DOI: 10.1093/bioinformatics/btq391. BioXSD: the common data-exchange format for everyday bioinformatics web services

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

10.1093/bioinformatics/btq391

Crossref journal-article

Oxford University Press (OUP)

Bioinformatics (286)

Abstract

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. Contact: matus.kalas@bccs.uib.no; developers@bioxsd.org; support@bioxsd.org

Bibliography

KalaÅ¡, M., Puntervoll, P., Joseph, A., BartaÅ¡eviÄiÅ«tÄ, E., TÃ¶pfer, A., Venkataraman, P., Pettifer, S., Bryne, J. C., Ison, J., Blanchet, C., Rapacki, K., & Jonassen, I. (2010). BioXSD: the common data-exchange format for everyday bioinformatics web services. Bioinformatics, 26(18), i540âi546.

Authors 12

Matúš Kalaš (first)
Pål Puntervoll (additional)
Alexandre Joseph (additional)
Edita Bartaševičiūtė (additional)
Armin Töpfer (additional)
Prabakar Venkataraman (additional)
Steve Pettifer (additional)
Jan Christian Bryne (additional)
Jon Ison (additional)
Christophe Blanchet (additional)
Kristoffer Rapacki (additional)
Inge Jonassen (additional)

References 27 Referenced 18

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10.1093/protein/gzh013 / Protein Eng. Des. Sel. / Prediction of proprotein convertase cleavage sites by Duckert (2004)
10.1186/gb-2005-6-5-r44 / Genome Biol. / The Sequence Ontology: a tool for the unification of genome annotations by Eilbeck (2005)
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Dates

Type	When
Created	14 years, 11 months ago (Sept. 7, 2010, 1:41 p.m.)
Deposited	2 years, 6 months ago (Jan. 25, 2023, 3:28 a.m.)
Indexed	2 years, 6 months ago (Jan. 28, 2023, 7:32 a.m.)
Issued	14 years, 11 months ago (Sept. 4, 2010)
Published	14 years, 11 months ago (Sept. 4, 2010)
Published Online	14 years, 11 months ago (Sept. 4, 2010)
Published Print	14 years, 11 months ago (Sept. 15, 2010)

Funders 0

None

BibTeX

@article{Kala__2010, title={BioXSD: the common data-exchange format for everyday bioinformatics web services}, volume={26}, ISSN={1367-4803}, url={http://dx.doi.org/10.1093/bioinformatics/btq391}, DOI={10.1093/bioinformatics/btq391}, number={18}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Kalaš, Matúš and Puntervoll, Pål and Joseph, Alexandre and Bartaševičiūtė, Edita and Töpfer, Armin and Venkataraman, Prabakar and Pettifer, Steve and Bryne, Jan Christian and Ison, Jon and Blanchet, Christophe and Rapacki, Kristoffer and Jonassen, Inge}, year={2010}, month=sep, pages={i540–i546} }

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