBVjrNJ_i_O9bgnY9z.Y3ROaLuZPA4joDDwXEIVw KZRENSjhVy3rJtpj30ZellF3HaE_lFCpaXzDaso0h2EXUlxhLYR50ROdfEsS GRvjw3Cw09dR2fiujo6COGsR98._M88FodpGHKYl6ms75andNjyt4rJ5wq8h SBh50v5YMQAg8.EHPDXtkFg1aBd6RHlheM3lt Received: from [132.213.8.3] by web140306.mail.bf1.yahoo.com via HTTP; Wed, 25 Sep 2013 06:56:33 PDT X-Rocket-MIMEInfo: 002.001,VGhhbmtzIERpbWEgZm9yIHRoZXNlIGV4dHJhIGluZm8uIHRoYXQgbWF5IGhlbHAgbWUKSSdsbCB0cnkgaXQgYW5kIGxldCB5b3Uga25vdy4KU2FtaXIKCgoKCl9fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fCiBGcm9tOiBEbWl0cml5IERsaWdhY2ggPGRtaXRyaXkuZGxpZ2FjaEBjaGlsZHJlbnMuaGFydmFyZC5lZHU.ClRvOiBkZXZAY3Rha2VzLmFwYWNoZS5vcmc7IHNhbWlyIGNoYWJvdSA8c2FtaXJjaGJAeWFob28uY29tPjsgInVzZXJAY3Rha2VzLmFwYWNoZS5vcmciIDx1c2VyQGN0YWtlcy5hcGEBMAEBAQE- X-Mailer: YahooMailWebService/0.8.157.561 References: <996FC801C05DF64A84246A106FACACD01BA8CC@MSGPEXCHA08A.mfad.mfroot.org> <924DE05C19409B438EB81DE683A942D9105AFACA@CHEXMBX1A.CHBOSTON.ORG> <1379775648.14371.YahooMailNeo@web140304.mail.bf1.yahoo.com> <5240A6CB.1040301@childrens.harvard.edu> <1379976224.70868.YahooMailNeo@web140302.mail.bf1.yahoo.com> <5241F963.4010100@childrens.harvard.edu> Message-ID: <1380117393.62690.YahooMailNeo@web140306.mail.bf1.yahoo.com> Date: Wed, 25 Sep 2013 06:56:33 -0700 (PDT) From: samir chabou Reply-To: samir chabou Subject: Re: examples of relation extractor annotations To: "dev@ctakes.apache.org" , "user@ctakes.apache.org" In-Reply-To: <5241F963.4010100@childrens.harvard.edu> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="-655264479-1486549426-1380117393=:62690" X-Virus-Checked: Checked by ClamAV on apache.org ---655264479-1486549426-1380117393=:62690 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Thanks Dima for these extra info. that may help me=0AI'll try it and let yo= u know.=0ASamir=0A=0A=0A=0A=0A________________________________=0A From: Dmi= triy Dligach =0ATo: dev@ctakes.apach= e.org; samir chabou ; "user@ctakes.apache.org" =0ASent: Tuesday, September 24, 2013 4:43:15 PM=0ASubject:= Re: examples of relation extractor annotations=0A =0A=0ASamir,=0A=0AActual= ly, the relations are represented in the type system differently. =0APlease= take a look at the BinaryTextRelation type. If you'd like an =0Aexample of= how to iterate over the relations, take a look at =0Actakes-relation-extra= ctor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationEx= tractorConsumer.java. =0AOnce you get a hold of each BinaryTextRelation, yo= u can determine the =0Arelation type by looking at the 'category' attribute= .=0A=0ADima=0A=0AOn 09/23/2013 06:43 PM, samir chabou wrote:=0A> Hi Dima,= =0A>=0A> I run RelationExtractorPipelineSingleCas.java and i got=0A> degree= _of(severe pain/3, severe/2)=0A> degree_of(pain/3, severe/2)=0A> location_o= f(pain/3, wrists/6)=0A>=0A> but when i run UIMA_CVD--relation-extractor.lau= nch - or UIMA_CPE--relation-extractor.launch=A0 on the hurd coded text=A0 "= He still is not able to work because of severe pain involving his wrists." = there is no annotation of type:=0A> org.apache.ctakes.typesystem.type.relat= ion.LocationOf=0A> org.apache.ctakes.typesystem.type.relation.DegreeOf=0A>= =0A>=0A> I need to identify the relations=A0 by their annotation type so i = can iterate on them=0A>=0A> Thanks=0A> Samir=0A>=0A>=0A>=0A>=0A> __________= ______________________=0A>=A0 From: Dmitriy Dligach =0A> To: dev@ctakes.apache.org; samir chabou ; "user@ctakes.apache.org" =0A> Sent: Monday= , September 23, 2013 4:38:35 PM=0A> Subject: Re: examples of relation extra= ctor annotations=0A>=A0 =0A>=0A> Samir,=0A>=0A> Could you please try to run= ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextracto= r/pipelines/RelationExtractorPipelineSingleCas.java and see if it finds any= relations in the hard-coded sample sentence. In that sentence=0A>=0A> "He = still is not able to work because of severe pain involving his wrists."=0A>= =0A> you should see the following relations:=0A>=0A> degree_of(severe pain/= 3, severe/2)=0A> degree_of(pain/3, severe/2)=0A> location_of(pain/3, wrists= /6)=0A>=0A> which will be printed to the console. The numbers next to each = argument are the UMLS semantic types (e.g. 6 =3D anatomical site).=0A>=0A> = Dima=0A>=0A> On 09/21/2013 11:00 AM, samir chabou wrote:=0A>> Hi,=0A>> I tr= ied to get examples of relation extractor annotations using RelationExtract= orAggregate.xml. I tried the RelationExtractorAggregate on many input medic= al text but there was no annotation for any kind of relation. I even tried = the bellow text used in RelationExtractorAnnotatorsTest but again no relati= on is annotated. Do you have idea or am i missing some thing ?=0A>>=A0 =A0 = =A0 =A0 =A0 "He had a slight fracture in the proximal right fibula.",=0A>>= =A0 =A0 =A0 =A0 =A0 =A0 "He had a slight fracture in the proximal right fib= ula .",=0A>>=A0 =A0 =A0 =A0 =A0 =A0 "PRP VBD DT JJ NN IN DT JJ JJ NN .");= =0A>>=0A>>=0A>> Thanks=0A>> Samir=0A>>=0A> -- Dmitriy Dligach, PhD=0A> Rese= arch Fellow=0A> Children's Hospital Informatics Program=0A> Boston Children= 's Hospital and Harvard Medical School=0A> (617) 919-3596=0A=0A-- =0ADmitri= y Dligach, PhD=0AResearch Fellow=0AChildren's Hospital Informatics Program= =0ABoston Children's Hospital and Harvard Medical School=0A(617) 919-3596 ---655264479-1486549426-1380117393=:62690 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Thanks Dima for these= extra info. that may help me
I'll try it and let you know.
Samir
=


From: Dmitriy Dligach <dmitriy.dligac= h@childrens.harvard.edu>
To: dev@ctakes.apache.org; samir chabou <samirchb@yahoo.com>; "= user@ctakes.apache.org" <user@ctakes.apache.org>
Sent: Tuesday, September 24, 2013 4:43:1= 5 PM
Subject: Re: exam= ples of relation extractor annotations
Samir,

Actually, the relations are represented in the type system = differently.
Please take a look at the BinaryTextRelation type. If you'= d like an
example of how to iterate over the relations, take a look at =
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextra= ctor/pipelines/RelationExtractorConsumer.java.
Once you get a hold of e= ach BinaryTextRelation, you can determine the
relation type by looking = at the 'category' attribute.

Dima

On 09/23/2013 06:43 PM, sam= ir chabou wrote:
> Hi Dima,
>
> I run RelationExtractorPi= pelineSingleCas.java and i got
> degree_of(severe pain/3, severe/2)> degree_of(pain/3, severe/2)
> location_of(pain/3, wrists/6)>
> but when i run UIMA_CVD--relation-extractor.launch - or UIMA_= CPE--relation-extractor.launch  on the hurd coded text  "He still is not able to work because of severe pain involving his wrists." th= ere is no annotation of type:
> org.apache.ctakes.typesystem.type.rel= ation.LocationOf
> org.apache.ctakes.typesystem.type.relation.DegreeO= f
>
>
> I need to identify the relations  by their a= nnotation type so i can iterate on them
>
> Thanks
> Sami= r
>
>
>
>
> ________________________________<= br>>  From: Dmitriy Dligach <dmitriy.dligach@childrens.harvard.edu>
> To: dev= @ctakes.apache.org; samir chabou <samirchb@yahoo.com>; "user@ctakes.apache.org" <user@ctakes.apache.org>
> Sent: Monday, September 23, 20= 13 4:38:35 PM
> Subject: Re: examples of relation extractor annotatio= ns
> 
>
> Samir,
>
> Could you please = try to run ctakes-relation-extractor/src/main/java/org/apache/ctakes/relati= onextractor/pipelines/RelationExtractorPipelineSingleCas.java and see if it= finds any relations in the hard-coded sample sentence. In that sentence>
> "He still is not able to work because of severe pain involvin= g his wrists."
>
> you should see the following relations:
&= gt;
> degree_of(severe pain/3, severe/2)
> degree_of(pain/3, se= vere/2)
> location_of(pain/3, wrists/6)
>
> which will be= printed to the console. The numbers next to each argument are the UMLS semantic types (e.g. 6 =3D anatomical site).
>
> Dima
><= br>> On 09/21/2013 11:00 AM, samir chabou wrote:
>> Hi,
>= > I tried to get examples of relation extractor annotations using Relati= onExtractorAggregate.xml. I tried the RelationExtractorAggregate on many in= put medical text but there was no annotation for any kind of relation. I ev= en tried the bellow text used in RelationExtractorAnnotatorsTest but again = no relation is annotated. Do you have idea or am i missing some thing ?
= >>          "He had a slight fracture in the= proximal right fibula.",
>>          &nb= sp; "He had a slight fracture in the proximal right fibula .",
>>&= nbsp;           "PRP VBD DT JJ NN IN DT JJ JJ NN .= ");
>>
>>
>> Thanks
>> Samir
>>= ;
> -- Dmitriy Dligach, PhD
> Research Fellow
> Children's Hospital Informatics Program
> Boston Children's Hospital= and Harvard Medical School
> (617) 919-3596

--
Dmitriy Dl= igach, PhD
Research Fellow
Children's Hospital Informatics ProgramBoston Children's Hospital and Harvard Medical School
(617) 919-3596


---655264479-1486549426-1380117393=:62690--