iEvoBio 2010 cdaostore
-
Upload
brandon-chisham -
Category
Technology
-
view
323 -
download
0
Transcript of iEvoBio 2010 cdaostore
![Page 1: iEvoBio 2010 cdaostore](https://reader033.fdocuments.net/reader033/viewer/2022052823/55508b34b4c905a85c8b4d68/html5/thumbnails/1.jpg)
Brandon Chisham, Trung Le, Enrico Pontelli, Tran Son, Ben Wright
IEvoBio 2010Portland, OR
CDAO-STORE: A New Vision for Data Integration
![Page 2: iEvoBio 2010 cdaostore](https://reader033.fdocuments.net/reader033/viewer/2022052823/55508b34b4c905a85c8b4d68/html5/thumbnails/2.jpg)
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.
![Page 3: iEvoBio 2010 cdaostore](https://reader033.fdocuments.net/reader033/viewer/2022052823/55508b34b4c905a85c8b4d68/html5/thumbnails/3.jpg)
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.
![Page 4: iEvoBio 2010 cdaostore](https://reader033.fdocuments.net/reader033/viewer/2022052823/55508b34b4c905a85c8b4d68/html5/thumbnails/4.jpg)
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
![Page 5: iEvoBio 2010 cdaostore](https://reader033.fdocuments.net/reader033/viewer/2022052823/55508b34b4c905a85c8b4d68/html5/thumbnails/5.jpg)
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.
![Page 6: iEvoBio 2010 cdaostore](https://reader033.fdocuments.net/reader033/viewer/2022052823/55508b34b4c905a85c8b4d68/html5/thumbnails/6.jpg)
Web-Based Queries
• Landing page for web-queries.
![Page 7: iEvoBio 2010 cdaostore](https://reader033.fdocuments.net/reader033/viewer/2022052823/55508b34b4c905a85c8b4d68/html5/thumbnails/7.jpg)
Trees Containing a Taxonomic Unit
• Shows a list of trees matching the Taxonomic Unit
• Has links to query these trees or View them graphically
![Page 8: iEvoBio 2010 cdaostore](https://reader033.fdocuments.net/reader033/viewer/2022052823/55508b34b4c905a85c8b4d68/html5/thumbnails/8.jpg)
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
![Page 9: iEvoBio 2010 cdaostore](https://reader033.fdocuments.net/reader033/viewer/2022052823/55508b34b4c905a85c8b4d68/html5/thumbnails/9.jpg)
Searching by Author
• List studies from a particular author.
![Page 10: iEvoBio 2010 cdaostore](https://reader033.fdocuments.net/reader033/viewer/2022052823/55508b34b4c905a85c8b4d68/html5/thumbnails/10.jpg)
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.
![Page 11: iEvoBio 2010 cdaostore](https://reader033.fdocuments.net/reader033/viewer/2022052823/55508b34b4c905a85c8b4d68/html5/thumbnails/11.jpg)
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.
![Page 12: iEvoBio 2010 cdaostore](https://reader033.fdocuments.net/reader033/viewer/2022052823/55508b34b4c905a85c8b4d68/html5/thumbnails/12.jpg)
Visualization with CDAO-Explorer
CDAO-Explorer Tree Viewer Matrix Viewer
![Page 13: iEvoBio 2010 cdaostore](https://reader033.fdocuments.net/reader033/viewer/2022052823/55508b34b4c905a85c8b4d68/html5/thumbnails/13.jpg)
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
![Page 14: iEvoBio 2010 cdaostore](https://reader033.fdocuments.net/reader033/viewer/2022052823/55508b34b4c905a85c8b4d68/html5/thumbnails/14.jpg)
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.
![Page 15: iEvoBio 2010 cdaostore](https://reader033.fdocuments.net/reader033/viewer/2022052823/55508b34b4c905a85c8b4d68/html5/thumbnails/15.jpg)
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.
![Page 16: iEvoBio 2010 cdaostore](https://reader033.fdocuments.net/reader033/viewer/2022052823/55508b34b4c905a85c8b4d68/html5/thumbnails/16.jpg)
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
![Page 17: iEvoBio 2010 cdaostore](https://reader033.fdocuments.net/reader033/viewer/2022052823/55508b34b4c905a85c8b4d68/html5/thumbnails/17.jpg)
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