Chandra, How are you wiring up the DrugMentionAnnotator? The default AggregatePlaintextFastUMLSProcessor.xml should already have the Drug NER included. http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml
In general, you'll most likely need to something like the below if you have a custom/modified pipeline: <typeSystemDescription> <imports> <import name="org.apache.ctakes.drugner.types.TypeSystem"/> </imports> </typeSystemDescription> Related Thread: http://mail-archives.apache.org/mod_mbox/ctakes-user/201403.mbox/%3CCAPqz87oUZ=hpzc_fo_zlaef3pvqcm9xsyums15iymgapsxx...@mail.gmail.com%3E If you're using uimaFIT to wire your pipeline together, I would highly recommend using the Automatic Type System Discovery. Hope that helps. On Sat, Aug 8, 2015 at 12:12 PM, RANGA CHANDRA GUDIVADA <chandhragupta...@hotmail.com> wrote: > Hello All, > > I am getting the below error while trying to run the analysis engine > "DrugMentionAnnotator.xml" from user install CVD. Please let me know if > anyone has similar issues and were able to successfully fix it. > > Ctakes Version used : apache-ctakes-3.2.2 > Ctakes Resources : ctakes-resources-3.2.1.1-bin > > > > Caused by: org.apache.uima.cas.CASRuntimeException: JCas type > "org.apache.ctakes.drugner.type.FrequencyAnnotation" used in Java code, but > was not declared in the XML type descriptor. > at org.apache.uima.jcas.impl.JCasImpl.getType(JCasImpl.java:412) > at org.apache.uima.jcas.impl.JCasImpl.getCasType(JCasImpl.java:436) > at > org.apache.uima.jcas.impl.JFSIndexRepositoryImpl.getAnnotationIndex(JFSIndexRepositoryImpl.java:80) > at > org.apache.ctakes.drugner.ae.DrugMentionAnnotator.removeAnnotations(DrugMentionAnnotator.java:306) > at > org.apache.ctakes.drugner.ae.DrugMentionAnnotator.removeDrugNerTypes(DrugMentionAnnotator.java:299) > at > org.apache.ctakes.drugner.ae.DrugMentionAnnotator.process(DrugMentionAnnotator.java:260) > ... 45 more > > Thanks > Chandra > > > > > > > >