ncbo web services: powering semantically aware applications
DESCRIPTION
Tutorial on NCBO Web services and examples of apps using NCBO Technology from ICBO 2013TRANSCRIPT
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THE NATIONAL CENTER FORBIOMEDICAL ONTOLOGY
NCBO Web Services: Powering Semantically Aware Applications
Trish WhetzelOutreach Coordinator
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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 of 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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Outline
• NCBO Web services Overview• Ontology Development and Visualization• Data Annotation• Data Integration
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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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Outline
• NCBO Web services• 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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Outline
• NCBO Web services• 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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Outline
• NCBO Web services• 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