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The National Center for Biomedical Ontology. Stanford – Berkeley Mayo – Victoria – Buffalo UCSF – Oregon – Cambridge http://www.bioontology.org. Ontologies are essential to make sense of biomedical data. Biologist have adopted ontologies.
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The National Center for Biomedical Ontology Stanford – Berkeley Mayo – Victoria – Buffalo UCSF – Oregon – Cambridge http://www.bioontology.org
Biologist have adopted ontologies • To provide canonical representation of scientific knowledge • To annotate experimental data to enable interpretation and comparison across databases • To facilitate knowledge-based applications for • Decision support • Natural language-processing • Data integration
Knowledge workers seem trapped in a pre-industrial age • Most ontologies are of relatively small scale • Most ontologies are built and refined by small groups working arduously in isolation • Success rests heavily on the particular talents of individual artisans, rather than on standard operating procedures • There is an urgent need for technologies to make this process “faster, better, cheaper”
Founded in September 2005 to provide a national focus on the use of ontologies in the biomedical sciences • A consortium that brings together investigators at • Stanford University (Ontology-management technology) • Lawrence Berkeley Labs (Use of ontologies for data annotation) • University of Victoria (Ontology and data visualization) • Mayo Clinic (Access to controlled clinical terminologies) • SUNY Buffalo (Best practices for ontology development) • Our goal: Industrial-strength technology for use of ontologies in e-science
National Center for Biomedical Ontology Capture and index experimental results Open Biomedical Ontologies (OBO) Open Biomedical Data (OBD) BioPortal Revise biomedicalunderstanding Relate experimental data to results from other sources
E-science needs technologies • To help build and extend ontologies • To locate ontologies and to relate them to one another • To visualize relationships and to aid understanding • To facilitate evaluation and annotation of ontologies
Goals for the National Center for Biomedical Ontology • Integrated ontology libraries in cyberspace • Meta-data standards for ontology annotation • Comprehensive methods for ontology indexing and retrieval • Easy-to-use portals for ontology access, annotation, and peer review • End-user platforms for putting ontologies to use for • Data annotation • Decision support • Natural-language processing • Information retrieval • And applications that we have not yet thought of!
Opportunities to collaborate with the Center • Using the Center’s technology • Contributing ontologies to the OBO library • Submitting a proposal to the NIH for a “collaborating R01” grant • Defining a biological driving project http://www.bioontology.org