CDAOStore: A Phylogenetic Repository Using Logic Programming and Web Services

The CDAOStore is a portal aimed at facilitating the storage and retrieval of data and metadata associated to studies in the field of evolutionary biology and phylogenetic analysis. The novelty of CDAOStore lies in the use of a semantic-based approach to the storage and querying of data. This enables CDAOStore to overcome the data format restrictions and complexities of other repositories (e.g., TreeBase) and to provide a domain-specific query interface, derived from studies of querying requirements for phylogenetic databases. CDAOStore represents the first full implementation of the EvoIO stack, an inter-operation stack composed of a formal ontology (the Comparative Data Analysis Ontology), an XML exchange format (NeXML), and a web services API (PhyloWS). CDAOStore has been implemented on top of an RDF triple store, using a combination of standard web technologies and logic programming technology. In particular, we employed Prolog to support some of the format transformation tasks and, more importantly, in the implementation of several of the domain-specific queries, whose structure is beyond the reach of standard RDF query languages (e.g., SPARQL). CDAOStore is operational and it already hosts over 90 million RDF triples, imported from TreeBase or submitted by other domain scientists

Initial Implementation of a Comparative Data Analysis Ontology

Comparative analysis is used throughout biology. When entities under comparison (e.g. proteins, genomes, species) are related by descent, evolutionary theory provides a framework that, in principle, allows N-ary comparisons of entities, while controlling for non-independence due to relatedness. Powerful software tools exist for specialized applications of this approach, yet it remains under-utilized in the absence of a unifying informatics infrastructure. A key step in developing such an infrastructure is the definition of a formal ontology. The analysis of use cases and existing formalisms suggests that a significant component of evolutionary analysis involves a core problem of inferring a character history, relying on key concepts: “Operational Taxonomic Units” (OTUs), representing the entities to be compared; “character-state data” representing the observations compared among OTUs; “phylogenetic tree”, representing the historical path of evolution among the entities; and “transitions”, the inferred evolutionary changes in states of characters that account for observations. Using the Web Ontology Language (OWL), we have defined these and other fundamental concepts in a Comparative Data Analysis Ontology (CDAO). CDAO has been evaluated for its ability to represent token data sets and to support simple forms of reasoning. With further development, CDAO will provide a basis for tools (for semantic transformation, data retrieval, validation, integration, etc.) that make it easier for software developers and biomedical researchers to apply evolutionary methods of inference to diverse types of data, so as to integrate this powerful framework for reasoning into their research

CDAO-Store: Ontology-driven Data Integration for Phylogenetic Analysis

<p>Abstract</p> <p>Background</p> <p>The <it>Comparative Data Analysis Ontology (CDAO) </it>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.</p> <p>Results</p> <p>Using CDAO as the semantic back-end, we developed a triple-store, named <it>CDAO</it>-<it>Store</it>. 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 <it>CDAO</it>-<it>Explorer</it>, 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, <monospace>nexml</monospace>, and NEXUS formats can be imported and their CDAO representations added to the triple-store.</p> <p>Conclusions</p> <p>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 <url>http://www.cs.nmsu.edu/~cdaostore</url>.</p

CDAO-Store: A New Vision in Data Integration

The Comparative Data Analysis Ontology (CDAO) 1 is an ontology developed, as part of the EvoInfo2 and EvoIO3 groups supported by NESCent4, to provide semantics to the descriptions of data and transformations commonly found in the domain of phylogenetic inference. The core concepts of the ontology enables the description of phylogenetic &#xd;&#xa;trees and associated character data matrices. &#xd;&#xa