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From digital paula <cybersat...@hotmail.com>
Subject RE: Dictionary and Assertion rules for the Aggregate Plaintext Processor
Date Wed, 20 Nov 2013 05:22:25 GMT
Thanks so much James for helping me to get my tiny dictionary to work.  If you look up James
in it....it states 'a great guy'  :-)
 
I really do appreciate your mentioning of the other options such as the lucene index (as well
as links to this) which I don't have any familiarity with, yet.   Also, like what you stated
on the better alternative on updating the SQL dictionaries.  However, I'm not familiar with
that either, is there any reference links or details that you can provide on how to update
SQL dictionaries?  
 
Thanks.
 
Regards,
Paula
 
From: Masanz.James@mayo.edu
To: user@ctakes.apache.org
Subject: RE: Dictionary and Assertion rules for the Aggregate Plaintext Processor
Date: Tue, 19 Nov 2013 03:50:10 +0000









Hi Paula,

 
There is a separate DictionaryLookupAnnotatorCSV.xml descriptor for using the delimited file
that you found.
You would have to update the aggregate to refer to DictionaryLookupAnnotatorCSV.xml instead
of DictionaryLookupAnnotator.xml in order to use the delimited files
 directly.
 
Or, to create a lucene index to replace the lucene index used by DictionaryLookupAnnotator.xml,
there are some posts on the old forum that talk about creating
 dictionaries.  You could take a look at those. 
 
https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=80&start=20#p1459

https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=423&p=1465
 
I think a better alternative would be update the SQL dictionaries – delete all the data
and replace with what you want. And remove the check for the UMLS user
 ID.
 
Hope that helps.
 
-- James
 


From: user-return-350-Masanz.James=mayo.edu@ctakes.apache.org [mailto:user-return-350-Masanz.James=mayo.edu@ctakes.apache.org]
On Behalf Of digital paula

Sent: Monday, November 18, 2013 8:48 PM

To: user@ctakes.apache.org

Subject: RE: Dictionary and Assertion rules for the Aggregate Plaintext Processor


 

Thanks James for the response. 




I'd like to update that tiny dictionary and see the changes take effect.   I looked in the
dictionary-lookup folders and found a dictionary1.csv file with these entires, I  added 'elbow
'to it  (just typed in and saved file).  




ankle|ankle

aspirin|aspirin

cm|cm 

cm|cm is a synonym of a UMLS term Cutaneous Mastocytosis which is in SNOMED but cm is not
by itself

hyperlipidemia|hyperlipidemia

knee|knee

knee|knee pain

ld|ld

ld|ld SNOMED procedure C0011911

medical|medical nutrition therapy

nutrition|nutrition

nutrition|nutrition therapy

pain|pain

pain|pain, chronic

weight|weight gain

elbow|elbow



 I typed in the following text in CVD using the plaintext processor that uses the DictionaryLookupAnnotator.xml
descriptor.



"patient has knee pain and gained significant weight gain due to injury.  Past history of
elbow pain.  family history includes hyperlipidemia. ."



There was no annotation for 'elbow' or 'weight' after executing the AggregatePlaintext AE
processor.  Does something else have to be done to get it to annotate, basically what are
the steps to add terms to the tiny dictionary?   




Thanks.



Regards,

Paula





> From: 
Masanz.James@mayo.edu

> To: user@ctakes.apache.org

> Subject: RE: Dictionary and Assertion rules for the Aggregate Plaintext Processor

> Date: Mon, 18 Nov 2013 20:17:32 +0000

> 

> The "pain" and "aspirin" terms are from a tiny dictionary that has just a handful of
terms with made-up codes/CUIs. (For the record, they are in a lucene index instead of an HSQL
database.) I think "knee" is also in that tiny dictionary.

> 

> As far as I know, the assertion component doesn't work any differently whether you use
the UMLS dictionary or the tiny, sample, made-up dictionary.

> 

> Which dictionary is used is determined by which Dictionary Lookup analysis engine is
included in the aggregate

> DictionaryLookupAnnotator.xml for the tiny one

> DictionaryLookupAnnotatorUMLS.xml for the one that has real UMLS terms and CUIs

> 

> -- James

> 

> 

> From: 
user-return-348-Masanz.James=mayo.edu@ctakes.apache.org [mailto:user-return-348-Masanz.James=mayo.edu@ctakes.apache.org]
On Behalf Of digital paula

> Sent: Monday, November 18, 2013 1:37 PM

> To: user@ctakes.apache.org

> Subject: RE: Dictionary and Assertion rules for the Aggregate Plaintext Processor

> 

> Oh, gosh....I meant 'Hello' again.   

>  

> ________________________________________

> From: cybersation@hotmail.com

> To: user@ctakes.apache.org

> Subject: Dictionary and Assertion rules for the Aggregate Plaintext Processor

> Date: Mon, 18 Nov 2013 14:36:13 -0500

> Hell again cTakes Community,

>  

> I think this will be an easy question.     Okay I've decided to start simple by first
exploring the Aggregate Plaintext Processor without ULMS.   Since it's not using ULMS, where
 is the dictionary and the assertion rules being defined?  Can these be modified
 easily?   For example,  I see that 'pain' and 'aspirin' gets annotated in text or if text
states 'family history'  this will be noted as well.   Can someone enlighten me as to how
cTakes generates this and if it's easily customizable?  


>  

> Thanks.

>  

> Regards,

> Paula


 		 	   		  
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