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
