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Cdao Evolution08
 

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

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    Cdao Evolution08 Cdao Evolution08 Presentation Transcript

    • Comparative Data Analysis Ontology
    • Presentation Outline
      • Motivation/ Goals
      • Implementation
      • NeXML Integration
      • Online Resources
      • Testing
      • Future Work
      • Acknowledgments
    • 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
    • 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.
    • 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.
    • 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
    • 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
    • Online Resources
      • Wiki
        • http://www.evolutionaryontology.org/CDAO
      • Artifacts
        • http://sourceforge.net/projects/cdao/
    • 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.
    • 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.
    • Acknowledgments
      • Institutions
        • NESCent
        • NMSU
        • NIST
        • IGBMC
      • Individuals
        • Enrico Pontelli
        • Francisco Prodocimi
        • Arlin Stoltzfus
        • Julie Thompson
        • The entire EvoInfo working group
    • Questions