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

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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

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Pn

PnTerms form a temporal series of tags

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DiseasesDiseases

ProceduresProcedures

DrugsDrugs

BioPortal – knowledge graph

Creating clean lexicons

NCBO Annotator

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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: support@bioontology.org

• Social media– Twitter: @bioontology– Facebook: http://on.fb.me/bioontology – LinkedIn: http://linkd.in/ncbo-group