1. Open Health Natural Language Processing Consortium
(part of caBIG Vocabulary Knowledge Center web presence)
Goal
foster an open-source collaborative community around clinical NLP that can deliver best-of-breed annotators, leverage the dynamic features of UIMA flow-control, and establish the infrastructure for clinical NLP.
Two open source releases as part of OHNLP
Mayo’s pipeline for processing clinical notes (cTAKES)
IBM’s pipeline for processing medical notes (MedKAT) and pathology reports (MedKAT/P)

4. cTAKES Technical Details
Open source release March 15, 2009
Downloads: Documentation and Downloads
Technical details: Publications
Framework
IBM’s Unstructured Information Management Architecture (UIMA) open source framework
Methods
Natural Language Processing methods (NLP)
Application
High-throughput phenotype extraction system (80M+ notes; 80B+ tokens)

5. cTAKES Components Core components
Sentence boundary detection (OpenNLP)
Tokenization (rule-based)
Morphologic normalization (NLM’s “norm”)
POS tagging (OpenNLP)
Shallow parsing (OpenNLP)
Named Entity Recognition
Diseases/disorders, signs/symptoms, procedures, anatomical sites, medications
Dictionary mapping (lookup algorithm)
Machine learning (MAWUI)
Negation and status identification (NegEx)

6. cTAKES Type System

7. cTAKES example

8. Current Efforts - I
Anaphoric relations and coreference (as part of the Ontology Development and Information Extraction project, University of Pittsburgh) ( )
In collaboration with Chapman and Crowley
Semantic processing of the clinical text (in collaboration with Palmer, Martin and Ward, University of Colorado) ( )
Treebanking (deep parses)
Predicate-argument structure and semantic labeling (PropBanking)
UMLS relations (except temporal relations)

9. Current Efforts - II Temporal relation discovery (2010-2014)
In collaboration with Palmer, Martin and Ward, University of Colorado
Lexical resources for the clinical domain ( )
In collaboration with Chapman, University of Colorado and Elhadad, Columbia University
A la Treebank and clinical named entities with attributes and modifiers