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From "Carrell, David" <carrel...@ghc.org>
Subject RE: configuring cTakes for getting input from a db table and persisting output to i2b2 and/or flat db table
Date Mon, 16 Sep 2013 23:03:19 GMT
Our NLP developers have created components that can be called in the collection processing
engine's (CPE) configurator to read from a relational database (via ODBC) and to either write
the structured data to a relational database or to a flat (CSV) file.  It is very useful.
 I think a wizard to allow non-developers to implement the same locally would be greatly appreciated.
-David Carrell
Group Health

-----Original Message-----
From: ksarma@gmail.com [mailto:ksarma@gmail.com] On Behalf Of Karthik Sarma
Sent: Monday, September 16, 2013 3:25 PM
To: dev@ctakes.apache.org
Subject: Re: configuring cTakes for getting input from a db table and persisting output to
i2b2 and/or flat db table

I was actually thinking about this use case earlier today -- it is not particularly easy to
set cTAKES up to work with a local database (either for lookup or for data, though the latter
is certainly easier). Setting up the appropriate database for a local UMLS installation is
also inconvenient for the non-developer. I have been thinking about putting together a wizard
or some such to help folks through the process -- do you think it'd be worthwhile? I'm not
really sure what proportion of users use a local UMLS install; personally I've found the web
API to be far too slow for my workflows.





--
Karthik Sarma
UCLA Medical Scientist Training Program Class of 20??
Member, UCLA Medical Imaging & Informatics Lab Member, CA Delegation to the House of Delegates
of the American Medical Association ksarma@ksarma.com
gchat: ksarma@gmail.com
linkedin: www.linkedin.com/in/ksarma


On Mon, Sep 16, 2013 at 3:11 PM, Chen, Pei
<Pei.Chen@childrens.harvard.edu>wrote:

>  > to a) take input from a ms sql db table****
>
> Something like a JdbcCollectionReader?****
>
>
> http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-core/src/main/java
> /org/apache/ctakes/core/cr/JdbcCollectionReader.java
> ****
>
> ** **
>
> >b) configure it so that it writes NLP results back to the db****
>
> Something like a CasConsumer?****
>
>
> http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-core/src/main/java
> /org/apache/ctakes/core/cc/CasConsumer.java
> ****
>
> ** **
>
> >, in i2b2 format as well as in a flat table format.****
>
> There was some early/prelim work done in sandbox on the i2b2 formats,
> but never really made it to mainstream ctakes (yet...).  ****
>
>
> http://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-gui/src/main/jav
> a/org/chboston/cnlp/ctakes/gui/runtime/result/
> ****
>
> ** **
>
> --Pei****
>
> ** **
>
> *From:* Vlad Valtchinov [mailto:vlad.valtchinov@gmail.com]
> *Sent:* Monday, September 16, 2013 5:13 PM
> *To:* user@ctakes.apache.org
> *Subject:* configuring cTakes for getting input from a db table and
> persisting output to i2b2 and/or flat db table****
>
> ** **
>
> Hello cTakes Users-****
>
> ** **
>
> we're relatively new to cTakes (even though not to NLP)****
>
> and are currently evaluating cTakes 3.0 for moving some of****
>
> our clinical radiology DSS pipeline to Apache cTakes.****
>
> ** **
>
> We have an evaluation install under Linux, and would like to start****
>
> with configuring cTakes to a) take input from a ms sql db table, and
> b)***
> *
>
> configure it so that it writes NLP results back to the db, in i2b2
> format as well****
>
> as in a flat table format. Somebody out there has probably implemented
> this already  -****
>
> can you point us to an online resource where this is detailed, or even
> better ****
>
> share binary implementation with us? cTakes is supposedly very similar
> to another ****
>
> Apache project, Solr, and yet we could not find a clear documentation
> of**
> **
>
> DataHandler configuration under cTakes... maybe not looking at the
> right
> place...****
>
> ** **
>
> Thanks much in advance.****
>
> ** **
>
> Vlad Valtchinov****
>
> Brigham Radiology, CEBI****
>

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