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From "Vlad Valtchinov" <vlad.valtchi...@gmail.com>
Subject RE: configuring cTakes for getting input from a db table and persisting output to i2b2 and/or flat db table
Date Tue, 17 Sep 2013 15:20:34 GMT
Thanks for the responses, Pei.

 

So what seems to be the prevailing and most mature deployment mode out there
-

deposit xml formatted input files in a given directory and cTakes write the 

results back in a similar format? Any idea how this compares in speed and
scalability to 

the db input/db output option?

 

Regarding JdbcCollectionReader (input) and CasConsumer (output) enabling - 

are there ways to add and configure those from the visual tool, CVD (as it
is done in the 

ctakes i2b2 tool on the i2b2 wiki)? Also, where do you

specify the mapping of the db columns to the internal filed names so cTakes
knows 

what to process (like i.e. in the DataHandler's section of the
solrconfig.xml file)?

 

If somebody has implemented a similar cTakes config and would be willing to 

share the details and the wisdom we will appreciate tremendously.

 

Regards,

vlad

 

From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu] 
Sent: Monday, September 16, 2013 6:12 PM
To: user@ctakes.apache.org; vlad.valtchinov@gmail.com
Subject: RE: configuring cTakes for getting input from a db table and
persisting output to i2b2 and/or flat db table

 

> 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/a
pache/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/a
pache/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/java/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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