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CDAO-STORE:
A New Vision for Data Integration



Brandon Chisham, Trung Le, Enrico Pontelli,
          Tran Son, Ben Wrigh...
CDAO

    Comparative Data Analysis Ontology
    
        Provides semantics to the descriptions of data
        commonl...
What We Did

    CDAO-Store
    
        A repository providing a rich set of API's for
        querying phyloinformatic...
CDAO-Store Repository

    What's in it?
    
        TreeBASE dump dated January 2009
    
        Also allows the imp...
Querying CDAO-Store

    PhyloWS
    
        Retrieve data sets via name, tree identifier, taxon,
        or size.
    ...
Web-Based Queries
•   Landing page for
    web-queries.
Trees Containing a Taxonomic Unit
•   Shows a list of trees
    matching the
    Taxonomic Unit
•   Has links to query
   ...
Tree Query
•   Shows a listing of
    nodes in the tree.
•   Allows user to select
    any set of them to
    find their m...
Searching by Author
•   List studies from a
    particular author.
Study Detail
•   Lists all authors,
    with links to their
    studies.
•   Abstract
•   Trees associated
    with the st...
Searching by Algorithm or Method
•    Can search by
     Algorithm or Method
•    As before listing
     shows tree name
 ...
Visualization with CDAO-Explorer

    CDAO-Explorer
    
        Tree Viewer
    
        Matrix Viewer
Tree Viewer

    Uses the Prefuse
    framework

    2 Layouts, “Force
    Layout” and “Node
    Layout”

    Can searc...
Matrix Viewer

    Custom built

    Color-coded cells

    Extract or 'crop' parts
    of the Matrix for
    closer vi...
Conclusion

    The CDAO-store tool set provides a robust
    foundation for a semantically aware, phylogeny
    resource...
Future

    Annotations / MIAPA / OBI

    User-defined SPARQL Queries

    Better Tree / Matrix integration

    Ambi...
Questions?

    Find us at:
    
        http://www.cs.nmsu.edu/~cdaostore
    
        http://cdaotools.sourceforge.ne...
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Ievobio2010cdaostore

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Transcript of "Ievobio2010cdaostore"

  1. 1. CDAO-STORE: A New Vision for Data Integration Brandon Chisham, Trung Le, Enrico Pontelli, Tran Son, Ben Wright IEvoBio 2010 Portland, OR
  2. 2. CDAO  Comparative Data Analysis Ontology  Provides semantics to the descriptions of data commonly found in the domain of phylogenetic inference.  Enables the rigorous description of phylogenetic trees and associated character data matrices.
  3. 3. What We Did  CDAO-Store  A repository providing a rich set of API's for querying phyloinformatics data.  CDAO-Explorer  A visualization tool for viewing data sets stored in the repository.
  4. 4. CDAO-Store Repository  What's in it?  TreeBASE dump dated January 2009  Also allows the importation of CDAO formatted files. − To get your files into CDAO, we can translate NEXUS, PHYLIP, and MEGA into CDAO format.  Files can be exported in RDF/XML using CDAO terms
  5. 5. Querying CDAO-Store  PhyloWS  Retrieve data sets via name, tree identifier, taxon, or size.  Supports computing the minimum spanning clade or the nearest common ancestor of a set of taxa.  Web-Based  Search for data sets by author or study  View data sets online by tree, taxon, algorithm, method, or size.
  6. 6. Web-Based Queries • Landing page for web-queries.
  7. 7. Trees Containing a Taxonomic Unit • Shows a list of trees matching the Taxonomic Unit • Has links to query these trees or View them graphically
  8. 8. Tree Query • Shows a listing of nodes in the tree. • Allows user to select any set of them to find their minimum spanning clade, or Nearest Common Ancestor
  9. 9. Searching by Author • List studies from a particular author.
  10. 10. Study Detail • Lists all authors, with links to their studies. • Abstract • Trees associated with the study. • Future: Matrices the data is available in the system but not exposed to the user.
  11. 11. Searching by Algorithm or Method • Can search by Algorithm or Method • As before listing shows tree name and links to query the tree or view it.
  12. 12. Visualization with CDAO-Explorer  CDAO-Explorer  Tree Viewer  Matrix Viewer
  13. 13. Tree Viewer  Uses the Prefuse framework  2 Layouts, “Force Layout” and “Node Layout”  Can search by node/edge name  View details of nodes or edges  Can save as jpg or png
  14. 14. Matrix Viewer  Custom built  Color-coded cells  Extract or 'crop' parts of the Matrix for closer views  Zoom in and out of the matrix  Annotation support in development.
  15. 15. Conclusion  The CDAO-store tool set provides a robust foundation for a semantically aware, phylogeny resource  The CDAO-Explorer portion of the store has achieved a good base-line functionality and provides a set of useful features to advance the current state of visualization of large data sets in this field.
  16. 16. Future  Annotations / MIAPA / OBI  User-defined SPARQL Queries  Better Tree / Matrix integration  Ambiguous Name Resolution (at taxon, tree, and study levels)  Integrating other stores besides TreeBASE
  17. 17. Questions?  Find us at:  http://www.cs.nmsu.edu/~cdaostore  http://cdaotools.sourceforge.net  http://www.twitter.com/cdaotools  Funding for this project provided by:  NSF CREST grant HRD-0420407  NSF IGERT grant DGE-0504304  Additional Support provided by:  NESCent  NMSU  CDAO Development Team
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