1. The NCBO Annotator and Enrichment Analysis with the
Human Disease Ontology
Trish Whetzel, Paea LePendu, Ray Fergerson, Mark Musen, Nigam Shah
Stanford University, Stanford, CA
250+ Biomedical Ontologies
• Create clean lexicons
• Normalize via mappings
• Aggregate via hierarchies
1
Pattern Analysis
1.04–million patients
• Use temporal ordering
NCBO Annotator Workflow
2.8–million terms
9.5–million clinical notes
• Adds negation detection
• Processes 1–million notes per hour
2
Patient t0 t1 … tn
Acknowledgements
The National Center for Biomedical Ontology is one of the National Centers for
Biomedical Computing supported by the NHGRI, the NHLBI, and the NIH Common
Fund under grant U54-HG004028.
1 A,B,X B,X,Y … A,X
2 B,X,Z C,Z … B,C
3 A,C,Y B,Z … X
Drug Safety Off-label Drug Use
3
Enrichment Analysis
For more information on the NCBO, visit http://www.bioontology.org
or email support@bioontology.org