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

• 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