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From Bonnie MacKellar <macke...@stjohns.edu>
Subject RE: do I need the UIMA SDK?
Date Mon, 27 Jul 2015 18:19:00 GMT
Thanks. I had actually read through that chain right before posting. It doesn’t address my
question on whether I need the UIMA SDK. I think that is where I am most confused.
I am looking at the ctakes-examples project right now. Is that similar to your set up? Is
it a good model to follow?

Bonnie MacKellar
Division of Computer Science, Math and Science
St John's University
Queens, NY
mackellb@stjohns.edu

From: Jeff Headley [mailto:jeffunf96@gmail.com]
Sent: Friday, July 24, 2015 11:08 PM
To: user@ctakes.apache.org
Subject: Re: do I need the UIMA SDK?

I am new to cTAKES as well and working on calling out to cTAKES from a Java application. The
advice I have seen here suggests adding cTAKES to your classpath. So <ctakes_home>/lib,
<ctakes_home>/desc, and <ctakes_home>/resources on your classpath in your java
project.

Look at http://mail-archives.apache.org/mod_mbox/ctakes-user/201506.mbox/browser and the June
thread in the users mailing list called "Running cTAKES through Java". I found Lance's reply
in that thread to be very helpful.

Jeff

On Fri, Jul 24, 2015 at 7:17 PM, Bonnie MacKellar <mackellb@stjohns.edu<mailto:mackellb@stjohns.edu>>
wrote:
Hi,

I am very new to cTakes. I want to work with it from Java. I followed the instructions in
developer-install, and loaded the code into Eclipse. I can run the CPE and CVD from the ctakes-ClinicalPipelines
project and I can use the FastUMLSAnnotator, so I know I have configured UMLS authentication
properly.

However, I am very confused. Looking at the Eclipse setup, I see many, many projects. What
are all these projects? I can’t find any documentation. I use the ctakes-ClinicalPipeline
project mainly because that is what the developer-install instructions say to use. Do I actually
need all those Eclipse projects?

More importantly, while I understand the relationship of cTakes to UIMA conceptually, on a
practical basis I am having trouble. For example, all the documentation is really UIMA documentation.
The UIMA documentation assumes I have UIMA SDK. For example, the instructions for running
the CPE Configurator tell me to run a .sh file in the UIMA SDK. Yet, the cTakes developer-install
instructions never mention the UIMA SDK. Do I need to install this?

And finsally, and I realize this may seem like a stupid question, but if I want to write an
application that uses the clinical pipeline and then accesses the jCAS structure to do something
additional, would I add my code to the ctakes-ClinicalPipeline project or just start another
Eclipse project?

Bonnie MacKellar
Division of Computer Science, Math and Science
St John's University
Queens, NY
mackellb@stjohns.edu<mailto:mackellb@stjohns.edu>


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