Transcript SHARP 4: Clinical Natural Language Processing

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 1st annotator, against
XML such as CDA document
 View annotations created (“debugger”)
 Export annotations to XML (XCAS or XMI)
cTAKES: Components
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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
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.
Sentences
Tokens
Chunks
Windows for Lookup
Named Entity
Questions?
Live Demo of CVD