previously OntologyConceptUtil was IdentifiedAnnotationUtil On Wed, Mar 8, 2017 at 11:12 AM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote:
> Hi Martijn, > > The dictionary creator gui is in sandbox just like the command line tool, > but it is newer and easier to use. > > OntologyConceptUtil is in org.apache.ctakes.core.util. > > Sean > > -----Original Message----- > From: Martijn [mailto:mgkersl...@uvic.ca] > Sent: Tuesday, March 07, 2017 5:38 PM > To: dev@ctakes.apache.org > Subject: Re: 2016AB UMLS (ctakessnorx) > > Hi Sean, > > Thanks so much for your quick reply. > I used the command line directorytool. Is that different than the gui? Can > that explain the decrease in tagged concepts? > > I’m not able to find the OntologyConceptUtil class, may I ask what the > path for that class is? > > - Martijn > > On 07/03/2017, 14:24, "Finan, Sean" <sean.fi...@childrens.harvard.edu> > wrote: > > Hi Martijn, > > Since you say that you've created your own dictionary I will assume > that you used the gui in sandbox to do so. If that isn't the case then let > me know. > > The any dictionary created using the default settings on the gui does > have snomedct and rxnorm codes in addition to the cuis. However, umls cui > is always used as the primary normalization code for ctakes annotations. > > To obtain codes for an annotation, check the OntologyConceptUtil in > ctakes core. It has methods that will return all associated codes as well > as one to get all associated codes for a scheme/vocabulary (like > snomedct_us, etc.). It can do this for a single annotation, a collection > of annotations, the entire document, or a section of the document > (sentence, paragraph, section). It also has methods that allow you to > fetch annotations found in the document by codes other than the umls cui. > > Sean > > > -----Original Message----- > From: Martijn [mailto:mgkersl...@uvic.ca] > Sent: Tuesday, March 07, 2017 5:13 PM > To: dev@ctakes.apache.org > Subject: 2016AB UMLS (ctakessnorx) > > Hi, > > I've been using cTAKES for a bit now, but I still can't figure out how > to upgrade the UMLS version to the most recent one. > If I create my own dictionary, cTAKES only returns UMLS concepts and > no SNOMED CT ones (I'm interested in those). The amount of concepts > returned is also way less compared to the 2011 UMLS that's included with > cTAKES. > > Can someone help me out by providing me a proper 2016 dictionary or > clear explanation how to implement the newest version of the UMLS (with > SNOMED CT). > > > Thanks! > > - Martijn > > > > > > >
