Download - BioPortal and NCBO Web services
![Page 1: BioPortal and NCBO Web services](https://reader035.vdocuments.us/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.us/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.us/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.us/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.us/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/5.jpg)
www.bioontology.org
![Page 6: BioPortal and NCBO Web services](https://reader035.vdocuments.us/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/6.jpg)
http://bioportal.bioontology.org
![Page 7: BioPortal and NCBO Web services](https://reader035.vdocuments.us/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.us/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/8.jpg)
Browse ontologies
![Page 9: BioPortal and NCBO Web services](https://reader035.vdocuments.us/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/9.jpg)
Search for terms
![Page 10: BioPortal and NCBO Web services](https://reader035.vdocuments.us/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.us/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/11.jpg)
Tag text with ontology terms
![Page 12: BioPortal and NCBO Web services](https://reader035.vdocuments.us/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/12.jpg)
![Page 13: BioPortal and NCBO Web services](https://reader035.vdocuments.us/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.us/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.us/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/15.jpg)
Search ontology-based index
![Page 16: BioPortal and NCBO Web services](https://reader035.vdocuments.us/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/16.jpg)
![Page 17: BioPortal and NCBO Web services](https://reader035.vdocuments.us/reader035/viewer/2022062314/56814969550346895db6bdc5/html5/thumbnails/17.jpg)
Who is using our Web services?
![Page 18: BioPortal and NCBO Web services](https://reader035.vdocuments.us/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.us/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