THE NATIONAL CENTER FORBIOMEDICAL ONTOLOGY
Enabling Semantically Aware Software Applications
Trish Whetzel, PhD Outreach Coordinator
Outline
• Overview of NCBO • NCBO Software
– BioPortal– Ontology Widgets– Annotator– Resource Index
• Future Plans
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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 Victoria - Dr. Margaret-Anne
Storey– University of Buffalo - Dr. Barry Smith
National Centers for Biomedical Computing(http://www.ncbcs.org)
BioPortal
http://bioportal.bioontology.org/http://bioportal.bioontology.org/
BioPortal
• Library of Ontologies– NCBO BioPortal includes Biomedical ontology
content, e.g. UMLS terminologies
• Architecture– Backend includes LexEVS and Protégé – Web Interface uses Ruby on Rails, Flex, and PHP
• Web services– REST Web services
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BioPortal
• Functionality– Search across all ontologies
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BioPortal
• Functionality– Browse ontology hierarchy– Details about a concept
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BioPortal
• Functionality– Visualize the ontology graph
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BioPortal
• Functionality– Mappings to/from other ontologies
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BioPortal
• Functionality– Notes
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BioPortal Notes
• Notes– Provide a mechanism to collect structured
information– Integration with ontology editing programs– Alerts – Email and RSS
Use Case for BioPortal Notes
• Ontology Enrichment– Expansion of the ontology based on user need for
terms
• Constraints – Existing trackers do not collect structured
information– No programmatic access to tracker– Lack of integration with ontology editing
programs
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BioPortal Notes
Ontology Widgets
• Ontology Widgets– Code to use in your web site
• Types– Jump To – Term auto-completion – View ontology graph – Ontology change alerts
• Available for all ontologies in BioPortal– Click on the Widgets tab
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Ontology Widgets
• BioPortal Widgets
RSS feedRSS feed
Term-selectionTerm-selection
Jump ToJump To
Ontology Widgets
• BioPortal Widgets
Tree widgetTree widget
VisualizationVisualization
NCBO Annotator
• Open access, ontology-based Web service that annotates or “tags” textual metadata
• Annotation is done using ontologies from BioPortal, including Unified Medical Language System terminologies
• Variety of parameters that can be customized
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Annotator: The Basic Idea
• Tag textual metadata with ontology terms
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Annotator Workflow
Annotator - Parameters
• longestOnly (boolean) - match longest term phrase– E.g. Purkinje cell versus Purkinje cell and cell
• stopWords (list) - words not to match• withDefaultStopWords (boolean)
– http://rest.bioontology.org/obs/stopwords• scored (boolean) - reflects the accuracy of the
annotation– E.g. Direct match scored higher than synonym
Annotator - Parameters
• ontologiesToExpand (list) - ontologies to check for mappings for expanded annotation
• ontologiesToKeepInResult (list) - ontologies to show in result
• semanticTypes (list) - refers to UMLS ontologies– http://rest.bioontology.org/obs/semanticTypes
• levelMax (integer) - hierarchy level to traverse for expanded annotation
• format - annotation result format – xml, text, or tabDelimited
Semantic Expansion
• is-a transitive closure– Traverses the ontology parent-child hierarchy creating
new annotations with the parent terms
Semantic Expansion
• Mapping expansion– Creates new annotations based on existing mappings
between ontologies
Code
Excel
UIMA platform
User Interface
Annotator Web service
Resource Index: The Basic Idea
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Resource Index: Use Case
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Resource Index: Use Case
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Resource Index: Use Case
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Future Plans
• Services that allow use of ontologies via an enhanced version of BioPortal
• Integration of ontology authoring, publishing, and peer review
• A comprehensive ontology-based index of online biomedical resources
• Analytic methods to summarize and profile biomedical data sets
References• BioPortal
– http://bioportal.bioontology.org • Annotator
– http://www.bioontology.org/wiki/index.php/Annotator_Web_service
• Resource Index– http://www.bioontology.org/wiki/index.php/
NCBO_Biomedical_Resources_Index • Web service documentation:
– http://www.bioontology.org/wiki/index.php/NCBO_REST_services
• Trish Whetzel – [email protected]