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The OXL format for the exchange of integrated datasets
Taubert, Jan ; Sieren, Klaus Peter ; Hindle, Matthew ; Hoekman, Berend ; Winnenburg, Rainer ; Philippi, Stephan ; Rawlings, Chris ; Köhler, Jacob
Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)
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.
||Faculty of Technology, Research Groups in Informatics
||Data processing, computer science, computer systems
Taubert, Jan ; Sieren, Klaus Peter ; Hindle, Matthew ; Hoekman, Berend ; Winnenburg, Rainer ; Philippi, Stephan ; Rawlings, Chris ; Köhler, Jacob (2007
) The OXL format for the exchange of integrated datasets.
Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 4(3), 2007. Special Issue: 4th Integrative Bioinformatics Workshop, Gent, Belgium