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Proteomics Data Collection (ProDaC): Publishing and Collecting Proteomics Data Sets in Public Repositories Using Standard Formats

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Proteome Bioinformatics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 604))

Abstract

In Proteomics, fast enhancements with regard to technology are responsible for the creation of huge data sets. Consequently, in 2006 the European Commission funded a Coordination Action named ProDaC (Proteomics Data Collection) within the 6th EU Framework Programme to foster a community-wide data collection and data sharing. The aims of ProDaC were the development of documentation and storage standards, setup of a standardized data submission pipeline and collection of data.

To reach these goals, the necessary work was structured in six thematic fields (work packages): Standards for Proteomics Data Representation, Standards Implementation, Data Integration Tools, Proteomics Repository Adaptation, Data Flow Management, and Proteomics Data Exploitation. The methods building the basis of the respective fields and the achieved results are described in the following sections.

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Abbreviations

HUPO:

Human Proteome Organisation

PSI:

Proteomics standards initiative

DCC:

Data collection center

ProDaC:

Proteomics data collection

LIMS:

Laboratory information management system

XML:

eXtensible markup language

PRIDE:

Proteomics identification database

CV:

Controlled vocabulary

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Acknowledgements

This work was funded by ProDaC (European Commis-sion project, 6th framework programme, project number LSHG-CT-2006-036814).

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Authors and Affiliations

  1. Medizinisches Proteom-Center (MPC), Ruhr-Universitaet Bochum, Bochum, Germany

    Christian Stephan, Martin Eisenacher, Michael Kohl & Helmut E. Meyer

Authors
  1. Christian Stephan
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  2. Martin Eisenacher
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  4. Helmut E. Meyer
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Editor information

Editors and Affiliations

  1. Fac. Life Sciences, University of Manchester, Oxford Rd., Manchester, M13 9PT, United Kingdom

    Simon J. Hubbard

  2. Fac. Veterinary Science, University of Liverpool, Liverpool, L69 7ZJ, United Kingdom

    Andrew R. Jones

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Stephan, C., Eisenacher, M., Kohl, M., Meyer, H.E. (2010). Proteomics Data Collection (ProDaC): Publishing and Collecting Proteomics Data Sets in Public Repositories Using Standard Formats. In: Hubbard, S., Jones, A. (eds) Proteome Bioinformatics. Methods in Molecular Biology™, vol 604. Humana Press. https://doi.org/10.1007/978-1-60761-444-9_24

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  • DOI: https://doi.org/10.1007/978-1-60761-444-9_24

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