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

Publication: Research - peer-reviewJournal article – Annual report year: 2010

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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
Publication date2010
Volume26
Issue18
Pagesi540-i546
ISSN1367-4803
DOIs
StatePublished
CitationsWeb of Science® Times Cited: 7
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