bioportal and ncbo web services
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BioPortal and NCBO Web services. Trish Whetzel Outreach 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 - PowerPoint PPT PresentationTRANSCRIPT
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:
//re
st.b
ioon
tolo
gy.o
rghtt
p://
rest
.bio
onto
logy
.org
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
rt
of
Inte
rest
DiseasesDiseases
ProceduresProcedures
DrugsDrugs
BioPortal – knowledge graph
Creating clean lexicons
NCBO Annotator
Furt
her A
naly
sis
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