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 0533D109B4 for ; Mon, 6 May 2013 18:50:20 +0000 (UTC) Received: (qmail 18182 invoked by uid 500); 6 May 2013 18:50:18 -0000 Delivered-To: apmail-ctakes-user-archive@ctakes.apache.org Received: (qmail 18159 invoked by uid 500); 6 May 2013 18:50:18 -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 18073 invoked by uid 99); 6 May 2013 18:50:18 -0000 Received: from nike.apache.org (HELO nike.apache.org) (192.87.106.230) by apache.org (qpsmtpd/0.29) with ESMTP; Mon, 06 May 2013 18:50:18 +0000 X-ASF-Spam-Status: No, hits=3.5 required=5.0 tests=FB_GET_MEDS,HTML_MESSAGE,RCVD_IN_DNSWL_LOW,SPF_PASS X-Spam-Check-By: apache.org Received-SPF: pass (nike.apache.org: domain of mminnah@gmail.com designates 209.85.128.171 as permitted sender) Received: from [209.85.128.171] (HELO mail-ve0-f171.google.com) (209.85.128.171) by apache.org (qpsmtpd/0.29) with ESMTP; Mon, 06 May 2013 18:50:12 +0000 Received: by mail-ve0-f171.google.com with SMTP id oy12so3516370veb.2 for ; Mon, 06 May 2013 11:49:51 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:x-received:in-reply-to:references:date:message-id :subject:from:to:cc:content-type; bh=0rze5/4rPpduA117AJzlFX0KVKUPOjAwd2zYVj9I6MY=; b=Cw3tpVwoqnbxcytBjvyCIvJrEBF6zWN0UVnA41W60I4HDO4Ngfu7DptVve4KqsIdPr ychpauXxCmUDO1/wMR2aUgqky46pF5xZxmf4/u+egRIpPrnM2oCIUh7B1GoGb2ROp0aE U/feXoajraKxL7dScY0c4CS8TzwOj54zxT5Gv4S1n8vjCkt7+b9rKX4iQwuU1hUvoY+T fAAJ139WNUF5h7EaSRTotubb3QNZ7L/g2FE6OUWJdymq21eLL7TPz1I3qrrQ/nI0EYaH J7A/d46vxOJy7d+fMCyWcuXABTURv5/69RoYiK9hLYKtRxJn7Jm/2FFkikAEmohyPI/R +kVA== MIME-Version: 1.0 X-Received: by 10.220.82.3 with SMTP id z3mr7267927vck.18.1367866191343; Mon, 06 May 2013 11:49:51 -0700 (PDT) Received: by 10.220.88.133 with HTTP; Mon, 6 May 2013 11:49:51 -0700 (PDT) In-Reply-To: <00f901ce4a89$5081ec70$f185c550$@Domain> References: <009b01ce4a6b$fcd55ac0$f6801040$@Domain> <924DE05C19409B438EB81DE683A942D91051B57A@CHEXMBX1A.CHBOSTON.ORG> <00f901ce4a89$5081ec70$f185c550$@Domain> Date: Mon, 6 May 2013 14:49:51 -0400 Message-ID: Subject: Re: Managing cTakes application output From: Murali Nagendranath To: user@ctakes.apache.org Cc: Pei.Chen@childrens.harvard.edu Content-Type: multipart/alternative; boundary=001a11c1ed326f788704dc112a2a X-Virus-Checked: Checked by ClamAV on apache.org --001a11c1ed326f788704dc112a2a Content-Type: text/plain; charset=ISO-8859-1 Austin, You may want to check out an existing RDFConsumer class: http://svn.apache.org/repos/asf/uima/sandbox/trunk/RDFCASConsumer/src/main/java/org/apache/uima/rdf/RDFCASConsumer.java This might shed additional insight into the output format and schema you are trying to get to. Murali On Mon, May 6, 2013 at 2:41 PM, <"Austin Ziehlke"@athena.apache.org> wrote: > Pei**** > > Thanks, this is helpful. I will look for the UIMA CAS Viewer and see what > that brings. I am still investigating options, and understanding how to get > info from medical record into a triple store is my ultimate goal. But > cTakes puts out way too much info. Before I invest in custom software > solution I want to make sure I am looking at a good path.**** > > ** ** > > Any further info you might have will be a blessing to me.**** > > ** ** > > Best Regards**** > > Austin**** > > ** ** > > ** ** > > *From:* Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu] > *Sent:* Monday, May 06, 2013 11:28 AM > *To:* user@ctakes.apache.org > *Subject:* RE: Managing cTakes application output**** > > ** ** > > Hi A.Ziehlke,**** > > Note: The CVD (CAS Visual Debugger) is an UIMA tool which is really > helpful visualizing a single result mainly for debugging purposes. There > are many ways to customize the output of cTAKES. Were you just looking for > something simple to visualize the xml output? If so, then there is a tool > called UIMA CAS viewer [1] where you can import the xml and pick and choose > the Types you are interested in.**** > > Alternatively, there are programmatic ways to customize the output: Some > examples include:**** > > **1) **Writing a custom Java CASConsumer [2] where you can select > the Types that your application may be interested in.**** > > **2) **There is a GU[3] I in the sandbox area which is intended to > make this easier for users to configure.**** > > ** ** > > Hope that helps.**** > > [1] > http://uima.apache.org/d/uimaj-2.4.0/tutorials_and_users_guides.html#ugr.tug.cpe.configurator_and_viewer > **** > > [2] > http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/ > **** > > [3] http://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-gui/**** > > ** ** > > *From:* AZiehlke @ knology [mailto:aziehlke@knology.net] > *On Behalf Of *"Austin Ziehlke"@nike.apache.org > *Sent:* Monday, May 06, 2013 11:15 AM > *To:* user@ctakes.apache.org > *Subject:* Managing cTakes application output**** > > ** ** > > Greetings all.**** > > ** ** > > I am relatively new to cTakes, and am seeking some guidance on best > use/practices. Specifically on the output generated by cTakes CVD. The XML > output is verbose. I need to make that output more succinct to user needs. > Is there a way in CVD to scale down the output, customize the output? Is > the generated output based/controlled on the data in the dictionaries? If > CVD does not allow customizing the output, do you have any suggestions on > secondary tools that will make it easier to get to the medical info and > hide/remove the lexical/grammar info. Is custom software necessary to parse > the data?**** > > ** ** > > When I import the xml generated from CVD directly into Allegrograph, and > display in Gruff, the resulting graph is enormous for one medical record > entry. Perhaps there is some step between the output from CVD and the input > to a datastore that can reduce the data to a manageable state?**** > > ** ** > > A.Ziehlke**** > > ** ** > --001a11c1ed326f788704dc112a2a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Austin,


This might shed additional insight into the= output format and schema you are trying to get to.

Murali


On Mon, May 6, 2013 at 2:41 PM, <"Austin = Ziehlke"@athena.apache.org> wrote:

Pei

Thanks, this is helpful. I will loo= k for the UIMA CAS Viewer and see what that brings. I am still investigatin= g options, and understanding how to get info from medical record into a tri= ple store is my ultimate goal. But cTakes puts out way too much info. Befor= e I invest in custom software solution I want to make sure I am looking at = a good path.

=A0

Any further info= you might have will be a blessing to me.

=A0

Best Regards

Austin

=A0

=A0

From: Chen, Pei [mailto:Pei.Chen@childrens.h= arvard.edu]
Sent: Monday, May 06, 2013 11:28 AM
To: user@ctakes.apache.org
= Subject: RE: Managing cTakes application output

=A0=

Hi A.Ziehlke,

No= te: The CVD (CAS Visual Debugger) is an UIMA tool which is really helpful v= isualizing a single result mainly for debugging purposes.=A0 There are many= ways to customize the output of cTAKES.=A0 Were you just looking for somet= hing simple to visualize the xml output?=A0 If so, then there is a tool cal= led UIMA CAS viewer [1] where you can import the xml and pick and choose th= e Types you are interested in.

Alternatively, there a= re programmatic ways to customize the output: Some examples include:=

1)=A0=A0=A0=A0=A0 Writing a custom Java CASConsu= mer [2] where you can select the Types that your application may be interes= ted in.

2)=A0=A0=A0=A0=A0 There is a GU[3] I in the sandbox area which is = intended to make this easier for users to configure.

=A0

Hope that helps.=

[1] http://uima.apache.org/d/uimaj-2.4.0/t= utorials_and_users_guides.html#ugr.tug.cpe.configurator_and_viewer

[2] http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-core/src/main/java= /org/apache/ctakes/core/cc/=

[3] http://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-gui/

=A0

From: AZiehlke= @ knology [mailt= o:aziehlke@knology.net] On Behalf Of "Austin Ziehlke"= @nike.apache.org
Sent: Monday, May 06, 2013 11:15 AM
To: user@ctakes.apache.org
= Subject: Managing cTakes application output

=A0

Gr= eetings all.

=A0

<= p class=3D"MsoNormal">I am relatively new to cTakes, and am seeking some gu= idance on best use/practices. Specifically on the output generated by cTake= s CVD. The XML output is verbose. I need to make that output more succinct = to user needs. Is there a way in CVD to scale down the output, customize th= e output? Is the generated output based/controlled on the data in the dicti= onaries? If CVD does not allow customizing the output, do you have any sugg= estions on secondary tools that will make it easier to get to the medical i= nfo and hide/remove the lexical/grammar info. Is custom software necessary = to parse the data?

=A0

When I i= mport the xml generated from CVD directly into Allegrograph, and display in= Gruff, the resulting graph is enormous for one medical record entry. Perha= ps there is some step between the output from CVD and the input to a datast= ore that can reduce the data to a manageable state?

=A0

A.Ziehlk= e<= u>

=A0

<= /div>

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