The National Center for Biomedical Ontology Stanford Berkeley

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The National Center for Biomedical Ontology Stanford – Berkeley Mayo – Victoria – Buffalo

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

Ontologies are essential to make sense of biomedical data

Biologist have adopted ontologies • To provide canonical representation of scientific knowledge • To

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

A Portion of the OBO Library

A Portion of the OBO Library

Knowledge workers seem trapped in a pre-industrial age • Most ontologies are of relatively

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

• 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)

National Center for Biomedical Ontology Capture and index experimental results Open Biomedical Ontologies (OBO) Revise biomedical understanding Open Biomedical Data (OBD) Bio. Portal Relate experimental data to results from other sources

E-science needs technologies • To help build and extend ontologies • To locate ontologies

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

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

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 R 01” grant • Defining a biological driving project http: //www. bioontology. org