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Molecular Information Fusion in Ondex

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Approaches in Integrative Bioinformatics

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Abstract

Current biological knowledge is buried in hundreds of proprietary and public life-science databases available on the World Wide Web (WWW) and millions of scientific publications. Gaining access to this knowledge can prove difficult as each database may provide different tools to query or show the data and may differ in their structure and user interface or uses a different interpretation of biological knowledge than others. Systems approaches to biological research require that existing biological knowledge (data) is made available to support on the one hand the analysis of experimental results and on the other hand the construction and enrichment of models. Data integration methods are being developed to address these issues by providing a consolidated view of molecular information fused together from multiple databases. However, a key challenge for data integration is the identification of links between closely related entries in different life sciences databases when there is no direct information that provides a reliable cross reference. Here we describe and evaluate three data integration methods to address this challenge in the context of a graph-based data integration framework (the Ondex system). We give a quantitative evaluation of their performance in two different situations: the integration and analysis of different metabolic pathways resources and the mapping of equivalent elements between the Gene Ontology and a nomenclature describing enzyme function.

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Acknowledgements

We would like to thank all current and previous contributors to the Ondex system (see www.ondex.org). The main part of this work has been carried out at Rothamsted Research. Rothamsted Research receives grant in aid from the Biotechnology and Biological Sciences Research Council (BBSRC). This work was supported by BBSRC SABR award BB/F006039/1 and TSB project TP 5082–33372. JT also would like to thank EMBL-EBI for allowing time to write this chapter.

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Authors and Affiliations

  1. Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK

    Jan Taubert

  2. Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN, 46268, USA

    Jacob Köhler

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Correspondence to Jan Taubert .

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Editors and Affiliations

  1. College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China

    Ming Chen

  2. Department of Bioinformatics and Medical Informatics, Bielefeld University, Bielefeld, Germany

    Ralf Hofestädt

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Taubert, J., Köhler, J. (2014). Molecular Information Fusion in Ondex. In: Chen, M., Hofestädt, R. (eds) Approaches in Integrative Bioinformatics. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-41281-3_5

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  • DOI: https://doi.org/10.1007/978-3-642-41281-3_5

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