enabling semantically aware software applications
DESCRIPTION
Overview of NCBO Technology for the Amgen Library meeting, 2011.TRANSCRIPT
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]