Collaborating with the National Center for Biomedical Ontology
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Transcript of Collaborating with the National Center for Biomedical Ontology
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Collaborating with the Collaborating with the National Center for National Center for
Biomedical OntologyBiomedical OntologyMark Musen and the NCBO Team
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http://www.ncbcs.org
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The National Center for Biomedical The National Center for Biomedical OntologyOntology
• One of three National Centers for Biomedical Computing launched by NIH in 2005
• Collaboration of Stanford, Mayo, Buffalo, Washington University, Johns Hopkins, and the Medical College of Wisconsin
• Primary goal is to make ontologies accessible and usable• Research will develop technologies for ontology dissemination, use,
indexing, alignment, and peer review
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NCBO: Key activitiesNCBO: 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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www.bioontology.orgwww.bioontology.org
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http://bioportal.bioontology.org
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BioPortal allows us to experiment BioPortal allows us to experiment with new models for with new models for
• Dissemination of knowledge on the Web• Integration and alignment of online content• Knowledge visualization and cognitive
support • Peer review of online content
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Users can view and create mappingsUsers can view and create mappings
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Biomedical Resource Ontology Biomedical Resource Ontology in BioPortalin BioPortal
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““Notes” in BioPortalNotes” in BioPortal
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Community-Based Annotation as Community-Based Annotation as Peer ReviewPeer Review
• Makes ontology evaluation a democratic process
• Assumes users’ application of ontologies will lead to insights not achievable by inspection alone
• Assumes end-users will be motivated to comment on and engage in dialog about ontologies in the repository
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BioPortal is building an online BioPortal is building an online community of users whocommunity of users who
• Develop, upload, and apply ontologies• Map ontologies to one another• Comment on ontologies via “notes” to give
feedback • To the ontology developers• To one another
• Make proposals for specific changes to ontologies• Stay informed about ontology changes and
proposed changes via “push” technology• Incorporate BioPortal services into their own
technologies
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http://ucsdbiolit.codeplex.comhttp://ucsdbiolit.codeplex.com
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Automated recognition of ontology terms before publication
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BioLit Web resource: automated recognition of ontology terms and database IDs after publication
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IO informatics uses Ontology ServicesIO informatics uses Ontology Services
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Wikipathways uses Ontology ServicesWikipathways uses Ontology Services
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ISAcreator uses Ontology Services
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ECG Gadget uses Ontology Services
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Biositemaps Editor
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Protégé BioPortal-reference plug-inProtégé BioPortal-reference plug-in
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Simbios usesSimbios usesNCBO OntologyNCBO OntologyWeb WidgetsWeb Widgets
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NCBO Annotator: The Basic IdeaNCBO Annotator: The Basic Idea
Process textual metadata to tag text automatically with as many ontology terms as possible.
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NCBO Annotator NCBO Annotator http://bioportal.bioontology.org/annotatehttp://bioportal.bioontology.org/annotate
• Give your text as input
• Select your parameters
• Get your results … in text or XML
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Resources Index: The Basic IdeaResources Index: The Basic Idea
• The index can be used for:• Search• Data mining
NCBO Annotator
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Example: Indexing GEOExample: Indexing GEO
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NCBO Indexed ResourcesNCBO Indexed Resources
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Links to specific resourcesLinks to specific resources
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See our wiki to learn more!See our wiki to learn more!
www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project
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Ways to collaborate with NCBOWays to collaborate with NCBO
• Be a user!• Propose a Driving Biological Project (DBP)• Get a collaborating research grant (NIH
R01)• Initiate an industrial or academic joint
projects
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Current Driving Biological ProjectsCurrent Driving Biological Projects
• caNanoLab: Workers at Stanford and Wash U developing searchable catalog of therapeutic nanoparticles
• Cardiovascular Research Grid: Workers at Hopkins developing ontology of ECGs and electrophysiological studies
• Rat Genome Database: Workers at MCW use ontologies to annotate genomic data
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Current “Collaborating R01” grantsCurrent “Collaborating R01” grants
• UW: Creating views of ontologies• UCSD: Using ontologies to annotate
neuroimaging data• UC Denver: Ontology enrichment through
published literature• Pittsburgh: Ontology enrichment through
EMR data• Wright State: Semantic data integration
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Some other collaborative activitiesSome other collaborative activities
• CollaboRx, Inc. — Resource annotation• NextBio, Inc. — Ontology-based search• Google, Inc. — Web of Trust• University of Karlsruhe — Use of OMV in
BioPortal metadata• World Health Organization — Ontology
support for ICD11
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Other NCBO componentsOther NCBO components
• Education and training• Graduate students• Post docs• Visiting researchers
• Outreach and dissemination• Specialized workshops• Support for conferences
• ISMB Bio-ontologies SIG• International Conference on Biomedical Ontology
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NCBO needs HCLS!NCBO needs HCLS!
• To push on our technology• To drive our requirements• To help disseminate ontology-based
methods in biomedicine• To help promote W3C recommendations in
biomedicine• To help us in our mission to educate the
community and to encourage best practices
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http://bioontology.org