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

被引:49
作者
Garwood, K
McLaughlin, T
Garwood, C
Joens, S
Morrison, N
Taylor, CF
Carroll, K
Evans, C
Whetton, AD
Hart, S
Stead, D
Yin, Z
Brown, AJP
Hesketh, A
Chater, K
Hansson, L
Mewissen, M
Ghazal, P
Howard, J
Lilley, KS
Gaskell, SJ
Brass, A
Hubbard, SJ
Oliver, SG
Paton, NW
机构
[1] Univ Manchester, Dept Comp Sci, Manchester M13 9PL, Lancs, England
[2] Univ Manchester, Sch Biol Sci, Manchester M13 9PT, Lancs, England
[3] European Bioinformat Inst, Hinxton CB10 1SD, Cambs, England
[4] Univ Manchester, Sch Biomol Sci, Manchester M60 1QD, Lancs, England
[5] Univ Aberdeen, Inst Med Sci, Sch Med Sci, Aberdeen AB25 2ZD, Scotland
[6] John Innes Ctr Plant Sci Res, Dept Mol Microbiol, Norwich NR4 7UH, Norfolk, England
[7] Univ Edinburgh, Sch Med, Scottish Ctr Genom Technol & Informat, Edinburgh EH16 4S, Midlothian, Scotland
[8] Univ Cambridge, Dept Biochem, Cambridge CB2 1QW, England
[9] Univ Manchester, Dept Chem, Manchester M60 1QD, Lancs, England
基金
英国生物技术与生命科学研究理事会;
关键词
D O I
10.1186/1471-2164-5-68
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
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 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. 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.
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页数:11
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