CDAO-store: ontology-driven data integration for phylogenetic analysis

Abstract

Background: The Comparative Data Analysis Ontology (CDAO) is an ontology developed, as part of the EvoInfo and EvoIO groups supported by the National Evolutionary Synthesis Center, to provide semantic descriptions of data and transformations commonly found in the domain of phylogenetic analysis. The core concepts of the ontology enable the description of phylogenetic trees and associated character data matrices.

Results: Using CDAO as the semantic back-end, we developed a triple-store, named CDAO-Store. CDAO-Store is a RDF-based store of phylogenetic data, including a complete import of TreeBASE. CDAO-Store provides a programmatic interface, in the form of web services, and a web-based front-end, to perform both user-defined as well as domain-specific queries; domain-specific queries include search for nearest common ancestors, minimum spanning clades, filter multiple trees in the store by size, author, taxa, tree identifier, algorithm or method. In addition, CDAO-Store provides a visualization front-end, called CDAO-Explorer, which can be used to view both character data matrices and trees extracted from the CDAO-Store. CDAO-Store provides import capabilities, enabling the addition of new data to the triple-store; files in PHYLIP, MEGA, nexml, and NEXUS formats can be imported and their CDAO representations added to the triple-store.

Conclusions: CDAO-Store is made up of a versatile and integrated set of tools to support phylogenetic analysis. To the best of our knowledge, CDAO-Store is the first semantically-aware repository of phylogenetic data with domain-specific querying capabilities. The portal to CDAO-Store is available at http://www.cs.nmsu.edu/~cdaostore.

Figure 1

The EvoIO Stack. This is the structure of the EvoIO stack developed by he EvoInfo working group of the National Evolutionary Synthesis Center.

Figure 2

The Principle View of OTUs and Characters. This figure summarizes the core concepts from phylogenetic analysis that are captured by the CDAO ontology.

Figure 3

Snapshot of the Key concepts of CDAO. This figure provides a very small summary of the core concepts and relations described in CDAO.

Figure 4

Structure of CDAO-store. This figure shows the overall structure of the implementation of the CDAO-store.

Figure 5

Tree Viewer with search. This is the TreeViewer Application displaying the tree Tree3099 from TreeBASE and searching for all nodes and edges with #Ilex_.

Figure 6

Matrix Viewer. This is a snapshot of the MatrixViewer component; it shows a DNA matrix, using colors to identify occurrences of identical nucleotides.