ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: dictionary questions
Date Thu, 15 Aug 2013 17:52:02 GMT
Thanks Sean.
I think this is a pretty common question- I added it to the FAQ's page:
http://ctakes.apache.org/user-faqs.html#why-doesnt-my-umls-term-get-indentified-by-the-system-but-it-exists-in-snomedctrxnorm


> -----Original Message-----
> From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> Sent: Thursday, August 15, 2013 1:35 PM
> To: dev@ctakes.apache.org
> Subject: RE: dictionary questions
> 
> 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.UmlsToSnomedDbCons
> umerImpl">
> 
> 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

Mime
View raw message