Download - BioPortal and NCBO Web services
THE NATIONAL CENTER FORBIOMEDICAL ONTOLOGY
BioPortal and NCBO Web services
Trish WhetzelOutreach Coordinator
National Center for Biomedical Ontology
• Mission – To create software for the application of
ontologies in biomedical science and clinical care
• NCBO Partners– Mark Musen, Stanford University– Christopher Chute, Mayo Clinic– Barry Smith, University at Buffalo– Margaret-Anne Storey, University of Victoria
National Centers for Biomedical Computing(http://www.ncbcs.org)
NCBO Key Activities
• We create and maintain a library of biomedical ontologies
• We build tools and Web services to enable the use of ontologies
• We collaborate with scientific communities that develop and use ontologies
www.bioontology.org
http://bioportal.bioontology.org
http:
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Ontology ServicesOntology Services
• Search• Traverse• Comment• Download
• Search• Traverse• Comment• Download
WidgetsWidgets• Tree-view• Auto-complete• Graph-view
• Tree-view• Auto-complete• Graph-view
AnnotationAnnotation
Data AccessData Access
Mapping ServicesMapping Services
• Create• Upload• Download
• Create• Upload• Download
ViewsViews
Term recognitionTerm recognition
Fetch “data” annotated with a given term
Fetch “data” annotated with a given term
http://bioportal.bioontology.orghttp://bioportal.bioontology.org
Browse ontologies
Search for terms
Widgets
Tree widget
Visualization
Term auto-complete
Tag text with ontology terms
Term – 1:::Term – nSyntactic typesSyntactic types
FrequencyFrequency
Term recognition tool NCBO Annotator
Term recognition tool NCBO Annotator NegEx
PatternsNegEx
Patterns
NegEx Rules – Negation detection
NegEx Rules – Negation detection
P1 ICD9 ICD9 ICD9 ICD9 ICD9 ICD9
P1 T1, T2, no T4
… T5, T4, T3
… T4, T3, T1
T8, T9, T4
… T6, T8, T10
T1, T2, no T4
P2
P2
P3
P3
:
:
Pn
PnTerms form a temporal series of tags
Co
ho
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of
Inte
rest
DiseasesDiseases
ProceduresProcedures
DrugsDrugs
BioPortal – knowledge graph
Creating clean lexicons
NCBO Annotator
Furt
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Text clinical note
Terms Recognized
Negation detection
Generation of tagged data
ROR of 2.058, CI of [1.804, 2.349]PRR of 1.828, CI of [1.645, 2.032]The uncorrected X2 statistic has p-value < 10-7.
ROR=1.524, CI=[0.872, 2.666] PRR=1.508, CI=[0.8768, 2.594]X2 p-value=0.06816.
Adverse drug events
Search ontology-based index
Who is using our Web services?
BioPortal SPARQL Endpoint
http://sparql.bioontology.org/
Links of Interest• Web service documentation
http://www.bioontology.org/wiki/index.php/NCBO_REST_services
• Software questions– Software support: [email protected]
• Social media– Twitter: @bioontology– Facebook: http://on.fb.me/bioontology – LinkedIn: http://linkd.in/ncbo-group
