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From Hung Hoang <hungkhanhho...@gmail.com>
Subject Running cTAKES for multiple plain texts
Date Thu, 14 Jul 2016 02:13:36 GMT
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.

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