This document introduces CDAO-Store, a repository for querying phyloinformatics data using the Comparative Data Analysis Ontology (CDAO). CDAO-Store includes a rich API for querying phylogenetic trees and associated character data stored from TreeBASE. It also includes CDAO-Explorer, a visualization tool for viewing stored data sets. CDAO-Store provides semantically-aware access and integration of phylogenetic data.

1. CDAO-STORE:
A New Vision for Data Integration
Brandon Chisham, Trung Le, Enrico Pontelli,
Tran Son, Ben Wright
IEvoBio 2010
Portland, OR

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. 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. 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. 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. Web-Based Queries
• Landing page for
web-queries.

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. 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. Searching by Author
• List studies from a
particular author.

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. 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. Visualization with CDAO-Explorer

CDAO-Explorer

Tree Viewer

Matrix Viewer

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. 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. 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. 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. 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