Comparative Data Analysis Ontology
Presentation Outline <ul><li>Motivation/ Goals </li></ul><ul><li>Implementation </li></ul><ul><li>NeXML Integration </li><...
Motivation/Goals <ul><li>Motivation </li></ul><ul><ul><li>Ease incompatibilities </li></ul></ul><ul><ul><ul><li>Software <...
Implementation <ul><li>OWL (Web Ontology Language) </li></ul><ul><ul><li>Positive Factors </li></ul></ul><ul><ul><ul><li>W...
Key Classes <ul><li>OTU represents a taxon name </li></ul><ul><li>CharacterStateDataMatrix relates OTU's to associated cha...
Additional Tools <ul><li>Translator </li></ul><ul><ul><li>Import formats </li></ul></ul><ul><ul><ul><li>Supported Input fi...
NeXML Annotation <ul><li>Annotating NeXML structures in terms of CDAO classes. </li></ul><ul><ul><li>Provides semantics fo...
Online Resources <ul><li>Wiki </li></ul><ul><ul><li>http://www.evolutionaryontology.org/CDAO </li></ul></ul><ul><li>Artifa...
Testing <ul><li>Translation </li></ul><ul><ul><li>Several nexus data files were translated into instances of CDAO classes....
Future Work <ul><li>Refine model </li></ul><ul><ul><li>Transition Model </li></ul></ul><ul><ul><li>Allow increased flexibi...
Acknowledgments <ul><li>Institutions </li></ul><ul><ul><li>NESCent </li></ul></ul><ul><ul><li>NMSU </li></ul></ul><ul><ul>...
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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

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Cdao Evolution08

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

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