PRIDE: new developments and new datasets.
作者： P. Jones , R. G. Cote , S. Y. Cho , S. Klie , L. Martens
DOI: 10.1093/NAR/GKM1021
关键词:
摘要: The PRIDE (http://www.ebi.ac.uk/pride) database of protein and peptide identifications was previously described in the NAR Database Special Edition 2006. Since this publication, volume public data relational has increased by more than an order magnitude. Several significant datasets have been added, including processed mass spectra generated HUPO Brain Proteome Project Liver Project. software development team made several changes additions to user interface tool set associated with PRIDE. focus these facilitate submission process improve mechanisms which can be queried. developed a Microsoft Excel workbook that allows required collated series relatively simple spreadsheets, automatic generation XML at end process. ability query augmented addition BioMart allowing complex queries constructed. Collaboration groups outside EBI fruitful extending PRIDE, approach encode iTRAQ quantitative XML.
oup.com
mpg.de
paperity.org
researchgate.net 参考文章(27)
Jonathan Bard, Seung Y Rhee, Michael Ashburner, An ontology for cell types Genome Biology. ,vol. 6, pp. 1- 5 ,(2005) , 10.1186/GB-2005-6-2-R21
Jennifer A Siepen, Neil Swainston, Andrew R Jones, Sarah R Hart, Henning Hermjakob, Philip Jones, Simon J Hubbard, An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQTM Proteome Science. ,vol. 5, pp. 4- 4 ,(2007) , 10.1186/1477-5956-5-4
RichardG Côté, Philip Jones, Rolf Apweiler, Henning Hermjakob, The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries BMC Bioinformatics. ,vol. 7, pp. 97- 97 ,(2006) , 10.1186/1471-2105-7-97
John T Prince, Mark W Carlson, Rong Wang, Peng Lu, Edward M Marcotte, The need for a public proteomics repository. Nature Biotechnology. ,vol. 22, pp. 471- 472 ,(2004) , 10.1038/NBT0404-471
Richard G Cote, Philip Jones, Lennart Martens, Samuel Kerrien, Florian Reisinger, Quan Lin, Rasko Leinonen, Rolf Apweiler, Henning Hermjakob, The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases BMC Bioinformatics. ,vol. 8, pp. 401- 401 ,(2007) , 10.1186/1471-2105-8-401
Marcus Bantscheff, Dirk Eberhard, Yann Abraham, Sonja Bastuck, Markus Boesche, Scott Hobson, Toby Mathieson, Jessica Perrin, Manfred Raida, Christina Rau, Valérie Reader, Gavain Sweetman, Andreas Bauer, Tewis Bouwmeester, Carsten Hopf, Ulrich Kruse, Gitte Neubauer, Nigel Ramsden, Jens Rick, Bernhard Kuster, Gerard Drewes, Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors Nature Biotechnology. ,vol. 25, pp. 1035- 1044 ,(2007) , 10.1038/NBT1328
Sheng Pan, David Zhu, Joseph F. Quinn, Elaine R. Peskind, Thomas J. Montine, Biaoyang Lin, David R. Goodlett, Greg Taylor, Jimmy Eng, Jing Zhang, A combined dataset of human cerebrospinal fluid proteins identified by multi-dimensional chromatography and tandem mass spectrometry. Proteomics. ,vol. 7, pp. 469- 473 ,(2007) , 10.1002/PMIC.200600756
Philip Jones, Richard G Côté, Lennart Martens, Antony F Quinn, Chris F Taylor, William Derache, Henning Hermjakob, Rolf Apweiler, PRIDE: a public repository of protein and peptide identifications for the proteomics community Nucleic Acids Research. ,vol. 34, pp. 659- 663 ,(2006) , 10.1093/NAR/GKJ138
Lennart Martens, Henning Hermjakob, Philip Jones, Marcin Adamski, Chris Taylor, David States, Kris Gevaert, Joël Vandekerckhove, Rolf Apweiler, PRIDE: The proteomics identifications database Proteomics. ,vol. 5, pp. 3537- 3545 ,(2005) , 10.1002/PMIC.200401303
Ian Lo, Vincent J. Denef, Nathan C. VerBerkmoes, Manesh B. Shah, Daniela Goltsman, Genevieve DiBartolo, Gene W. Tyson, Eric E. Allen, Rachna J. Ram, J. Chris Detter, Paul Richardson, Michael P. Thelen, Robert L. Hettich, Jillian F. Banfield, Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria Nature. ,vol. 446, pp. 537- 541 ,(2007) , 10.1038/NATURE05624