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From "Masanz, James J." <Masanz.Ja...@mayo.edu>
Subject RE: CEM Template Filler
Date Wed, 07 May 2014 17:10:49 GMT
You could look at SideEffectCasConsumer.java for an example of outputting delimited files.

Or ParserTreeWriterConsumer.java might be a better place to start, since it outputs a single
type.

A more complex example, which extracts medication concept codes, would be ConsumeNamedEntityRecordModel.java.
But parts of that look like it was written in a hurry -- it doesn’t do a very efficient
job of iterating through annotations within other annotations, so I wouldn’t pattern your
loops after that.

Others might have other suggestions.

From: Anirban Chakraborti [mailto:chakraborti.anirban@googlemail.com]
Sent: Wednesday, May 07, 2014 11:24 AM
To: Masanz, James J.
Subject: Fwd: CEM Template Filler

Hi,

Not reaching the group so direct email. Feel free to post reply on the group for benefit of
all.

Thanks,
Anirban
---------- Forwarded message ----------
From: Anirban Chakraborti <chakraborti.anirban@googlemail.com<mailto:chakraborti.anirban@googlemail.com>>
Date: Wed, May 7, 2014 at 9:14 PM
Subject: Fwd: CEM Template Filler
To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>



Thanks again.

Would you happen to have a template of CAS consumer which I can customize.

What I need is to structure a template so that all medications and downstream concepts, all
disease, all anatomical site mentions are grouped together for a particular processed record.

Anir

On Wed, May 7, 2014 at 12:15 AM, Masanz, James J. <Masanz.James@mayo.edu<mailto:Masanz.James@mayo.edu>>
wrote:
The XXXXXXXMention annotations such  DiseaseDisorderMention, SignSymptomMention correspond
to the CEMs.

You could customize a CAS Consumer to just output the annotations you are interested in, plus
the related annotation such as OntologyConcept and UmlsConcept and the MedicationXXXX annotations
like MedicationDosage and MedicationDosageModifier.

Perhaps we are thinking of different things when we refer to CEMs.  What do you mean by CEMs
or where did you hear about CEMs?

There is also a data normalization pipeline that takes cTAKES output and stores it into a
database
http://informatics.mayo.edu/sharp/index.php/Data_Normalization

But I suspect that is more involved than what you are looking for and I’m not sure if that
output is quite what you are looking for either


From: Anirban Chakraborti [mailto:chakraborti.anirban@googlemail.com<mailto:chakraborti.anirban@googlemail.com>]
Sent: Tuesday, May 06, 2014 5:30 AM
To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
Subject: CEM Template Filler

Hi,

I ran Aggregatemplatefiller.xml on a text file and got the attached output in XMI format.
How do I convert the same into CEMs supported by Ctakes.

The output by itself is very bulky to read.

Anir



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