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cTAKES: Demo Clinical Text Analysis and Knowledge Extraction System

cTAKES: Demo Clinical Text Analysis and Knowledge Extraction System. James Masanz Mayo Clinic. UIMA CAS Visual Debugger (CVD). Provided by / part of UIMA Run a pipeline against free text With appropriate 1 st annotator, against XML such as CDA document

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cTAKES: Demo Clinical Text Analysis and Knowledge Extraction System

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  1. cTAKES: DemoClinical Text Analysis and Knowledge Extraction System James Masanz Mayo Clinic

  2. UIMA CAS Visual Debugger (CVD) • Provided by / part of UIMA • Run a pipeline against free text • With appropriate 1st annotator, against XML such as CDA document • View annotations created (“debugger”) • Export annotations to XML (XCAS or XMI)

  3. cTAKES: Components • Sentence boundary detection (OpenNLP technology) • Tokenization (rule-based) • Morphologic normalization (NLM’s LVG) • POS tagging (OpenNLP technology) • Shallow parsing (OpenNLP technology) • Named Entity Recognition • Negation and context identification (NegEx) • Dependency parser • Drug Profile module • Smoking status classifier • CEM normalization module

  4. Extend Earlier Example Tamoxifen 20 mg po daily started on March 1, 2005 for 6 mo. Aspirin prn. Fx history of breast cancer. History of migraines.

  5. Sentences

  6. Tokens

  7. Chunks

  8. Windows for Lookup

  9. Named Entity

  10. Questions?

  11. Live Demo of CVD

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