title: 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.
authors.affiliation: Department of Computer Science, New Mexico State University, Las Cruces, USA.
authors.forename: Brandon
authors.initials: B
authors.lastname: Chisham
authors.forename: Ben
authors.initials: B
authors.lastname: Wright
authors.forename: Trung
authors.initials: T
authors.lastname: Le
authors.forename: Tran Cao
authors.initials: TC
authors.lastname: Son
authors.forename: Enrico
authors.initials: E
authors.lastname: Pontelli
mesh_terms: D000465:Algorithms; D005075:Biological Evolution; D002965:Classification / Q000379:methods*; D016247:Information Storage and Retrieval; D020407:Internet; D010802:Phylogeny; D012660:Semantics; D012984:Software