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

Kevin Garwood, Thomas McLaughlin, Chris Garwood, Scott Joens, Norman Morrison, Christopher F Taylor, Kathleen Carroll, Caroline Evans, Anthony D Whetton, Sarah Hart, David Stead, Zhikang Yin, Alistair J P Brown, Andrew Hesketh, Keith Chater, Lena Hansson, Muriel Mewissen, Peter Ghazal, Julie Howard, Kathryn S LilleySimon J Gaskell, Andy Brass, Simon J Hubbard, Stephen G Oliver, Norman W Paton

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Abstract

Background
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.

Results
This paper describes the design, implementation and use of a

P
roteome
E
xperimental
D
ata
R
ep
o
sitory (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.
Conclusions
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 activity through the Proteome Standards Initiative of the Human Proteome Organisation.
Original languageEnglish
Article number68
Number of pages11
JournalBMC Genomics
Volume5
DOIs
Publication statusPublished - 17 Sep 2004

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Garwood, K., McLaughlin, T., Garwood, C., Joens, S., Morrison, N., Taylor, C. F., Carroll, K., Evans, C., Whetton, A. D., Hart, S., Stead, D., Yin, Z., Brown, A. J. P., Hesketh, A., Chater, K., Hansson, L., Mewissen, M., Ghazal, P., Howard, J., ... Paton, N. W. (2004). PEDRo: A database for storing, searching and disseminating experimental proteomics data. BMC Genomics, 5, [68]. https://doi.org/10.1186/1471-2164-5-68