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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: dictionary questions
Date Thu, 15 Aug 2013 17:34:14 GMT
Hi Chase,

I just ran a search in the bundled UMLS dictionary and the full term and cui does existfrom
SnomedCT and NCI, with tui T007.

The Dictionary Lookup that you are using filters out terms that don't have tui codes registered
in the resources/org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml file.  Edit that file
and add "T007" to the value list for "disorderTuis" property as below:
<property key="disorderTuis" value="T019,T020,T037,T046,T047,T048,T049,T050,T190,T191,T007"/>
For <lookupConsumer className="org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedDbConsumerImpl">

Sean

-----Original Message-----
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu] 
Sent: Thursday, August 15, 2013 11:32 AM
To: dev@ctakes.apache.org
Subject: RE: dictionary questions

Hi Chase,

> -----Original Message-----
> From: Chase Master [mailto:chasemaster9@gmail.com]
> Sent: Thursday, August 15, 2013 11:22 AM
> To: dev@ctakes.apache.org
> Subject: dictionary questions
> 
> Hi,
> 
> If I am using DictionaryLookupAnnotatorUMLS.xml as the descriptor for 
> that module, with my valid UMLS username and password, does this use 
> the full SNOMED CT and RxNorm dictionaries?  (I believe it connects to 
> the online
> database.)  Because it misses ""VANCOMYCIN RESISTANT ENTEROCOCCI", 
> C1265175, so I was wondering why?

The below UMLS subsets are bundled in the umls resource files:
*	International Classification of Diseases, Ninth Revision, Clinical Modification, 2012	ICD9CM_2012
ICD9CM	ENG	0	20997
*	International Classification of Diseases, Ninth Revision, Clinical Modification, Metathesaurus
additional entry terms, 2012	MTHICD9_2012	ICD9CM	ENG	0	16304
*	Medical Subject Headings, 2012_2011_09_09	MSH2012_2011_09_09	MSH	ENG	0	321367
*	NCI Thesaurus, 2011_02D	NCI2011_02D	NCI	ENG	0	90135
*	SNOMED Clinical Terms, 2011_07_31	SNOMEDCT_2011_07_31	SNOMEDCT	ENG	9	324494
*	RxNorm

> Is it possible to specify that only "child" UMLS CUIs are output- ie. 
> the most descriptive matches?
One will probably either need a custom dictionary or some additional code that will consume
only the more specific matches.

I hope that helps.
--Pei

> 
> Thanks

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