The National Center for Biomedical Ontology

Stanford – Berkeley Mayo – Victoria – Buffalo

UCSF – Oregon – Cambridgehttp://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”

• 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

Open Biomedical Ontologies

(OBO)

Open Biomedical Data (OBD)

BioPortal

Capture and index experimental results

Revise biomedicalunderstanding

Relate experimental data to results from other sources

National Center for Biomedical Ontology

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