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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

Open Access
Online
ISSN
1613-4516
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Volume 4, Issue 3

Issues

The OXL format for the exchange of integrated datasets

Jan Taubert
  • Corresponding author
  • Department of Biomathematics and Bioinformatics, Rothamsted Research, AL5 2JQ, Harpenden, United Kingdom of Great Britain and Northern Ireland
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/ Klaus Peter Sieren / Matthew Hindle
  • Department of Biomathematics and Bioinformatics, Rothamsted Research, AL5 2JQ, Harpenden, United Kingdom of Great Britain and Northern Ireland
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/ Berend Hoekman / Rainer Winnenburg
  • Department of Biomathematics and Bioinformatics, Rothamsted Research, AL5 2JQ, Harpenden, United Kingdom of Great Britain and Northern Ireland
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/ Stephan Philippi / Chris Rawlings
  • Department of Biomathematics and Bioinformatics, Rothamsted Research, AL5 2JQ, Harpenden, United Kingdom of Great Britain and Northern Ireland
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/ Jacob Köhler
  • Department of Biomathematics and Bioinformatics, Rothamsted Research, AL5 2JQ, Harpenden, United Kingdom of Great Britain and Northern Ireland
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Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2007-62

Abstract

A prerequisite for systems biology is the integration and analysis of heterogeneous experimental data stored in hundreds of life-science databases and millions of scientific publications. Several standardised formats for the exchange of specific kinds of biological information exist. Such exchange languages facilitate the integration process; however they are not designed to transport integrated datasets. A format for exchanging integrated datasets needs to i) cover data from a broad range of application domains, ii) be flexible and extensible to combine many different complex data structures, iii) include metadata and semantic definitions, iv) include inferred information, v) identify the original data source for integrated entities and vi) transport large integrated datasets. Unfortunately, none of the exchange formats from the biological domain (e.g. BioPAX, MAGE-ML, PSI-MI, SBML) or the generic approaches (RDF, OWL) fulfil these requirements in a systematic way.

We present OXL, a format for the exchange of integrated data sets, and detail how the aforementioned requirements are met within the OXL format. OXL is the native format within the data integration and text mining system ONDEX. Although OXL was developed with the ONDEX system in mind, it also has the potential to be used in several other biological and non-biological applications described in this paper.

Availability: The OXL format is an integral part of the ONDEX system which is freely available under the GPL at http://ondex.sourceforge.net/. Sample files can be found at http://prdownloads.sourceforge.net/ondex/ and the XML Schema at http://ondex.svn.sf.net/viewvc/*checkout*/ondex/trunk/backend/data/xml/ondex.xsd.

About the article

Published Online: 2016-10-18

Published in Print: 2007-12-01


Citation Information: Journal of Integrative Bioinformatics, Volume 4, Issue 3, Pages 27–40, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2007-62.

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© 2007 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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[1]
Keywan Hassani-Pak, Martin Castellote, Maria Esch, Matthew Hindle, Artem Lysenko, Jan Taubert, and Christopher Rawlings
Applied & Translational Genomics, 2016, Volume 11, Page 18

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