NCBO Technology Overview
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![Page 1: NCBO Technology Overview](https://reader035.fdocuments.net/reader035/viewer/2022062313/557dc1d4d8b42a8a188b511e/html5/thumbnails/1.jpg)
THE NATIONAL CENTER FORBIOMEDICAL ONTOLOGY
NCBO Technology Overview
Trish WhetzelOutreach Coordinator
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Links of Interest
• http://www.bioontology.org/wiki/index.php/NCBO_Web_Services_and_the_Development_of_Semantic_Applications
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Outline
• Learning Objectives• REST Web services• BioPortal• NCBO Web Services• BioPortal SPARQL Endpoint
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Learning Objectives
• Learn what Web services are available from NCBO
• Learn how to programmatically use these Web services
• Learn how to combine these Web services to perform tasks
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REST Web Services
• Accessed via HTTP– http://rest.bioontology.org/{parameters}
• Each unique URL is a representation of some object
• Operations include GET, POST, PUT, DELETE • Lightweight, easy to build
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Web Services
Code
User Interface
Browser
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Outline
• REST Web services• BioPortal• NCBO Web Services• BioPortal SPARQL Endpoint
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http://bioportal.bioontology.org
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Outline
• REST Web services• BioPortal• NCBO Web Services• BioPortal SPARQL Endpoint
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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
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Ontology Web Services
Accessing, browsing, searching and traversing ontologies in Your application
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Ontology Web Services
• List All Ontologies– List all ontologies in BioPortal – Documentation: http://bit.ly/sxL2Qi – GoogleDoc Excel example:
http://bit.ly/ncbo-list-all-ontologies
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Ontology version id
Ontology id
One ontology idhas many ontology version ids
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Ontology Web Services cont.
• Search– Search by term or term identifier across all ontologies
in BioPortal• Documentation: http://bit.ly/tMDkr6 • Example clients
– Java: http://bit.ly/ttTb1G – Perl: http://bit.ly/sPXC2X
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Ontology Web Services cont.
• Term– get details about a term including it’s definition,
synonyms, URI, super- and sub-classes, and other properties http://bit.ly/teedbd
• Hierarchy– get parent, children, and sibling terms
http://bit.ly/tPzm75
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Notes Web Services
Propose new terms and comment on ontologies
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Notes Web Service
• Add terms proposals and comments on ontology terms
• Documentation: http://www.bioontology.org/wiki/index.php/Ontology_Notes
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WebProtégé
http://protegewiki.stanford.edu/wiki/WebProtegehttp://protegewiki.stanford.edu/wiki/WebProtege
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VIEWs
Custom subset of large ontologies
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Views and Value Sets
• Users can submit their own derivatives of BioPortal ontologies – these which become first-class objects in BioPortal and
can be used as all other Web services
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Views in BioPortal
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Views and Value Sets
• View Extraction Web service – Given a root node term, extracts all child terms
http://bit.ly/uXeh2s • Access directly from Protégé via the BioPortal
Import plugin http://protegewiki.stanford.edu/wiki/BioPortal_Import_Plugin
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MAPPING Web Services
Using NCBO technology to integrate terminologies and ontologies
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MappingsMappings
Root
Term-1 Term-2
Term-3 Term-4
Term-5
R
t1 t2
t4
t5 t6 t7
t3
Term-2 t1
Term-5 t5
Ontology A Upload or Download mapping subsets
Ontology B
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Mappings
• Mappings Web service– Documentation:
http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service
• Functions– Get – Create/Upload
• Example Perl client to Get mappings: http://bit.ly/tDKPQd
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widgets
Using NCBO technology on your web pages
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Widgets
• Form auto-complete – auto-complete function and can return term URI, term ID or term name
• Jump To – auto-complete function to select term and Jump To BioPortal to view term details
• Visualize widget – view the ontology structure and relations
• Tree widget – view the ontology tree
Code for widgets is available on BioPortal
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Widgets
RSS feed
Form auto-complete
Jump To
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Widgets
Tree widget
Visualization
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Break
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Annotator web service
Using Ontologies to Annotate Your Data
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Annotator: The Basic Idea
• Tag textual metadata with ontology terms
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Annotator Workflow
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Annotator Web Service
• Tag free text with ontology terms• Documentation:
http://www.bioontology.org/wiki/index.php/Annotator_Web_service
• Example clients:– Perl: http://bit.ly/vKYpCP – Java: http://bit.ly/rRFoKd
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Data service
Using Ontologies to Access Public Data
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Resource Index: The Basic Idea
• The index can be used for• Search• Data mining
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Data Access
• Resource Index Web service– Documentation:
http://www.bioontology.org/wiki/index.php/Resource_Index
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BioPortal SPARQL Endpoint
• Documentation: http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal
• Query interface: http://alphasparql.bioontology.org/
• Example queries: http://alphasparql.bioontology.org/examples
• Sample code: https://github.com/ncbo/sparql-code-examples
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Thank you!
• Web service documentation: http://www.bioontology.org/wiki/
index.php/NCBO_REST_services• Keep in touch
– NCBO Announce mailing list: http://bit.ly/osLzng– Software support: [email protected] – Twitter: @bioontology– Facebook and LinkedIn
• Questions: [email protected]
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RightField
http://www.sysmo-db.org/rightfieldhttp://www.sysmo-db.org/rightfield
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ECG Gadget
http://wiki.cvrgrid.org/index.php/ECGGadgethttp://wiki.cvrgrid.org/index.php/ECGGadget
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ISAcreator
http://isatab.sourceforge.net/isacreator.htmlhttp://isatab.sourceforge.net/isacreator.html
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DOG4DAG Ontology Generation Tool for OBO-Edit and Protégé
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Word Add-in
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cgMDR
http://cancergrid.org/index.phphttp://cancergrid.org/index.php
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openMDR
http://citih.osumc.edu/projects/project&r=1032http://citih.osumc.edu/projects/project&r=1032
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eleMap
https://victr.vanderbilt.edu/eleMAP/https://victr.vanderbilt.edu/eleMAP/
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BioPortal Import Plugin
http://protegewiki.stanford.edu/wiki/BioPortal_Import_Pluginhttp://protegewiki.stanford.edu/wiki/BioPortal_Import_Plugin
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RedFly
http://redfly.ccr.buffalo.edu/index.phphttp://redfly.ccr.buffalo.edu/index.php
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Radiological Society of North America
http://radlex.org/http://radlex.org/
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GMiner
http://gminer.mcw.edu/http://gminer.mcw.edu/
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Knowledge Egg
http://www.kunnskapsegget.no/http://www.kunnskapsegget.no/
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Gene Wiki
Annotator
http://en.wikipedia.org/wiki/Portal:Gene_Wikihttp://en.wikipedia.org/wiki/Portal:Gene_Wiki
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Statistical Tracking of Ontological Phrases (STOP)
http://www.mooneygroup.org/content/webtoolshttp://www.mooneygroup.org/content/webtools
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Ontological Discovery Environment
http://ontologicaldiscovery.org/http://ontologicaldiscovery.org/
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STRIDE
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ODiSSea