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Cdao Evolution08

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This presentation gives a brief introduction to the comparative data analysis ontology. It was presented at Evolution 08, June 2008

This presentation gives a brief introduction to the comparative data analysis ontology. It was presented at Evolution 08, June 2008

Published in: Education, Technology

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Transcript

  • 1. Comparative Data Analysis Ontology
  • 2. Presentation Outline
    • Motivation/ Goals
    • Implementation
    • NeXML Integration
    • Online Resources
    • Testing
    • Future Work
    • Acknowledgments
  • 3. Motivation/Goals
    • Motivation
      • Ease incompatibilities
        • Software
        • File formats
    • Goals
      • Provide a Framework for Comparative Analysis
        • Controlled Vocabulary
          • Synonym support
          • Facilitate data exchange
        • Validation
          • Semantic problems can be identified more readily.
        • Applications
          • Smart Querying
            • The ontology will allow one to query for inferred data.
          • Work-flows and Service Composition
  • 4. Implementation
    • OWL (Web Ontology Language)
      • Positive Factors
        • W3C Standard
        • Tool support
          • Protege: editing
          • Pellet: query too
        • Existing Ontologies can be readily be used.
      • Negative Factors
        • Support for many advanced features is missing or not yet well implemented in tools.
          • Especially OWL 1.1 constructs
        • Types of relationships and queries can be limited.
  • 5. Key Classes
    • OTU represents a taxon name
    • CharacterStateDataMatrix relates OTU's to associated characters and the states of those characters.
    • Network: is the most general type of tree. We also define several more specific classes for trees.
    • Node
      • Node instances are connected by edge instances and attached by a property to an OTU instance.
    • Edge
      • Edge instances relate node instances to each other.
  • 6. Additional Tools
    • Translator
      • Import formats
        • Supported Input files
          • Imports Nexus files to CDAO
            • Uses Paul Lewis' NCL to parse files
                • Does not support continuous characters (yet).
              • We are adding support of these characters
        • Planned support
          • NeXML
          • Mega
          • Phylip
      • Output CDAO compliant Owl instances.
      • Other attributes
        • Written in C++
        • Licensed under GNU GPL
  • 7. NeXML Annotation
    • Annotating NeXML structures in terms of CDAO classes.
      • Provides semantics for NeXML syntax
      • NeXML users get this additional rigor transparently.
      • Should also help with:
        • Service integration
        • Translation to other formats
        • Validation of semantics in addition to syntax
  • 8. Online Resources
    • Wiki
      • http://www.evolutionaryontology.org/CDAO
    • Artifacts
      • http://sourceforge.net/projects/cdao/
  • 9. Testing
    • Translation
      • Several nexus data files were translated into instances of CDAO classes.
    • Queries
      • Pellet is being used to query matrix and tree instances
        • Pros:
          • Standard, widely used tool
          • Easy to learn query language
        • Cons:
          • Very slow for queries on large or complex instances.
  • 10. Future Work
    • Refine model
      • Transition Model
      • Allow increased flexibility with community curators or a temporary term system.
        • RDBOM sounds promising as a candidate for this role.
    • Outreach
      • MIAPA
      • Data providers
      • Provide an instance creation/validation webservice.
  • 11. Acknowledgments
    • Institutions
      • NESCent
      • NMSU
      • NIST
      • IGBMC
    • Individuals
      • Enrico Pontelli
      • Francisco Prodocimi
      • Arlin Stoltzfus
      • Julie Thompson
      • The entire EvoInfo working group
  • 12. Questions

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