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Enabling Medical Experts to navigate clinical text
for cohort identification (meTAKES)
Stephen Wu, Mayo Clinic
SHARPn Summit 2012June 12, 2012
Outline
• Motivation
• Methods (current)• System architecture• Data retrieval• Search• Cohort management
• Conclusion & Future Work
Motivation
• Clinical NLP out-of-the-box• Comprehensive knowledge• Customize? Collaborate!
• Diverse requirements
• Physician/Researcher tasks• Enroll patients in study• Define retrospective cohort• Case abstraction
Somali patients (unique terms)
Drug-induced liver injury (rel’ns)
Pediatric asthma (temporal)
“Medical expert”-driven NLP
• Use case-specific• Streamlined• On-the-fly NLP Diverse requirements
• Interactive interface• Delivery mechanism• Available data vs. expert knowledge
• Use case-agnostic• Comprehensive• Pre-computed NLP Known requirements
text semantics expert criteriasource
Client Server
• Web interface (GWT)
GUI
Lucene
ranked records
EHRdata pool parameters
records
NLP (MedTagger)
query parser
query
cohort manipulation
records
cohort mgmt
Data retrieval
• Parameters (current)• Patient ID• Date
• Sources (current)• Enterprise Data Trust (EDT)
@ Mayo Clinic• Text files on server
Search
• Parameters (current)• Term lists• Logic• Expansion
• Techniques (current)• Dictionary (Lucene)• NLP results
(e.g., negation)
Cohort Management
• Parameters:• Cohort name/tag• Selecting patients
• Export
• Iterative refinement
Conclusion and Future Work
• NLP / search• Text characteristics• Semantic search• Relationships
• HCI / cohort management• Learning• Collaboration
• Interoperability• Structured data• API
• Mayo delivery: DDQB Clinical Notes
Search Tool
Evaluation framework
THANK YOU.
https://sites.google.com/site/stephentzeinnwu
meTAKES team: Stephen Wu Ravikumar K.E. Hongfang Liu
Special thanks to: Siddhartha Jonnalagadda James Masanz Vinod Kaggal Sean Murphy Tom Suther Erik Voldal Carlos Garcia Melissa Gregg
This work was supported in part by the SHARPn (Strategic Health IT Advanced Research Projects) Area 4: Secondary Use of EHR Data Cooperative Agreement from the HHS Office of the National Coordinator, Washington, DC. DHHS 90TR000201.