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From "Austin Ziehl...@athena.apache.org
Subject RE: Managing cTakes application output
Date Mon, 06 May 2013 19:16:09 GMT
Is there a workflow for these tools that I have not seen? Like use CVD to
parse a Medical Record, Then run the results XML through CPE to produce RDF
like info?
Just looking to get as much info as possible.
From: Murali Nagendranath [mailto:mminnah@gmail.com] 
Sent: Monday, May 06, 2013 2:50 PM
To: user@ctakes.apache.org
Cc: Pei.Chen@childrens.harvard.edu
Subject: Re: Managing cTakes application output
You may want to check out an existing RDFConsumer class:
This might shed additional insight into the output format and schema you are
trying to get to.
On Mon, May 6, 2013 at 2:41 PM, <"Austin Ziehlke"@athena.apache.org
<mailto:%22Austin%20Ziehlke%22@athena.apache.org> > wrote:
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
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.
[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 <mailto:%22Austin%20Ziehlke%22@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?

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