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From giri vara prasad nambari <girinamb...@gmail.com>
Subject Re: cTakes with java web application
Date Tue, 02 Apr 2013 15:44:56 GMT
Hi Tim and Team,

I see. Now I am getting more clarity on the way I need to spend my time.

cTakes is more on defining type systems and pipeline. UIMA/UIMA-Fit is the
code which really process the text based on cTakes definitions to extract
information. Am I correct?

I know your time is valuable, but, could some one help me with any
documentation for UIMA-Fit client code (and/or) related documentation? (I
just started on this domain, so any pointers would be really helpful).

Thanks for your time.

Thank you,
Giri


On Tue, Apr 2, 2013 at 11:28 AM, Tim Miller <
timothy.miller@childrens.harvard.edu> wrote:

>  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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