Abstract
BackgroundThe 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.ResultsUsing 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.ConclusionsCDAO-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.
Highlights
The Comparative Data Analysis Ontology (CDAO) is an ontology developed, as part of the Evolutionary Informatics (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
Our PhyloWS implementation is the basis for all the data access features of CDAO-Store
Its connection with TreeBASE and the ability to import arbitrary files from several different formats allows the repository to dynamically grow through communitycontributed submissions; the ability to provide additional annotations, driven by a formal ontology, allows community curation of data and facilitates the reuse of phylogenetic trees in different investigations
Summary
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 novelty of CDAO-Store lies in the use of a semanticbased approach to the storage and querying of data, building on established ontologies for the semantic annotation of data. This approach enables scientists to overcome the restrictions imposed by the use of specific data formats-facilitating inter-operation among phylogenetic analysis applications-and makes it possible to design and implement more meaningful domain-specific queries. Phylogenies are used with increasing frequency in several fields, e.g., comparative genomics [1], meta-genomics [2], and community ecology [3]
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