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

Research output: Contribution to journalArticle

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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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Proteomics
Databases
Proteome
Information Dissemination
Information Systems
Gels
Technology
Datasets

Cite this

Garwood, K., McLaughlin, T., Garwood, C., Joens, S., Morrison, N., Taylor, C. F., ... 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

PEDRo : A database for storing, searching and disseminating experimental proteomics data. / Garwood, Kevin; McLaughlin, Thomas; Garwood, Chris; Joens, Scott; Morrison, Norman; Taylor, Christopher F; Carroll, Kathleen; Evans, Caroline; Whetton, Anthony D; Hart, Sarah; Stead, David; Yin, Zhikang; Brown, Alistair J P; Hesketh, Andrew; Chater, Keith; Hansson, Lena; Mewissen, Muriel; Ghazal, Peter; Howard, Julie; Lilley, Kathryn S; Gaskell, Simon J; Brass, Andy; Hubbard, Simon J; Oliver, Stephen G; Paton, Norman W.

In: BMC Genomics, Vol. 5, 68, 17.09.2004.

Research output: Contribution to journalArticle

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 2004, 'PEDRo: A database for storing, searching and disseminating experimental proteomics data', BMC Genomics, vol. 5, 68. https://doi.org/10.1186/1471-2164-5-68
Garwood K, McLaughlin T, Garwood C, Joens S, Morrison N, Taylor CF et al. PEDRo: A database for storing, searching and disseminating experimental proteomics data. BMC Genomics. 2004 Sep 17;5. 68. https://doi.org/10.1186/1471-2164-5-68
Garwood, Kevin ; McLaughlin, Thomas ; Garwood, Chris ; Joens, Scott ; Morrison, Norman ; Taylor, Christopher F ; Carroll, Kathleen ; Evans, Caroline ; Whetton, Anthony D ; Hart, Sarah ; Stead, David ; Yin, Zhikang ; Brown, Alistair J P ; Hesketh, Andrew ; Chater, Keith ; Hansson, Lena ; Mewissen, Muriel ; Ghazal, Peter ; Howard, Julie ; Lilley, Kathryn S ; Gaskell, Simon J ; Brass, Andy ; Hubbard, Simon J ; Oliver, Stephen G ; Paton, Norman W. / PEDRo : A database for storing, searching and disseminating experimental proteomics data. In: BMC Genomics. 2004 ; Vol. 5.
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abstract = "BackgroundProteomics 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.ResultsThis paper describes the design, implementation and use of aProteomeExperimentalDataRepository (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.ConclusionsThe 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.",
author = "Kevin Garwood and Thomas McLaughlin and Chris Garwood and Scott Joens and Norman Morrison and Taylor, {Christopher F} and Kathleen Carroll and Caroline Evans and Whetton, {Anthony D} and Sarah Hart and David Stead and Zhikang Yin and Brown, {Alistair J P} and Andrew Hesketh and Keith Chater and Lena Hansson and Muriel Mewissen and Peter Ghazal and Julie Howard and Lilley, {Kathryn S} and Gaskell, {Simon J} and Andy Brass and Hubbard, {Simon J} and Oliver, {Stephen G} and Paton, {Norman W}",
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AU - Garwood, Kevin

AU - McLaughlin, Thomas

AU - Garwood, Chris

AU - Joens, Scott

AU - Morrison, Norman

AU - Taylor, Christopher F

AU - Carroll, Kathleen

AU - Evans, Caroline

AU - Whetton, Anthony D

AU - Hart, Sarah

AU - Stead, David

AU - Yin, Zhikang

AU - Brown, Alistair J P

AU - Hesketh, Andrew

AU - Chater, Keith

AU - Hansson, Lena

AU - Mewissen, Muriel

AU - Ghazal, Peter

AU - Howard, Julie

AU - Lilley, Kathryn S

AU - Gaskell, Simon J

AU - Brass, Andy

AU - Hubbard, Simon J

AU - Oliver, Stephen G

AU - Paton, Norman W

PY - 2004/9/17

Y1 - 2004/9/17

N2 - BackgroundProteomics 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.ResultsThis paper describes the design, implementation and use of aProteomeExperimentalDataRepository (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.ConclusionsThe 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.

AB - BackgroundProteomics 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.ResultsThis paper describes the design, implementation and use of aProteomeExperimentalDataRepository (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.ConclusionsThe 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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