bioportal and ncbo web services
DESCRIPTION
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
![Page 1: BioPortal and NCBO Web services](https://reader035.vdocuments.mx/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/1.jpg)
THE NATIONAL CENTER FORBIOMEDICAL ONTOLOGY
BioPortal and NCBO Web services
Trish WhetzelOutreach Coordinator
![Page 2: BioPortal and NCBO Web services](https://reader035.vdocuments.mx/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/2.jpg)
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
![Page 3: BioPortal and NCBO Web services](https://reader035.vdocuments.mx/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/3.jpg)
National Centers for Biomedical Computing(http://www.ncbcs.org)
![Page 4: BioPortal and NCBO Web services](https://reader035.vdocuments.mx/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/4.jpg)
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
![Page 5: BioPortal and NCBO Web services](https://reader035.vdocuments.mx/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/5.jpg)
www.bioontology.org
![Page 6: BioPortal and NCBO Web services](https://reader035.vdocuments.mx/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/6.jpg)
http://bioportal.bioontology.org
![Page 7: BioPortal and NCBO Web services](https://reader035.vdocuments.mx/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/7.jpg)
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
![Page 8: BioPortal and NCBO Web services](https://reader035.vdocuments.mx/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/8.jpg)
Browse ontologies
![Page 9: BioPortal and NCBO Web services](https://reader035.vdocuments.mx/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/9.jpg)
Search for terms
![Page 10: BioPortal and NCBO Web services](https://reader035.vdocuments.mx/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/10.jpg)
Widgets
Tree widget
Visualization
Term auto-complete
![Page 11: BioPortal and NCBO Web services](https://reader035.vdocuments.mx/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/11.jpg)
Tag text with ontology terms
![Page 12: BioPortal and NCBO Web services](https://reader035.vdocuments.mx/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/12.jpg)
![Page 13: BioPortal and NCBO Web services](https://reader035.vdocuments.mx/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/13.jpg)
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
![Page 14: BioPortal and NCBO Web services](https://reader035.vdocuments.mx/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/14.jpg)
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
![Page 15: BioPortal and NCBO Web services](https://reader035.vdocuments.mx/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/15.jpg)
Search ontology-based index
![Page 16: BioPortal and NCBO Web services](https://reader035.vdocuments.mx/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/16.jpg)
![Page 17: BioPortal and NCBO Web services](https://reader035.vdocuments.mx/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/17.jpg)
Who is using our Web services?
![Page 18: BioPortal and NCBO Web services](https://reader035.vdocuments.mx/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/18.jpg)
BioPortal SPARQL Endpoint
http://sparql.bioontology.org/
![Page 19: BioPortal and NCBO Web services](https://reader035.vdocuments.mx/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/19.jpg)
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