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.fi...@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:chen...@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 < > snika...@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 > > > > snika...@montefiore.org > > > > www.emerginghealthit.com > > > > www.montefiore.org > > > > > > > > [image: logo-montefiore-it] > > > > > >
