Workshop Bethesda 2007 July case review

July Bethesda OBI Workshop - Use Case Review

This page provides a general outline of the Use Cases we'd like to review at the meeting, a brief definition of Use Case in this context, and aggregates links to Use Cases from specific OBI Branch Use Case pages.

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Use Case Scope and Definition

<<We need to have a clear definition and statement of scope for these Use Cases, so all branches & communities can use this as a guide when assembling their Use Cases>>

General Use Case Hierarchy

• Use of OBI within other ontologies
  • NMR Instruments (for metabolomics investigation)
  • BIRNLex - from BIRN
• Representation of biomedical investigation instances - experiment provenance - referencing OBI elements
  • Representation of biomedical investigation instances using current formats (XML Schemas, flat file formats, etc.) designed by specific communities for export/exchange of provenance data
    • gene expression studies
      • FuGE
      • MicroArray and Gene Expression (MAGE)
        • v1.1
        • v2.0 (layered on top of FuGE)
    • bioimaging studies
      • XML-based Clinical Experiment Data Exchange Schema (XCEDE) (from BIRN)
      • Digital Imaging and Communications in Medicine (DICOM)
  • Representation of biomedical investigation instances using Minimal Information Lists
    • Minimal Information for Biological and Biomedical Investigations (MIBBI)

Related Links

OBI Branch Use Case Summaries

• link to Biomaterial Branch Use Cases
• link to Data Transformation Branch Use Cases
• link to Digital Entity and Non-realizable Entity Branch Use Cases
• Function Branch Use Cases
• link to Plan (Investigation Design & Protocol) Branch Use Cases
• link to Protocol Application Branch Use Cases
• link to Qualities Branch Use Cases
• link to Role Branch Use Cases
• link to Relation Branch Use Cases

OBI Community Use Case Summaries

• link to Cellular Assays Community Use Cases
• link to Crop Sciences Community Use Cases
• link to Clinical Trials Community Use Cases
• link to Environmental Biology Community Use Cases
• link to Flow Cytometry Community Use Cases
• link to Genomics/Metagenomics Community Use Cases
• link to ImmPort Community Use Cases
• link to Immune Epitope Database and Analysis Resource Community Use Cases
• link to In Situ Hybridization and Immunohistochemistry Community Use Cases
• link to Metabol/nomics Community Use Cases
• link to Neuroinformatics and Bio-imaging Community Use Cases
• link to Nutrigenomics Community Use Cases
• link to Polymorphism Community Use Cases
• link to Proteomics Community Use Cases
• link to Toxicogenomics Community Use Cases
• link to Transcriptomics Community Use Cases