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The National Center for Biomedical Ontology

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

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The National Center for Biomedical Ontology

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  1. 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

  2. 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)

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

  4. 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

  5. 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

  6. A Small Portion of ICD9-CM 724 Unspecified disorders of the back 724.0 Spinal stenosis, other than cervical 724.00 Spinal stenosis, unspecified region 724.01 Spinal stenosis, thoracic region 724.02 Spinal stenosis, lumbar region 724.09 Spinal stenosis, other 724.1 Pain in thoracic spine 724.2 Lumbago 724.3 Sciatica 724.4 Thoracic or lumbosacral neuritis 724.5 Backache, unspecified 724.6 Disorders of sacrum 724.7 Disorders of coccyx 724.70 Unspecified disorder of coccyx 724.71 Hypermobility of coccyx 724.71 Coccygodynia 724.8 Other symptoms referable to back 724.9 Other unspecified back disorders

  7. The Foundational Model of Anatomy

  8. A Portion of the OBO Library

  9. National Center for Biomedical Ontology Annotations on experimental data Capture and index experimental results Open Biomedical Ontologies (OBO) Open Biomedical Database (OBD) BioPortal Revise biomedicalunderstanding Relate experimental data to results from other sources Visualization and analysis

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