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Proteome Bioinformatics

Volume 604 of the series Methods in Molecular Biology™ pp 333-343

Date:

Managing Experimental Data Using FuGE

  • Andrew R. JonesAffiliated withDepartment of Pre-clinical Veterinary Science, Faculty of Veterinary Science, University of Liverpool Email author 
  • , Allyson L. ListerAffiliated withCISBAN and School of Computing Science, Newcastle University

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Abstract

Data management and sharing in omics science is highly challenging due to the constant evolution of experimental techniques, the range of instrument types and software used for analysis, and the high volumes of data produced. The Functional Genomics Experiment (FuGE) Model was created to provide a model for capturing descriptions of sample processing, experimental protocols and multidimensional data for any kind of omics experiment. FuGE has two modes of action: (a) as a storage architecture for experimental workflows and (b) as a framework for building new technology-specific data standards.

FuGE is an object model that is converted into an XML implementation for data exchange. Software toolkits have been developed for data handling and for bridging between XML data files and relational database implementations. FuGE has been adopted by the Proteomics Standards Initiative (PSI, http://​www.​psidev.​info) for building several new data formats, and it is being used in a variety of other experimental contexts, thus allowing data to be integrated across a range of experimental types to support Systems Biology approaches. This chapter provides a practical guide for laboratories or groups wishing to manage their data, and for developers wishing to create new data formats using FuGE.

Key words

Data standards Functional genomics Data exchange Database development