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CDAOStore: A Phylogenetic Repository Using Logic Programming and Web Services

Authors Brandon Chisham, Enrico Pontelli, Tran Cao Son, Ben Wright



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LIPIcs.ICLP.2011.209.pdf
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Brandon Chisham
Enrico Pontelli
Tran Cao Son
Ben Wright

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Brandon Chisham, Enrico Pontelli, Tran Cao Son, and Ben Wright. CDAOStore: A Phylogenetic Repository Using Logic Programming and Web Services. In Technical Communications of the 27th International Conference on Logic Programming (ICLP'11). Leibniz International Proceedings in Informatics (LIPIcs), Volume 11, pp. 209-219, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2011)
https://doi.org/10.4230/LIPIcs.ICLP.2011.209

Abstract

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.
Keywords
  • Bioinformatics
  • Phylogenetic Analysis
  • Prolog
  • Ontologies

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