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From "Masanz, James J." <Masanz.Ja...@mayo.edu>
Subject RE: Retrieving CUIs
Date Tue, 08 Jul 2014 18:54:21 GMT
What gets annotated depends on which pipeline you use.
The pipeline mentioned in the User Guide should also annotate diseases/disorders, signs/symptoms,
procedures, and anatomical sites. So first would be to check which pipeline you are using.

Or perhaps you do not have the separately downloadable dictionary. To test that, try text
that includes the words "knee" and "pain". If those are annotated and other anatomical sites
and signs/symptoms are not, you probably don't have the dictionary resources or don't have
them on your classpath.

Good things to post to help us help you are:
 - whether you are using CVD or CPE GUI, or a program/script
 - the name of pipeline you are running (are you loading an XML descriptor into CVD or CPE),
or the name of the script/program 
 - a sample output file (xcas/xmi) [make sure not to include any PHI in the sample text that
you process if you are going to post the output]

-- James

-----Original Message-----
From: Nick Nikandish [mailto:snikandi@emerginghealthit.com] 
Sent: Tuesday, July 08, 2014 1:43 PM
To: dev@ctakes.apache.org
Subject: Retrieving CUIs

Hi there,

I was wondering if there is any way to retrieve CUIs for the tokens of a free text in CTakes
without changing the codebase? I am able to retrieve CUIs for only medications  in a text.


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