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BY-NC-ND 4.0 license Open Access Published by De Gruyter October 18, 2016

The OXL format for the exchange of integrated datasets

  • Jan Taubert EMAIL logo , Klaus Peter Sieren , Matthew Hindle , Berend Hoekman , Rainer Winnenburg , Stephan Philippi , Chris Rawlings and Jacob Köhler


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 Sample files can be found at and the XML Schema at*checkout*/ondex/trunk/backend/data/xml/ondex.xsd.

Published Online: 2016-10-18
Published in Print: 2007-12-1

© 2007 The Author(s). Published by Journal of Integrative Bioinformatics.

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

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