BioXSD: the common data-exchange format for everyday bioinformatics web services

M. Kalas, P. Puntervoll, A. Joseph, Edita Bartaseviciute, A. Topfer, P. Venkataraman, S. Pettifer, J.C. Bryne, J. Ison, C. Blanchet, Kristoffer Rapacki, I. Jonassen

    Research output: Contribution to journalJournal articleResearchpeer-review

    Abstract

    Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of the resources offer programmatic web-service interface. However, efficient use of the resources is hampered by the lack of widely used, standard data-exchange formats for the basic, everyday bioinformatics data types. Results: BioXSD has been developed as a candidate for standard, canonical exchange format for basic bioinformatics data. BioXSD is represented by a dedicated XML Schema and defines syntax for biological sequences, sequence annotations, alignments and references to resources. We have adapted a set of web services to use BioXSD as the input and output format, and implemented a test-case workflow. This demonstrates that the approach is feasible and provides smooth interoperability. Semantics for BioXSD is provided by annotation with the EDAM ontology. We discuss in a separate section how BioXSD relates to other initiatives and approaches, including existing standards and the Semantic Web.
    Original languageEnglish
    JournalBioinformatics
    Volume26
    Issue number18
    Pages (from-to)i540-i546
    ISSN1367-4803
    DOIs
    Publication statusPublished - 2010

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