The NCBO Annotator and Enrichment Analysis with the Human Disease Ontology

Trish Whetzel, Paea LePendu, Ray Fergerson, Mark Musen, Nigam ShahStanford University, Stanford, CA

AcknowledgementsThe 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.

250+ Biomedical Ontologies• Create clean lexicons• Normalize via mappings• Aggregate via hierarchies

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Pattern Analysis1.04–million patients

• Use temporal ordering

Patient t0 t1 … tn

1 A,B,X B,X,Y … A,X

2 B,X,Z C,Z … B,C

3 A,C,Y B,Z … X

NCBO Annotator Workflow2.8–million terms9.5–million clinical notes

• Adds negation detection• Processes 1–million notes per hour

Drug Safety Off-label Drug Use

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Enrichment Analysis

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