ncbo technology
DESCRIPTION
Tutorial presentation of NCBO Technology for the EBI Industry Programme meeting, 2013.TRANSCRIPT
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THE NATIONAL CENTER FORBIOMEDICAL ONTOLOGY
NCBO Technology
Trish WhetzelOutreach Coordinator
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Outline
• NCBO Overview• BioPortal and NCBO Web Services• BioPortal SPARQL Endpoint• Applications using NCBO Technology
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National Center for Biomedical Ontology
• Mission – To create software for the application of
ontologies in biomedical science and clinical care
• NCBO Partners– Stanford University - Dr. Mark A. Musen– Mayo Clinic - Dr. Christopher G. Chute– University at Buffalo - Dr. Barry Smith– University of Victoria - Dr. Margaret-Anne
Storey
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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
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National Centers for Biomedical Computing(http://www.ncbcs.org)
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www.bioontology.org
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Social Media
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Outline
• NCBO Overview• BioPortal and NCBO Web Services• BioPortal SPARQL Endpoint• Applications using NCBO Technology
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bioportal.bioontology.orgbioportal.bioontology.org
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BioPortal
• Repository of biomedical ontologies• Infrastructure is domain independent• Stores ontologies developed in OWL, Protégé
frames, OBO format, and Rich Release Format• Access to ontologies via Web interface, Web
services, and SPARQL • Access control for private ontologies• Supports subsets/views of ontologies
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BioPortal Architecture
OWL, RDF, Protégé frames
RDF Data Store LexEVSProtégé DB
Hibernate ORM
Spring Framework
Restlet
Tomcat
Ruby on Rails
OBO format, UMLS RRF, LexGrid XML
Third partyapplications
SPARQLAccess
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Virtual Appliance Installations
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Virtual Appliance User Locations
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Outline
• NCBO Overview• BioPortal and NCBO Web Services• BioPortal SPARQL Endpoint• Applications using NCBO Technology
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REST Web Services
• Accessed via HTTP– http://rest.bioontology.org/{parameter}
• Each unique URL is a representation of some object
• Operations include GET, POST, PUT, DELETE • Lightweight, easy to build
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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
Term recognitionTerm recognition
Search “data” annotated with a given term
Search “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
• Search– Search by term or term identifier across all ontologies
in BioPortal– Results are ranked by Web page views– Parameters to expand or constrict search
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Ontology Web Services
• Term– Get details about a term including it’s definition,
synonyms, URI, super- and sub-classes, and other properties
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Ontology Web Services
• Hierarchy– Get parent, children, and sibling terms
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Notes Web Services
Propose new terms and comment on ontologies
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Notes Web Service
• Add comments or terms proposals to an ontology
• Maintained as metadata associated with the ontology
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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
• 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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Mapping Access
• Get a list of mappings for an ontology to all other ontologies
• Get a list of mappings between two ontologies• Get a list of mappings for a single term• Get a list of mappings between two terms
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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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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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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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Outline
• NCBO Overview• BioPortal and NCBO Web Services• BioPortal SPARQL Endpoint• Applications using NCBO Technology
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http://sparql.bioontology.org/http://sparql.bioontology.org/
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BioPortal SPARQL Data (beta)
• Ontology Content• Ontology Metadata• Ontology Term Mapping Data
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BioPortal SPARQL Data (beta)
• All ontologies from BioPortal– Original ontology format transformed into RDF
• OBO and OWL converted via OWL API• RRF converted via UMLS2RDF custom code
– Latest version only in beta release
• Statistics (as of Dec. 2012)– 415 ontologies– 4.2M terms– 2419 different predicates– 80M triples
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BioPortal Ontology Metadata
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BioPortal Metadata Ontology
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Globals
• Provides rdfs:subPropertyOf reasoning to enable querying over multiple ontologies while using the same predicate– http://bioportal.bioontology.org/ontologies/globals
• Implemented for:– Preferred name – skos:prefLabel– Synonyms – skos:altLabel– Term definition – skos:definition– Term author – dc:author
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Outline
• NCBO Overview• BioPortal and NCBO Web Services• BioPortal SPARQL Endpoint• Applications using NCBO Technology
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Applications using NCBO Technology
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Applications using NCBO Technology
• Ontology Development and Visualization• Data Annotation• Data Integration
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http://protegewiki.stanford.edu/wiki/BioPortal_Import_Pluginhttp://protegewiki.stanford.edu/wiki/BioPortal_Import_Plugin
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http://ols2owl.sourceforge.net/ http://ols2owl.sourceforge.net/
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http://webprotege/ http://webprotege/
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http://www.biotec.tu-dresden.de/research/schroeder/dog4dag/http://www.biotec.tu-dresden.de/research/schroeder/dog4dag/
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http://radlex.org/http://radlex.org/
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Applications using NCBO Technology
• Ontology Development and Visualization• Data Annotation• Data Integration
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http://www.sysmo-db.org/rightfieldhttp://www.sysmo-db.org/rightfield
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http://isatab.sourceforge.net/isacreator.htmlhttp://isatab.sourceforge.net/isacreator.html
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http://wiki.cvrgrid.org/index.php/ECGGadgethttp://wiki.cvrgrid.org/index.php/ECGGadget
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http://redfly.ccr.buffalo.edu/index.phphttp://redfly.ccr.buffalo.edu/index.php
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Applications using NCBO Technology
• Ontology Development and Visualization• Data Annotation• Data Integration
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Annotator
http://en.wikipedia.org/wiki/Portal:Gene_Wikihttp://en.wikipedia.org/wiki/Portal:Gene_Wiki
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http://www.kunnskapsegget.no/http://www.kunnskapsegget.no/
Knowledge EggKnowledge Egg
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http://ontologicaldiscovery.org/http://ontologicaldiscovery.org/
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ODiSSea
http://www.hub.sciverse.com/http://www.hub.sciverse.com/
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Thank you!
• Web service documentation: http://www.bioontology.org/wiki/
index.php/NCBO_REST_services• Keep in touch
– Software support: [email protected]
– Twitter: @bioontology– Facebook: http://on.fb.me/bioontology – LinkedIn: http://linkd.in/ncbo-group