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 16EDF11B6B for ; Sun, 11 May 2014 14:27:11 +0000 (UTC) Received: (qmail 92452 invoked by uid 500); 11 May 2014 14:00:31 -0000 Delivered-To: apmail-ctakes-user-archive@ctakes.apache.org Received: (qmail 92413 invoked by uid 500); 11 May 2014 14:00:31 -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 92406 invoked by uid 99); 11 May 2014 14:00:31 -0000 Received: from Unknown (HELO nike.apache.org) (192.87.106.230) by apache.org (qpsmtpd/0.29) with ESMTP; Sun, 11 May 2014 14:00:31 +0000 X-ASF-Spam-Status: No, hits=1.5 required=5.0 tests=HTML_MESSAGE,RCVD_IN_DNSWL_LOW,SPF_PASS X-Spam-Check-By: apache.org Received-SPF: pass (nike.apache.org: domain of chakraborti.anirban@googlemail.com designates 209.85.216.172 as permitted sender) Received: from [209.85.216.172] (HELO mail-qc0-f172.google.com) (209.85.216.172) by apache.org (qpsmtpd/0.29) with ESMTP; Sun, 11 May 2014 14:00:28 +0000 Received: by mail-qc0-f172.google.com with SMTP id l6so6632047qcy.17 for ; Sun, 11 May 2014 07:00:05 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=googlemail.com; s=20120113; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type; bh=/fHGmOcPBKKSUYcx4KCbySY8rZFwmlOv3FgI8S9lglA=; b=MW1yn9pabM6uHLAELh+G/5EwCoSzJff7bO/Fh/EXSN9BRpSCnbB6TrxopJn3Cneqpl eA65gnVJ19JrsIjIWd2DBRHnLvyLdDKEyXkQHpsjuFNFSPR12ChNvXEaJcB1jrrR/Ev+ Hh5yWarTqfM3Tqgr9dZwDPLWCAom/qvybMc3oLekuynxEpyYnMRVgDF2TuK8iMJ5/gCB Rjo4nhN/orxUw95mizqjo62627aA0VBLTmhgcDmyTmcn1UuTl8fi9nRrNVYd2sH2Vir0 mBUCUMMmRyUpR9sIWLJmAd9vVYwX63o8SFCu4L9axbMhEUm65KkV/DYbr+/41tii7Drr V4tg== MIME-Version: 1.0 X-Received: by 10.140.23.7 with SMTP id 7mr29392116qgo.0.1399816805224; Sun, 11 May 2014 07:00:05 -0700 (PDT) Received: by 10.140.91.82 with HTTP; Sun, 11 May 2014 07:00:05 -0700 (PDT) In-Reply-To: <1399814861979.94492@anu.edu.au> References: <1399799328751.6893@anu.edu.au> <1399813219136.49658@anu.edu.au> <1399814861979.94492@anu.edu.au> Date: Sun, 11 May 2014 19:30:05 +0530 Message-ID: Subject: Re: cTAKES Information Extraction From: Anirban Chakraborti To: "user@ctakes.apache.org" Content-Type: multipart/alternative; boundary=001a11c13db26d639e04f9203f52 X-Virus-Checked: Checked by ClamAV on apache.org --001a11c13db26d639e04f9203f52 Content-Type: text/plain; charset=UTF-8 that's the desired output. What were you anticipating. On Sun, May 11, 2014 at 6:57 PM, Tamzidur Rahman wrote: > I have used > ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextProcessor.xml > for this. > > > Without UMLS: > > http://i.imgur.com/TWg1kzG.png > > > With UMLS: > > http://i.imgur.com/btZdNtS.png > > > I am still having the same issue. > > > ------------------------------ > *From:* Anirban Chakraborti > *Sent:* Sunday, 11 May 2014 11:02 PM > > *To:* user@ctakes.apache.org > *Subject:* Re: cTAKES Information Extraction > > Startwith AggregatePlainText.xml , you should get annotations on target > text > > > On Sun, May 11, 2014 at 6:30 PM, Tamzidur Rahman wrote: > >> Thanks for the reply, >> >> >> I haven't created any custom AEs, I've only used the default AE found >> in the vanilla install. >> >> >> The AEs I've used: >> >> >> >> ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml >> >> >> ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate >> >> >> ctakes-template-filler/desc/analysis_engine/AggregateTemplateFiller >> >> >> >> ------------------------------ >> *From:* Anirban Chakraborti >> *Sent:* Sunday, 11 May 2014 10:51 PM >> *To:* user@ctakes.apache.org >> *Subject:* Re: cTAKES Information Extraction >> >> Tam, >> >> What AE engines are you using. There might be an issue there. >> >> >> On Sun, May 11, 2014 at 2:38 PM, Tamzidur Rahman wrote: >> >>> Hi, >>> >>> I've been working on a project which uses cTAKES annotations for a >>> search algorithm in a database. What we would like to extract is >>> information such as body Laterality, alleviating Factor, etc. >>> We've been using cTAKES CVD with various AE but we seem to be mostly >>> producing annotations with no information. I have used an working sample >>> from a keynote on cTAKES as evidence of this problem. >>> >>> Working sample >>> https://uima.apache.org/downloads/gscl2013/keynote_ctakes.pdf page >>> 68 >>> >>> Running with sample input >>> http://i.imgur.com/3n6WyHE.png >>> >>> Any help would be appreciated. >>> >>> Thanks >>> >>> >>> >> > --001a11c13db26d639e04f9203f52 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
that's the desired output. What were you anticipating.=


On Sun,= May 11, 2014 at 6:57 PM, Tamzidur Rahman <u5184041@anu.edu.au> wrote:

I have used ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlain= textProcessor.xml for this.


Without UMLS:

http://i.im= gur.com/TWg1kzG.png


With UMLS:

http://i.im= gur.com/btZdNtS.png


I am still having the same issue.


From: Anirban Chakraborti <chakraborti.anirban@g= ooglemail.com>
Sent: Sunday, 11 May 2014 11:02 PM

To: user= @ctakes.apache.org
Subject: Re: cTAKES Information Extraction
=C2=A0
Startwith AggregatePlainText.xml , you should get annotati= ons on target text


On Sun, May 11, 2014 at 6:30 PM, Tamzidur Rahman= <u5184041@anu.e= du.au> wrote:

Thanks for the reply,


I haven't created any custom AEs, I've only used the default AE = found in the vanilla install.


The AEs=C2=A0I've used:


ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProc= essor.xml


ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate


ctakes-template-filler/desc/analysis_engine/AggregateTemplateFiller



From: Anirban Chakraborti <chakraborti.anirban@g= ooglemail.com>
Sent: Sunday, 11 May 2014 10:51 PM
To: user= @ctakes.apache.org
Subject: Re: cTAKES Information Extraction
=C2=A0
Tam,
=C2=A0
What AE engines are you using. There might be an issue there.


On Sun, May 11, 2014 at 2:38 PM, Tamzidur Rahman= <u5184041@anu.e= du.au> wrote:
Hi,

I've been working on = a project which uses cTAKES annotations for a search algorithm in a databas= e. What we would like to extract is information such as body Laterality, al= leviating Factor, etc.
We've been using cTAKES CVD with various AE but we seem to be mostly pr= oducing annotations with no information. I have used an working sample from= a keynote on cTAKES as evidence of this problem.
Working sample

Running with sample input
=C2=A0=C2=A0=C2=A0=C2=A0http://i.imgur.com/3n6WyHE.png

Any help would be appreciated.

Thanks





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