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 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

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”

A consortium that brings together investigators at 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

Capture and index experimental results National Center for Biomedical Ontology Capture and index experimental results Open Biomedical Ontologies (OBO) Open Biomedical Data (OBD) BioPortal Revise biomedical understanding Relate experimental data to results from other sources 2005

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