Enabling Semantically Aware Software Applications

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 – whetzel@stanford.edu