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

Authors :
Kalas M
Puntervoll P
Joseph A
Bartaseviciūte E
Töpfer A
Venkataraman P
Pettifer S
Bryne JC
Ison J
Blanchet C
Rapacki K
Jonassen I
Source :
Bioinformatics (Oxford, England) [Bioinformatics] 2010 Sep 15; Vol. 26 (18), pp. i540-6.
Publication Year :
2010

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.<br />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.<br />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.

Details

Language :
English
ISSN :
1367-4811
Volume :
26
Issue :
18
Database :
MEDLINE
Journal :
Bioinformatics (Oxford, England)
Publication Type :
Academic Journal
Accession number :
20823319
Full Text :
https://doi.org/10.1093/bioinformatics/btq391