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The National Center for Biomedical Ontology One of three National Centers for Biomedical Computing launched by NIH in 2005 Collaboration of Stanford, Berkeley,

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Presentation on theme: "The National Center for Biomedical Ontology One of three National Centers for Biomedical Computing launched by NIH in 2005 Collaboration of Stanford, Berkeley,"— Presentation transcript:

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 724Unspecified disorders of the back 724.0Spinal stenosis, other than cervical Spinal stenosis, unspecified region Spinal stenosis, thoracic region Spinal stenosis, lumbar region Spinal stenosis, other 724.1Pain in thoracic spine 724.2Lumbago 724.3Sciatica 724.4Thoracic or lumbosacral neuritis 724.5Backache, unspecified 724.6Disorders of sacrum 724.7Disorders of coccyx Unspecified disorder of coccyx Hypermobility of coccyx Coccygodynia 724.8Other symptoms referable to back 724.9Other unspecified back disorders

7 The Foundational Model of Anatomy

8 A Portion of the OBO Library

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


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