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From Nick Nikandish <snika...@emerginghealthit.com>
Subject RE: Bacterium Dictionary
Date Mon, 30 Jun 2014 19:48:43 GMT
Hi Sean,

Thanks for the info. I have written an application for clinical text using Ctakes where one
of the  annotator  retrieves and identifies the bacterium in clinical  texts but it uses a
small library that I created. Therefore I would like to check those texts against a comprehensive
library like UML. I have UMLS account and but I was wondering how to utilize Ctakes to use
that library. It will be great if there were some documents on building a separate dictionary
using the dictionary creator.


Thanks again,
Nick

-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu] 
Sent: Monday, June 30, 2014 3:37 PM
To: dev@ctakes.apache.org
Subject: RE: Bacterium Dictionary

Hi Nick,
There are ~26,000 T007 Bacterium (falls under Living Being) entries in UMLS 2013aa.  They
aren't in the cTakes dictionary, but you can build a separate bacteria dictionary using the
dictionary creator tool in cTakes sandbox.  It can create dictionaries formatted for use with
both available cTakes-dictionary-lookup modules.  I have a full living beings dictionary,
if you want to somehow confirm your umls license then I could pull out the bacteria for you.
Sean

> -----Original Message-----
> From: Pei Chen [mailto:chenpei@apache.org]
> Sent: Monday, June 30, 2014 12:50 PM
> To: dev@ctakes.apache.org
> Subject: Re: Bacterium Dictionary
> 
> Nick,
> I am not sure how complete it is, but I believe the UMLS has the 
> semantic type of
> 
> Bacterium
> <https://uts.nlm.nih.gov//semanticnetwork.html#Bacterium;0;0;2014AA>
> 
>  [T007]
>   It's most likely not included in the default cTAKES dictionaries though...
> 
> Thanks,
> Pei
> 
> 
> On Mon, Jun 30, 2014 at 10:31 AM, Nick Nikandish < 
> snikandi@emerginghealthit.com> wrote:
> 
> >  Hi there,
> >
> >
> >
> > I was wondering if Ctakes has any Bacterium Dictionary? I need to 
> > extract information for bacteria like “Enterococcus Faecium”, 
> > “Pseudomonas Aeruginosa “ , etc  and I was wondering if I can do it 
> > by using Ctakes annotators?
> >
> >
> >
> > Thanks,
> >
> >
> >
> > *Nick Nikandish*
> >
> > *Product Development Software Engineer*
> >
> > Clinical Research Informatics
> >
> >
> >
> > *Emerging Health*
> >
> > *Montefiore Information Technology*
> >
> > 6 Executive Blvd. Suite 290, Yonkers, NY 10701
> >
> > 914-457-6792 Office
> >
> > snikandi@montefiore.org
> >
> > www.emerginghealthit.com
> >
> > www.montefiore.org
> >
> >
> >
> > [image: logo-montefiore-it]
> >
> >
> >
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