THE NATIONAL CENTER FORBIOMEDICAL ONTOLOGY

NCBO Web Services: Powering Semantically Aware Applications

Trish WhetzelOutreach Coordinator

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

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

National Centers for Biomedical Computing(http://www.ncbcs.org)

www.bioontology.org

Outline

• NCBO Web services Overview• Ontology Development and Visualization• Data Annotation• Data Integration

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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

Term recognitionTerm recognition

Search “data” annotated with a given term

Search “data” annotated with a given term

http://bioportal.bioontology.orghttp://bioportal.bioontology.org

Outline

• NCBO Web services• Ontology Development and Visualization• Data Annotation• Data Integration

http://protegewiki.stanford.edu/wiki/BioPortal_Import_Pluginhttp://protegewiki.stanford.edu/wiki/BioPortal_Import_Plugin

http://ols2owl.sourceforge.net/ http://ols2owl.sourceforge.net/

http://webprotege/ http://webprotege/

http://www.biotec.tu-dresden.de/research/schroeder/dog4dag/http://www.biotec.tu-dresden.de/research/schroeder/dog4dag/

http://radlex.org/http://radlex.org/

Outline

• NCBO Web services• Ontology Development and Visualization• Data Annotation• Data Integration

http://www.sysmo-db.org/rightfieldhttp://www.sysmo-db.org/rightfield

http://isatab.sourceforge.net/isacreator.htmlhttp://isatab.sourceforge.net/isacreator.html

http://wiki.cvrgrid.org/index.php/ECGGadgethttp://wiki.cvrgrid.org/index.php/ECGGadget

http://redfly.ccr.buffalo.edu/index.phphttp://redfly.ccr.buffalo.edu/index.php

Outline

• NCBO Web services• Ontology Development and Visualization• Data Annotation• Data Integration

Annotator

http://en.wikipedia.org/wiki/Portal:Gene_Wikihttp://en.wikipedia.org/wiki/Portal:Gene_Wiki

http://www.kunnskapsegget.no/http://www.kunnskapsegget.no/

Knowledge EggKnowledge Egg

http://ontologicaldiscovery.org/http://ontologicaldiscovery.org/

ODiSSea

http://www.hub.sciverse.com/http://www.hub.sciverse.com/

Thank you!

• Web service documentation: http://www.bioontology.org/wiki/

index.php/NCBO_REST_services• Keep in touch

– Software support: support@bioontology.org – Twitter: @bioontology– Facebook: http://on.fb.me/bioontology – LinkedIn: http://linkd.in/ncbo-group