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From Leonard Jacuzzo <jacu...@gmail.com>
Subject Re: Managing cTakes application output
Date Mon, 06 May 2013 20:42:15 GMT
Hi All,

I had the same problem. So I used TopBraid Composer to make a SPARQL motion
script that takes the XML in and converts it to RDF and used SPARQL to get
to the triples that I was interested in. But this required manually reading
the XML to see how things were organized.

I tried the RDF Consumer, but wasn't able to get it to work very well. So I
went with what I knew.

Has that project progressed any since mid-summer?

LFJ

On Mon, May 6, 2013 at 2:53 PM, <"Austin Ziehlke"@nike.apache.org> wrote:

> Thanks****
>
> 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****
>
> ** **
>
> Austin,****
>
> ** **
>
> You may want to check out an existing RDFConsumer class:
> http://svn.apache.org/repos/asf/uima/sandbox/trunk/RDFCASConsumer/src/main/java/org/apache/uima/rdf/RDFCASConsumer.java
> ****
>
> ** **
>
> This might shed additional insight into the output format and schema you
> are trying to get to.****
>
> ** **
>
> Murali****
>
> ** **
>
> On Mon, May 6, 2013 at 2:41 PM, <"Austin Ziehlke"@athena.apache.org>
> wrote:****
>
> Pei****
>
> 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****
>
> Austin****
>
>  ****
>
>  ****
>
> *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.****
>
> [1]
> http://uima.apache.org/d/uimaj-2.4.0/tutorials_and_users_guides.html#ugr.tug.cpe.configurator_and_viewer
> ****
>
> [2]
> http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/
> ****
>
> [3] http://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-gui/****
>
>  ****
>
> *From:* AZiehlke @ knology [mailto:aziehlke@knology.net<aziehlke@knology.net>]
> *On Behalf Of *"Austin Ziehlke"@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?****
>
>  ****
>
> A.Ziehlke****
>
>  ****
>
> ** **
>

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