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PRIDE: new developments and new datasets

The PRIDE (http://www.ebi.ac.uk/pride) database of protein and peptide identifications was previously described in the NAR Database Special Edition in 2006. Since this publication, the volume of public data in the PRIDE relational database has increased by more than an order of magnitude. Several si...

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Autores principales: Jones, Philip, Côté, Richard G., Cho, Sang Yun, Klie, Sebastian, Martens, Lennart, Quinn, Antony F., Thorneycroft, David, Hermjakob, Henning
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238846/
https://www.ncbi.nlm.nih.gov/pubmed/18033805
http://dx.doi.org/10.1093/nar/gkm1021
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author Jones, Philip
Côté, Richard G.
Cho, Sang Yun
Klie, Sebastian
Martens, Lennart
Quinn, Antony F.
Thorneycroft, David
Hermjakob, Henning
author_facet Jones, Philip
Côté, Richard G.
Cho, Sang Yun
Klie, Sebastian
Martens, Lennart
Quinn, Antony F.
Thorneycroft, David
Hermjakob, Henning
author_sort Jones, Philip
collection PubMed
description The PRIDE (http://www.ebi.ac.uk/pride) database of protein and peptide identifications was previously described in the NAR Database Special Edition in 2006. Since this publication, the volume of public data in the PRIDE relational database has increased by more than an order of magnitude. Several significant public datasets have been added, including identifications and processed mass spectra generated by the HUPO Brain Proteome Project and the HUPO Liver Proteome Project. The PRIDE software development team has made several significant changes and additions to the user interface and tool set associated with PRIDE. The focus of these changes has been to facilitate the submission process and to improve the mechanisms by which PRIDE can be queried. The PRIDE team has developed a Microsoft Excel workbook that allows the required data to be collated in a series of relatively simple spreadsheets, with automatic generation of PRIDE XML at the end of the process. The ability to query PRIDE has been augmented by the addition of a BioMart interface allowing complex queries to be constructed. Collaboration with groups outside the EBI has been fruitful in extending PRIDE, including an approach to encode iTRAQ quantitative data in PRIDE XML.
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spelling pubmed-22388462008-02-12 PRIDE: new developments and new datasets Jones, Philip Côté, Richard G. Cho, Sang Yun Klie, Sebastian Martens, Lennart Quinn, Antony F. Thorneycroft, David Hermjakob, Henning Nucleic Acids Res Articles The PRIDE (http://www.ebi.ac.uk/pride) database of protein and peptide identifications was previously described in the NAR Database Special Edition in 2006. Since this publication, the volume of public data in the PRIDE relational database has increased by more than an order of magnitude. Several significant public datasets have been added, including identifications and processed mass spectra generated by the HUPO Brain Proteome Project and the HUPO Liver Proteome Project. The PRIDE software development team has made several significant changes and additions to the user interface and tool set associated with PRIDE. The focus of these changes has been to facilitate the submission process and to improve the mechanisms by which PRIDE can be queried. The PRIDE team has developed a Microsoft Excel workbook that allows the required data to be collated in a series of relatively simple spreadsheets, with automatic generation of PRIDE XML at the end of the process. The ability to query PRIDE has been augmented by the addition of a BioMart interface allowing complex queries to be constructed. Collaboration with groups outside the EBI has been fruitful in extending PRIDE, including an approach to encode iTRAQ quantitative data in PRIDE XML. Oxford University Press 2008-01 2007-11-22 /pmc/articles/PMC2238846/ /pubmed/18033805 http://dx.doi.org/10.1093/nar/gkm1021 Text en © 2007 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Jones, Philip
Côté, Richard G.
Cho, Sang Yun
Klie, Sebastian
Martens, Lennart
Quinn, Antony F.
Thorneycroft, David
Hermjakob, Henning
PRIDE: new developments and new datasets
title PRIDE: new developments and new datasets
title_full PRIDE: new developments and new datasets
title_fullStr PRIDE: new developments and new datasets
title_full_unstemmed PRIDE: new developments and new datasets
title_short PRIDE: new developments and new datasets
title_sort pride: new developments and new datasets
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238846/
https://www.ncbi.nlm.nih.gov/pubmed/18033805
http://dx.doi.org/10.1093/nar/gkm1021
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