General Information
| Description | The common data-exchange format for everyday bioinformatics web services |
| Homepage | http://www.bioxsd.org/BioXSD-1.0.xsd |
Publications
BioXSD: the common data-exchange format for everyday bioinformatics web services
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
Related Tools
Geneious Basic
Published April 2012
An integrated and extendable desktop software platform for the organization and analysis of sequence data
EDAM
Published March 2013
An ontology of bioinformatics operations, types of data and identifiers, topics and formats
BioServices
Published September 2013
A common Python package to access biological Web Services programmatically
ms-data-core-api
Published April 2015
An open-source, metadata-oriented library for computational proteomics
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