PEDRo: a database for storing, searching and disseminating experimental proteomics data

BMC Genomics
Kevin L GarwoodNorman W Paton

Abstract

Proteomics is rapidly evolving into a high-throughput technology, in which substantial and systematic studies are conducted on samples from a wide range of physiological, developmental, or pathological conditions. Reference maps from 2D gels are widely circulated. However, there is, as yet, no formally accepted standard representation to support the sharing of proteomics data, and little systematic dissemination of comprehensive proteomic data sets. This paper describes the design, implementation and use of a Proteome Experimental Data Repository (PEDRo), which makes comprehensive proteomics data sets available for browsing, searching and downloading. It is also serves to extend the debate on the level of detail at which proteomics data should be captured, the sorts of facilities that should be provided by proteome data management systems, and the techniques by which such facilities can be made available. The PEDRo database provides access to a collection of comprehensive descriptions of experimental data sets in proteomics. Not only are these data sets interesting in and of themselves, they also provide a useful early validation of the PEDRo data model, which has served as a starting point for the ongoing standardisation activ...Continue Reading

References

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Citations

Sep 18, 2007·Journal of Proteome Research·Mark A ShifmanKenneth R Williams
Aug 10, 2007·Nature Biotechnology·Chris F TaylorHenning Hermjakob
Jun 15, 2005·Nature Reviews. Microbiology·Douglas B KellStephen G Oliver
Dec 31, 2005·Nucleic Acids Research·Thomas McLaughlinSimon J Hubbard
Apr 29, 2008·Nucleic Acids Research·Jennifer A SiepenSimon J Hubbard
Mar 10, 2006·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Stephen G Oliver
Sep 29, 2005·BMC Bioinformatics·Andrew R Jones, Norman W Paton
Mar 29, 2006·Molecular & Cellular Proteomics : MCP·David A SteadAlistair J P Brown
Mar 21, 2007·Proteomics·Vladimir BrusicEllis L Reinherz
Oct 14, 2005·Bioscience Reports·Andreas KremerGeorg C Terstappen
Mar 27, 2019·Journal of Medical Internet Research·Seo Jeong ShinRae Woong Park
Jan 16, 2013·Proteomics·J Alberto Medina-AunonAndrew J Jones
Jun 15, 2005·Analytical Chemistry·Jean-Philippe LambertDaniel Figeys
Jul 26, 2007·Chemical Reviews·Marjorie L FournierMichael P Washburn

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Software Mentioned

WORLD
2DPAGE
GIMS
GEO
SBEAMS
PEDRo Database Access
ProDB
MIAME
Pedro
UAB

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