The National Center for Biomedical Ontology

• One of three National Centers for Biomedical Computing launched by NIH in 2005

• Collaboration of Stanford, Berkeley, Mayo, Buffalo, Victoria, UCSF, Oregon, and Cambridge

• Primary goal is to make ontologies accessible and usable

• Research will develop technologies for ontology indexing, alignment, and peer review

• Stanford: Tools for ontology alignment, indexing, and management (Musen)

• Lawrence–Berkeley Labs: Tools to use ontologies for data annotation (Lewis)

• Mayo Clinic: Tools for access to large controlled terminologies (Chute)

• Victoria: Tools for ontology visualization (Story)• University at Buffalo: Dissemination of best practices

for ontology engineering (Smith)

cBio Driving Biological Projects

• Flybase (Cambridge, Ashburner)

• ZFIN (Oregon, Westerfield)

• Trial Bank (UCSF, Sim)

cBio plans to offer 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

Why Develop an Ontology?

• To share common understanding of the structure of descriptive information – among people– among software agents– between people and software

• To enable reuse of domain knowledge– to avoid “re-inventing the wheel”– to introduce standards to allow interoperability

A Small Portion of ICD9-CM724 Unspecified disorders of the

back724.0 Spinal stenosis, other than

cervical724.00 Spinal stenosis,

unspecified region724.01 Spinal stenosis, thoracic

region724.02 Spinal stenosis, lumbar

region724.09 Spinal stenosis, other724.1 Pain in thoracic spine724.2 Lumbago724.3 Sciatica724.4 Thoracic or lumbosacral neuritis724.5 Backache, unspecified724.6 Disorders of sacrum724.7 Disorders of coccyx724.70 Unspecified disorder of

coccyx724.71 Hypermobility of coccyx724.71 Coccygodynia724.8 Other symptoms referable to back724.9 Other unspecified back disorders

The Foundational Model of AnatomyThe Foundational Model of Anatomy

A Portion of the OBO Library

Open Biomedical Ontologies

(OBO)

Open Biomedical Database (OBD)

BioPortal

Capture and index experimental results

Revise biomedicalunderstanding

Relate experimental data to results from other sources

Annotations on experimental data

Visualization and analysis

National Center for Biomedical Ontology