Hi Richard, Did you add SNOMED-CT when creating your UMLS Subset? The dictionary that YTEX ships with has ~1.5 million entries. If that doesn't work, you can also try running the stock cTAKES AggregatePlaintextUMLSProcessor to see if that creates different annotations.
HTH, -vj On Fri, May 23, 2014 at 4:58 PM, Lee, Richard A. [USA] <[email protected]>wrote: > Hi, folks. > > > > I’ve been trying to use the new cTAKES 3.1.2 with ytex, using the > AggregatePlaintextUMLSProcessor.xml AE under ctakes-ytex-uima, and so far > it’s not been producing the numerous medical annotations (eg > DiseaseDisorderMention) that I was getting on the same documents with > cTAKES 3.1.1. Attached screenshot will hopefully make this clear. > > > > I did use MetamorphoSys to set up the UMLS tables, and then the ytex > script to populate its schema, and I now have ytex tables with hundreds of > thousands of entries. > > > > I’ve upped the logging level in the hopes the log file would provide a > clue, and the only thing I’m seeing is a lot of “DEBUG > [FirstTokenPermutationImpl] Window size of 8 exceeds the max permutation > level of 7.”; that number varies from 8 to 12. > > > > Would that explain the problem? If so, how do I fix it? If not, how do I > find the problem? Thanks. > > > > >
