BioXSD: the common data-exchange format for everyday bioinformatics web services.
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.
Kalas
Matús
M
Bergen Center for Computational Science, Uni Research, Bergen, Norway. matus.kalas@bccs.uib.no
Puntervoll
Pål
P
Joseph
Alexandre
A
Bartaseviciūte
Edita
E
Töpfer
Armin
A
Venkataraman
Prabakar
P
Pettifer
Steve
S
Bryne
Jan Christian
JC
Ison
Jon
J
Blanchet
Christophe
C
Rapacki
Kristoffer
K
Jonassen
Inge
I
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
BMC Bioinformatics. 2007 Sep 12;8:333
17850653
Protein Eng Des Sel. 2004 Jan;17(1):107-12
14985543
Genome Biol. 2005;6(5):R44
15892872
Bioinformatics. 2009 Aug 15;25(16):2090-1
19460889
BMC Bioinformatics. 2006 Nov 06;7:490
17087823
Nat Genet. 2000 May;25(1):25-9
10802651
Brief Bioinform. 2008 Nov;9(6):493-505
18621748
Genome Biol. 2002 Aug 23;3(9):RESEARCH0046
12225585
Nucleic Acids Res. 2010 Jan;38(Database issue):D142-8
19843607
Bioinformatics. 2005 Apr 1;21(7):988-92
15509603
Bioinformatics. 2008 Dec 1;24(23):2767-72
18936051
Brief Bioinform. 2002 Dec;3(4):331-41
12511062
J Mol Biol. 1990 Oct 5;215(3):403-10
2231712
BMC Bioinformatics. 2007 Aug 28;8:312
17725821
Protein Eng Des Sel. 2004 Jun;17(6):527-36
15314210
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W729-32
16845108
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W683-8
20462862
BMC Bioinformatics. 2009 Oct 27;10:356
19860910
Nucleic Acids Res. 2010 Jan;38(Database issue):D366-70
19900969
Nature. 2002 May 9;417(6885):119-20
12000935
OMICS. 2008 Jun;12(2):115-21
18479204
Bioinformatics. 2003 Mar 1;19(4):524-31
12611808
Methods Enzymol. 1996;266:540-53
8743705
Nat Biotechnol. 2004 Feb;22(2):177-83
14755292
Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
7984417