The National Center for Biomedical Ontology One of

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The National Center for Biomedical Ontology • One of three National Centers for Biomedical

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:

• 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)

c. Bio Driving Biological Projects • Flybase (Cambridge, Ashburner) • ZFIN (Oregon, Westerfield) •

c. Bio Driving Biological Projects • Flybase (Cambridge, Ashburner) • ZFIN (Oregon, Westerfield) • Trial Bank (UCSF, Sim)

c. Bio plans to offer technologies • To help build and extend ontologies •

c. Bio 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

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 ICD 9 -CM 724. 01 724. 02 724. 09 724.

A Small Portion of ICD 9 -CM 724. 01 724. 02 724. 09 724. 1 724. 2 724. 3 724. 4 724. 5 724. 6 724. 70 724. 71 724. 8 724. 9 Unspecified disorders of the back Spinal stenosis, other than cervical Spinal stenosis, unspecified region Spinal stenosis, thoracic region Spinal stenosis, lumbar region Spinal stenosis, other Pain in thoracic spine Lumbago Sciatica Thoracic or lumbosacral neuritis Backache, unspecified Disorders of sacrum Disorders of coccyx Unspecified disorder of coccyx Hypermobility of coccyx Coccygodynia Other symptoms referable to back Other unspecified back disorders

The Foundational Model of Anatomy

The Foundational Model of Anatomy

A Portion of the OBO Library

A Portion of the OBO Library

National Center for Biomedical Ontology Annotations on Open experimenta l data Biomedical Capture and

National Center for Biomedical Ontology Annotations on Open experimenta l data Biomedical Capture and index experimental results Open Biomedical Ontologies (OBO) Revise biomedical understanding Database (OBD) Bio. Portal Visualization and analysis Relate experimental data to results from other sources