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Bioinformatics. 2010 Sep 15;26(18):i540-6. doi: 10.1093/bioinformatics/btq391.

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

Author information

1
Bergen Center for Computational Science, Uni Research, Bergen, Norway. matus.kalas@bccs.uib.no

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.

AVAILABILITY:

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.

PMID:
20823319
PMCID:
PMC2935419
DOI:
10.1093/bioinformatics/btq391
[Indexed for MEDLINE]
Free PMC Article
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