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 28D21FB39 for ; Tue, 2 Apr 2013 15:29:38 +0000 (UTC) Received: (qmail 96976 invoked by uid 500); 2 Apr 2013 15:29:37 -0000 Delivered-To: apmail-ctakes-user-archive@ctakes.apache.org Received: (qmail 96843 invoked by uid 500); 2 Apr 2013 15:29:37 -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 96810 invoked by uid 99); 2 Apr 2013 15:29:36 -0000 Received: from nike.apache.org (HELO nike.apache.org) (192.87.106.230) by apache.org (qpsmtpd/0.29) with ESMTP; Tue, 02 Apr 2013 15:29:36 +0000 X-ASF-Spam-Status: No, hits=2.2 required=5.0 tests=HTML_MESSAGE,SPF_PASS X-Spam-Check-By: apache.org Received-SPF: pass (nike.apache.org: domain of Timothy.Miller@childrens.harvard.edu designates 134.174.20.73 as permitted sender) Received: from [134.174.20.73] (HELO mailsmtp3.childrenshospital.org) (134.174.20.73) by apache.org (qpsmtpd/0.29) with ESMTP; Tue, 02 Apr 2013 15:29:30 +0000 Received: from pps.filterd (mailsmtp3.childrenshospital.org [127.0.0.1]) by mailsmtp3.childrenshospital.org (8.14.5/8.14.5) with SMTP id r32FSlXR017376; Tue, 2 Apr 2013 11:29:08 -0400 Received: from smtpndc2.chboston.org (smtpndc2.chboston.org [10.20.50.105]) by mailsmtp3.childrenshospital.org with ESMTP id 1bergbres9-1 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT); Tue, 02 Apr 2013 11:29:08 -0400 Received: from pps.filterd (smtpndc2.chboston.org [127.0.0.1]) by smtpndc2.chboston.org (8.14.5/8.14.5) with SMTP id r32FP3mb004470; Tue, 2 Apr 2013 11:29:07 -0400 Received: from chexhubcas2.chboston.org (internal-ndc-nat-v1260.tch.harvard.edu [10.20.50.4]) by smtpndc2.chboston.org with ESMTP id 1ayt405dsk-1 (version=TLSv1/SSLv3 cipher=AES128-SHA bits=128 verify=NOT); Tue, 02 Apr 2013 11:29:07 -0400 Received: from [10.7.2.218] (10.7.2.218) by email.tch.harvard.edu (10.20.50.93) with Microsoft SMTP Server (TLS) id 14.2.309.2; Tue, 2 Apr 2013 11:29:06 -0400 Message-ID: <515AF935.1020308@childrens.harvard.edu> Date: Tue, 2 Apr 2013 11:28:53 -0400 From: Tim Miller User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:17.0) Gecko/20130308 Thunderbird/17.0.4 MIME-Version: 1.0 To: CC: Subject: Re: cTakes with java web application References: <924DE05C19409B438EB81DE683A942D9104CFC59@CHEXMBX1A.CHBOSTON.ORG> <924DE05C19409B438EB81DE683A942D9104CFD73@CHEXMBX1A.CHBOSTON.ORG> In-Reply-To: Content-Type: multipart/alternative; boundary="------------090308050304080105050002" X-Originating-IP: [10.7.2.218] X-Proofpoint-Virus-Version: vendor=fsecure engine=2.50.10432:5.10.8626,1.0.431,0.0.0000 definitions=2013-04-02_06:2013-04-02,2013-04-02,1970-01-01 signatures=0 X-Proofpoint-Virus-Version: vendor=fsecure engine=2.50.10432:5.10.8626,1.0.431,0.0.0000 definitions=2013-04-02_06:2013-04-02,2013-04-02,1970-01-01 signatures=0 X-Virus-Checked: Checked by ClamAV on apache.org --------------090308050304080105050002 Content-Type: text/plain; charset="windows-1252"; format=flowed Content-Transfer-Encoding: 8bit Gira, Your use case is probably one that will become more and more common, and cTAKES devs do similar things all the time. I think the hangup to new or non-dev users (and probably something we need to document better) is that cTAKES is built on top of UIMA, and so the techniques for running pipelines and extracting information are actually UIMA and UIMAFit-based, and so there is nothing like the traditional javadocs explaining a cTAKES API to rely on. Pei's sample code is basically UIMA and UIMAFit standard code that points at cTAKES pipelines, then once that is working the real cTAKES part is basically just understanding the type system so you know how to use UIMA API calls to extract the information you need. So maybe better documentation of the type system (maybe in javadoc style) is something that cTAKES should prioritize. Tim On 04/02/2013 10:45 AM, giri vara prasad nambari wrote: > Hi Pei, > Thanks for your time! > Sort of this is what I am looking for. I will do some research on > javadoc to see what I could do with the API. > May I ask you one more question? Isn't ctakes build to accommodate > these types of requirements (like integrating with other application)? > Am I missing something important? > The reason is, I would need to read the out put of ctakes and perform > some other analysis using WEKA. If ctakes is not yet ready for these > types of requirements I may need to go back re-evaluate the software > stack. > Thank you, > Giri > > > On Tue, Apr 2, 2013 at 10:20 AM, Chen, Pei > > wrote: > > Hi Giri, > > I presume, essentially, you�re planning to include the cTAKES > lib(s) (via mvn?) into your existing app > > 1)Programmatically configure the pipeline > > 2)Pass in a document(s) to cTAKES for processing > > 3)Do XYZ with the output from the jCAS using the UIMA API�s (such > as writing to disk or saving it to a db) > > It is not quite prime time ready but, take a look peek at the > below (It uses uimaFIT to do the above): > > http://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-gui/src/main/java/org/chboston/cnlp/ctakes/gui/service/LauncherService.java > > Essentially, it boils down to a few lines of code: > > AnalysisEngine aggregateAE = AnalysisEngineFactory.createAggregate( > > engines, componentNames, typeSystemDescription, null, > > new SofaMapping[0]); > > JCas jcas = aggregateAE.newJCas(); > > jcas.setDocumentText(doc.getText()); > > aggregateAE.process(jcas); > > *From:*giri vara prasad nambari [mailto:girinambari@gmail.com > ] > *Sent:* Tuesday, April 02, 2013 10:04 AM > *To:* user@ctakes.apache.org > *Subject:* Re: cTakes with java web application > > Hi Pei, > > Thanks for your time on answering this. > > Actually I am not looking for pre built web application (or) GUI. > I was expecting something like "include ctakes jars in my web > application ((or) even for the matter any client java program)" > and start using ctakes API. Is this possible with ctakes api? If > so, any sample ctakes client code available? > > I am not moving towards any SOA (or) pre-built GUI. > > I would be happy to contribute to GUI, but first I need to finish > this ctakes integration task into my web application ASAP. > > I hope this time my question is more clear. > > Thank you, > > Giri > > On Tue, Apr 2, 2013 at 9:51 AM, Chen, Pei > > wrote: > > Hi Giri, > > Apache cTAKES is mainly in Java built on top of the UIMA Framework. > > Currently, there isn�t out of the box web application with cTAKES, > however there is a GUI currently in the sandbox area but isn�t > quite ready for prime time yet. Is this something that you might > be interested in contributing to? > > http://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-gui/ > > There are also some UIMA options that may point you in the right > direction. > > UIMA-AS (If you�re gearing towards a Service Architecture for your > web app.) > > http://uima.apache.org/d/uima-as-2.4.0/uima_async_scaleout.html > > There is also a Simple Rest service (but runs in-process): > > UIMA Simple Server > > http://uima.apache.org/sandbox.html#simple-server > > Thanks, > > Pei > > *From:*giri vara prasad nambari [mailto:girinambari@gmail.com > ] > *Sent:* Tuesday, April 02, 2013 12:29 AM > *To:* ctakes-user@incubator.apache.org > > *Subject:* Fwd: cTakes with java web application > > Hi Community, > > I did lot of google for sample java code to integrate cTakes into > web application, can some one please point me in right direction. > > I would like to use clinical pipeline with plain text instead of > XML documents. > > Any help would be appreciated. > > Thank you, > > Giri > > --------------090308050304080105050002 Content-Type: text/html; charset="windows-1252" Content-Transfer-Encoding: 8bit Gira,
Your use case is probably one that will become more and more common, and cTAKES devs do similar things all the time. I think the hangup to new or non-dev users (and probably something we need to document better) is that cTAKES is built on top of UIMA, and so the techniques for running pipelines and extracting information are actually UIMA and UIMAFit-based, and so there is nothing like the traditional javadocs explaining a cTAKES API to rely on.

Pei's sample code is basically UIMA and UIMAFit standard code that points at cTAKES pipelines, then once that is working the real cTAKES part is basically just understanding the type system so you know how to use UIMA API calls to extract the information you need. So maybe better documentation of the type system (maybe in javadoc style) is something that cTAKES should prioritize.

Tim

On 04/02/2013 10:45 AM, giri vara prasad nambari wrote:
Hi Pei,
�
Thanks for your time!
�
Sort of this is what I am looking for. I will do some research on javadoc to see what I could do with the API.
�
May I ask you one more question? Isn't ctakes build to accommodate these types of requirements (like integrating with other application)? Am I missing something important?
�
The reason is, I would need to read the out put of ctakes and perform some other analysis using WEKA. If ctakes is not yet ready for these types of requirements I may need to go back re-evaluate the software stack.
�
Thank you,
Giri


On Tue, Apr 2, 2013 at 10:20 AM, Chen, Pei <Pei.Chen@childrens.harvard.edu> wrote:

Hi Giri,

I presume, essentially, you�re planning to include the cTAKES lib(s) (via mvn?) into your existing app

1)����� Programmatically configure the pipeline

2)����� Pass in a document(s) to cTAKES for processing

3)����� Do XYZ with the output from the jCAS using the UIMA API�s (such as writing to disk or saving it to a db)

It is not quite prime time ready but, take a look peek at the below (It uses uimaFIT to do the above):

http://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-gui/src/main/java/org/chboston/cnlp/ctakes/gui/service/LauncherService.java

�

Essentially, it boils down to a few lines of code:

AnalysisEngine aggregateAE = AnalysisEngineFactory.createAggregate(

�������������� engines, componentNames, typeSystemDescription, null,

�������������� new SofaMapping[0]);

��������������

JCas jcas = aggregateAE.newJCas();

jcas.setDocumentText(doc.getText());

aggregateAE.process(jcas);

�

�

From: giri vara prasad nambari [mailto:girinambari@gmail.com]
Sent: Tuesday, April 02, 2013 10:04 AM
To: user@ctakes.apache.org
Subject: Re: cTakes with java web application

�

Hi Pei,

�

Thanks for your time on answering this.

�

Actually I am not looking for pre built web application (or) GUI. I was expecting something like "include ctakes jars in my web application ((or) even for the matter any client java program)" and start using ctakes API. Is this possible with ctakes api? If so, any sample ctakes client code available?

�

I am not moving towards any SOA (or) pre-built GUI.

�

�

I would be happy to contribute to GUI, but first I need to finish this ctakes integration task into my web application ASAP.

�

I hope this time my question is more clear.

�

Thank you,

Giri

On Tue, Apr 2, 2013 at 9:51 AM, Chen, Pei <Pei.Chen@childrens.harvard.edu> wrote:

Hi Giri,

Apache cTAKES is mainly in Java built on top of the UIMA Framework.

Currently, there isn�t out of the box web application with cTAKES, however there is a GUI currently in the sandbox area but isn�t quite ready for prime time yet.� Is this something that you might be interested in contributing to?

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

�

There are also some UIMA options that may point you in the right direction.

UIMA-AS (If you�re gearing towards a Service Architecture for your web app.)

http://uima.apache.org/d/uima-as-2.4.0/uima_async_scaleout.html

�

There is also a Simple Rest service (but runs in-process):

UIMA Simple Server

http://uima.apache.org/sandbox.html#simple-server

�

Thanks,

Pei

�

From: giri vara prasad nambari [mailto:girinambari@gmail.com]
Sent: Tuesday, April 02, 2013 12:29 AM
To: ctakes-user@incubator.apache.org
Subject: Fwd: cTakes with java web application

�

�

Hi Community,

�

I did lot of google for sample java code to integrate cTakes into web application, can some one please point me in right direction.

�

I would like to use clinical pipeline with plain text instead of XML documents.

�

Any help would be appreciated.

�

Thank you,

Giri

�

�

�



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