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Linking Ontologies and ISO/IEC 11179 in the CEDAR Metadata Repository

Linking Ontologies and ISO/IEC 11179 in the CEDAR Metadata Repository. Martin J. O’Connor Technical Lead, CEDAR Project Stanford University. What is this colored picture about?. Minimal information checklists, such as MIAME, are being advanced from all sectors of the biomedical community

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Linking Ontologies and ISO/IEC 11179 in the CEDAR Metadata Repository

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  1. Linking Ontologies and ISO/IEC 11179 in the CEDAR Metadata Repository Martin J. O’Connor Technical Lead, CEDAR Project Stanford University

  2. What is this colored picture about?

  3. Minimal information checklists, such as MIAME, are being advanced from all sectors of the biomedical community • Investigators view requests for even “minimal” information as burdensome • There is an urgent need to lower the bar for authoring good metadata

  4. 68 168

  5. The BioSharing approach is limited • Emphasis has been on development of simple checklists of metadata elements • Little consideration of • How to supply values for the metadata elements • Standard ontologies that might be used • We need a more expressive—and computable—framework for describing metadata

  6. Unguided Data Entry is Problematic

  7. Example entity–relationship diagram for describing metadata for annotating multiplex bead array assays (e.g., Luminex) HIPC centerssubmit data directly to the NIAID ImmPortdata repository using detailed, experiment-specific templates

  8. A Metadata Ecosystem • HIPC investigators perform experiments in human immunology • HIPC Standards Working Group creates metadata templates to annotate experimental data in a uniform manner • ImmPort stores HIPC data (and metadata) in its public repository • Researchers use resulting metadata resources.

  9. The CEDAR Approach to Metadata

  10. CEDAR Technology Will Give Us • Mechanisms • To author metadata template elements • To assemble them into composite templates (a la forms) • To fill out templates to encode experimental metadata • A repository of metadata • To enable metadata discovery • To learn metadata patterns • To guide predictive entry of new metadata • To inform creation of templates • Links to unique, rigorous encodings and open data • To ensure that metadata fields are well described (a la CDEs) • To ensure that metadata are encoded using appropriate terms • To ensure that references can be found and clearly cited

  11. CEDAR and Ontologies, Value Sets, and ISO/IEC 11179 • CEDAR has direct access to a comprehensive set of BioMedical ontologies via BioPortal • Recently we incorporated value sets into BioPortal for use in CEDAR. Added National Library of Medicine Value Sets. • Current goal: leverage ISO/IEC 11179 repositories, particularly CDEs

  12. The CEDAR Approach to Metadata

  13. CDEs as Value Sets • Can leverage CDEs in CEDAR • Can use some csDSR CDEs in CEDAR tools, e.g., build forms containing CDEs • Incomplete experimental solution: • Not leverage all CDE metadata • Currently not handling numerical CDEs • Semantics not fully understood • However: useful first step

  14. http://metadatacenter.org

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