title: BioXSD: the common data-exchange format for everyday bioinformatics web services.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  The BioXSD 1.0 XML Schema is freely available at http://www.bioxsd.org/BioXSD-1.0.xsd under the Creative Commons BY-ND 3.0 license. The http://bioxsd.org web page offers documentation, examples of data in BioXSD format, example workflows with source codes in common programming languages, an updated list of compatible web services and tools and a repository of feature requests from the community.
authors.affiliation: Bergen Center for Computational Science, Uni Research, Bergen, Norway. matus.kalas@bccs.uib.no
authors.forename: Matús
authors.initials: M
authors.lastname: Kalas
authors.forename: Pål
authors.initials: P
authors.lastname: Puntervoll
authors.forename: Alexandre
authors.initials: A
authors.lastname: Joseph
authors.forename: Edita
authors.initials: E
authors.lastname: Bartaseviciūte
authors.forename: Armin
authors.initials: A
authors.lastname: Töpfer
authors.forename: Prabakar
authors.initials: P
authors.lastname: Venkataraman
authors.forename: Steve
authors.initials: S
authors.lastname: Pettifer
authors.forename: Jan Christian
authors.initials: JC
authors.lastname: Bryne
authors.forename: Jon
authors.initials: J
authors.lastname: Ison
authors.forename: Christophe
authors.initials: C
authors.lastname: Blanchet
authors.forename: Kristoffer
authors.initials: K
authors.lastname: Rapacki
authors.forename: Inge
authors.initials: I
authors.lastname: Jonassen
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D016247:Information Storage and Retrieval / Q000592:standards; D020407:Internet; D008969:Molecular Sequence Data; D011381:Programming Languages; D012660:Semantics; D012984:Software; D057188:Workflow
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