The NCBO Annotator and Enrichment Analysis with the Human Disease Ontology
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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 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. 250+ Biomedical Ontologies • Create clean lexicons • Normalize via mappings • Aggregate via hierarchies 1 Pattern Analysis 1.04–million patients • Use temporal ordering Patien t t 0 t 1 … t n 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 Workflow 2.8–million terms 9.5–million clinical notes • Adds negation detection • Processes 1–million notes per hour Drug Safety Off-label Drug Use 2 3 Enrichment Analysis For more information on the NCBO, visit http:// www.bioontology.org or email support@ bioontology.org
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Poster presentation at CSHALS 2012.
Transcript of The NCBO Annotator and Enrichment Analysis with the Human Disease Ontology
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
1
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
2
3
Enrichment Analysis
For more information on the NCBO, visit http://www.bioontology.org or email [email protected]
