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From Pei Chen <pei.c...@wiredinformatics.com>
Subject Re: do I need the UIMA SDK?
Date Mon, 27 Jul 2015 18:34:31 GMT
Bonnie,
It really depends.  One typically shouldn't need a separate UIMA SDK download (if that is
what you mean); cTAKES uses it programmatically and it pulls the required uima-j jars from
maven central.

If you are planning to use cTAKES as a library/API and just want to build an application on
top of it (w/o touching the source), then you can also take a look at:
http://healthnlp.github.io/examples/
[The idea to automatically pull in cTAKES jars from maven central; note this is still being
improved upon.  So feel free to give it a try and let us know if you have any issues]

Hope that helps,
Pei
> On Jul 27, 2015, at 2:19 PM, Bonnie MacKellar <mackellb@stjohns.edu> wrote:
> 
> 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 <mailto: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 <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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