Nucleic Acids Research Advance Access originally published online on November 22, 2007
Nucleic Acids Research 2008 36(Database issue):D878-D883; doi:10.1093/nar/gkm1021
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2008, Vol. 36, Database issue D878-D883
© 2007 The Author(s)
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.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
Articles |
PRIDE: new developments and new datasets
1EMBL Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK, 2Department of Biochemistry, Yonsei Proteome Research Center and Biomedical Proteome Research Center, Yonsei University, Seoul, Korea and 3Martin Luther University, Halle-Wittenberg, Halle-Saale, Germany
*To whom correspondence should be addressed. Tel: +44 1223 492610; Fax: +44 1223 494484; Email: pjones{at}ebi.ac.uk
Received September 19, 2007. Revised October 24, 2007. Accepted October 27, 2007.
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.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  P. J. Kersey, D. Lawson, E. Birney, P. S. Derwent, M. Haimel, J. Herrero, S. Keenan, A. Kerhornou, G. Koscielny, A. Kahari, et al. Ensembl genomes: Extending ensembl across the taxonomic space Nucleic Acids Res., November 1, 2009; (2009) gkp871v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Li, X. Xing, G. Ding, Q. Li, C. Wang, L. Xie, R. Zeng, and Y. Li SysPTM: A Systematic Resource for Proteomic Research on Post-translational Modifications Mol. Cell. Proteomics, August 1, 2009; 8(8): 1839 - 1849. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Haider, B. Ballester, D. Smedley, J. Zhang, P. Rice, and A. Kasprzyk BioMart Central Portal--unified access to biological data Nucleic Acids Res., July 1, 2009; 37(suppl_2): W23 - W27. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Reiland, G. Messerli, K. Baerenfaller, B. Gerrits, A. Endler, J. Grossmann, W. Gruissem, and S. Baginsky Large-Scale Arabidopsis Phosphoproteome Profiling Reveals Novel Chloroplast Kinase Substrates and Phosphorylation Networks Plant Physiology, June 1, 2009; 150(2): 889 - 903. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. W. Deutsch, H. Lam, and R. Aebersold Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics Physiol Genomics, October 8, 2008; 33(1): 18 - 25. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. G. Cote, P. Jones, L. Martens, R. Apweiler, and H. Hermjakob The Ontology Lookup Service: more data and better tools for controlled vocabulary queries Nucleic Acids Res., July 1, 2008; 36(suppl_2): W372 - W376. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Baerenfaller, J. Grossmann, M. A. Grobei, R. Hull, M. Hirsch-Hoffmann, S. Yalovsky, P. Zimmermann, U. Grossniklaus, W. Gruissem, and S. Baginsky Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics Science, May 16, 2008; 320(5878): 938 - 941. [Abstract] [Full Text] [PDF]
|
|