Dear all, I am trying to annotate multiple clinical notes with cTAKES 3.2 in user mode. First, I ran the command ./bin/runctakes.CPE.sh to launch the CPE. I selected the file "test_plaintext.xml" in the CPE descriptor and the default AggregatePlainTextProcessor.
It ran smoothly, but I found that the AggregatePlainTextProcessor just annotated text with a few types of labels. Then I tried to use the AggregatePlaintextFastUMLSProcessor. Unfortunately, the program took a long time to stop at the following lines without response. 14 Jul 2016 11:09:55 INFO ChunkAdjuster - process(JCas) 14 Jul 2016 11:09:55 INFO CopyAnnotator - process(JCas) 14 Jul 2016 11:09:55 INFO OverlapAnnotator - process(JCas) 14 Jul 2016 11:09:55 INFO DictionaryLookupAnnotator - process(JCas) 14 Jul 2016 11:09:55 INFO MaxentParserWrapper - Started processing: testpatient_plaintext_1.txt 14 Jul 2016 11:09:56 INFO MaxentParserWrapper - Done parsing: testpatient_plaintext_1.txt 14 Jul 2016 11:09:56 INFO SentenceDetector - Starting processing. 14 Jul 2016 11:09:56 INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 14 Jul 2016 11:09:56 INFO LvgAnnotator - process(JCas) 14 Jul 2016 11:09:57 INFO ContextDependentTokenizerAnnotator - process(JCas) 14 Jul 2016 11:09:57 INFO POSTagger - process(JCas) 14 Jul 2016 11:09:57 INFO Chunker - process(JCas) 14 Jul 2016 11:09:59 INFO ChunkAdjuster - process(JCas) 14 Jul 2016 11:09:59 INFO ChunkAdjuster - process(JCas) 14 Jul 2016 11:09:59 INFO AbstractJCasTermAnnotator - Starting processing 14 Jul 2016 11:09:59 INFO AbstractJCasTermAnnotator - Finished processing 14 Jul 2016 11:09:59 INFO DrugMentionAnnotator - process(JCas) Can anybody help me out with this? I am new with cTAKES. Any help is highly appreciated.
