Hi My piper file had the following analysis engines for drug mention annotation purpose however on executing the piper file through builder.run() I do not see any annotations related to drug annotation like medication strength, frequency, frequency modifier types being added to XMI output.
Is flow control required here like in Aggregate engines? PiperFile name: UmlsLookupPipeline.piper Text file content: Administration of Prilosac ( omeprazole ) 20 mg twice daily for 4 days Piper file Content: =========================================== reader org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader InputDirectory=D:\xxx\cTAKES_docs\Inbound\Medication add org.apache.ctakes.core.ae.SimpleSegmentAnnotator // Sentence Detector // Annotates Sentences based upon an OpenNLP model. add org.apache.ctakes.core.ae.SentenceDetector // PTB Tokenizer // Annotates Document Penn TreeBank Tokens. add org.apache.ctakes.core.ae.TokenizerAnnotatorPTB // LVG Annotator // Adds cononical form of words. addDescription LvgAnnotator // Context Dependent Annotator // Finds tokens based upon context. Time, Date, Roman numeral, Fraction, Range, Measurement, Person title. add org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator // Part of Speech Tagger // Annotate Parts of Speech. add org.apache.ctakes.postagger.POSTagger // Chunker // Annotator that generates chunks of any kind as specified by the chunker model and the chunk creator. addDescription Chunker addDescription adjuster.ChunkAdjuster NP,NP 1 addDescription adjuster.ChunkAdjuster NP,PP,NP 2 set ctakes.umlsuser=bhatnl ctakes.umlspw=Test1234 // Dictionary Lookup (Default) // Annotates clinically-relevant terms. Terms must match dictionary entries exactly. add org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator // Constituency Parser addDescription ConstituencyParser // Drug Mention Annotator // Creates modifier annotations needed to handle the drug mentions. add org.apache.ctakes.drugner.ae.DrugMentionAnnotator // XMI Writer // Writes XMI files with full representation of input text and all extracted information. # OutputDirectory Output directory to write xmi files add org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes OutputDirectory=D:\xxx\cTAKES_docs\Outbound\xmi =========================================================== -- Thanks and Regards Narayan L Bhat +91 9740237967
