dc.contributor.author | Kalaš, Matúš | eng |
dc.contributor.author | Puntervoll, Pål | eng |
dc.contributor.author | Joseph, Alexandre | eng |
dc.contributor.author | Bartaševičiūtė, Edita | eng |
dc.contributor.author | Töpfer, Armin | eng |
dc.contributor.author | Venkataraman, Prabakar | eng |
dc.contributor.author | Pettifer, Steve | eng |
dc.contributor.author | Bryne, Jan Christian | eng |
dc.contributor.author | Ison, Jon | eng |
dc.contributor.author | Blanchet, Christophe | eng |
dc.contributor.author | Rapacki, Kristoffer | eng |
dc.contributor.author | Jonassen, Inge | eng |
dc.date.accessioned | 2015-11-17T09:26:01Z | |
dc.date.available | 2015-11-17T09:26:01Z | |
dc.date.issued | 2010 | |
dc.Published | Bioinformatics 2010, 26(18):i540-i546 | eng |
dc.identifier.issn | 1367-4803 | en_US |
dc.identifier.uri | https://hdl.handle.net/1956/10660 | |
dc.description.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. | en_US |
dc.language.iso | eng | eng |
dc.publisher | Oxford University Press | en_US |
dc.relation.ispartof | <a href="http://hdl.handle.net/1956/10658" target="_blank">Efforts towards accessible and reliable bioinformatics</a> | en_US |
dc.rights | Attribution CC BY-NC | eng |
dc.rights.uri | http://creativecommons.org/licenses/by-nc/2.5 | eng |
dc.title | BioXSD: the common data-exchange format for everyday bioinformatics web services | en_US |
dc.type | Peer reviewed | |
dc.type | Journal article | |
dc.date.updated | 2015-11-17T09:21:42Z | |
dc.description.version | publishedVersion | en_US |
dc.rights.holder | Copyright 2010 The Authors | en_US |
dc.identifier.doi | https://doi.org/10.1093/bioinformatics/btq391 | |