A guide to the Proteomics Identifications Database proteomics data repository

The Proteomics Identifications Database (PRIDE, http://www.ebi.ac.uk/pride) is one of the main repositories of MS derived proteomics data. Here, we point out the main functionalities of PRIDE both as a submission repository and as a source for proteomics data. We describe the main features for data...

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Detalles Bibliográficos
Autores principales: Vizcaíno, Juan Antonio, Côté, Richard, Reisinger, Florian, M. Foster, Joseph, Mueller, Michael, Rameseder, Jonathan, Hermjakob, Henning, Martens, Lennart
Formato: Texto
Lenguaje:English
Publicado: WILEY-VCH Verlag 2009
Materias:
Standardisation & Guidelines
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970915/
https://www.ncbi.nlm.nih.gov/pubmed/19662629
http://dx.doi.org/10.1002/pmic.200900402
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author Vizcaíno, Juan Antonio
Côté, Richard
Reisinger, Florian
M. Foster, Joseph
Mueller, Michael
Rameseder, Jonathan
Hermjakob, Henning
Martens, Lennart
author_facet Vizcaíno, Juan Antonio
Côté, Richard
Reisinger, Florian
M. Foster, Joseph
Mueller, Michael
Rameseder, Jonathan
Hermjakob, Henning
Martens, Lennart
author_sort Vizcaíno, Juan Antonio
collection PubMed
description The Proteomics Identifications Database (PRIDE, http://www.ebi.ac.uk/pride) is one of the main repositories of MS derived proteomics data. Here, we point out the main functionalities of PRIDE both as a submission repository and as a source for proteomics data. We describe the main features for data retrieval and visualization available through the PRIDE web and BioMart interfaces. We also highlight the mechanism by which tailored queries in the BioMart can join PRIDE to other resources such as Reactome, Ensembl or UniProt to execute extremely powerful across-domain queries. We then present the latest improvements in the PRIDE submission process, using the new easy-to-use, platform-independent graphical user interface submission tool PRIDE Converter. Finally, we speak about future plans and the role of PRIDE in the ProteomExchange consortium.
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spelling pubmed-29709152010-11-10 A guide to the Proteomics Identifications Database proteomics data repository Vizcaíno, Juan Antonio Côté, Richard Reisinger, Florian M. Foster, Joseph Mueller, Michael Rameseder, Jonathan Hermjakob, Henning Martens, Lennart Proteomics Standardisation & Guidelines The Proteomics Identifications Database (PRIDE, http://www.ebi.ac.uk/pride) is one of the main repositories of MS derived proteomics data. Here, we point out the main functionalities of PRIDE both as a submission repository and as a source for proteomics data. We describe the main features for data retrieval and visualization available through the PRIDE web and BioMart interfaces. We also highlight the mechanism by which tailored queries in the BioMart can join PRIDE to other resources such as Reactome, Ensembl or UniProt to execute extremely powerful across-domain queries. We then present the latest improvements in the PRIDE submission process, using the new easy-to-use, platform-independent graphical user interface submission tool PRIDE Converter. Finally, we speak about future plans and the role of PRIDE in the ProteomExchange consortium. WILEY-VCH Verlag 2009-09 /pmc/articles/PMC2970915/ /pubmed/19662629 http://dx.doi.org/10.1002/pmic.200900402 Text en Copyright © 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim http://creativecommons.org/licenses/by/2.5/ Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation.
spellingShingle Standardisation & Guidelines
Vizcaíno, Juan Antonio
Côté, Richard
Reisinger, Florian
M. Foster, Joseph
Mueller, Michael
Rameseder, Jonathan
Hermjakob, Henning
Martens, Lennart
A guide to the Proteomics Identifications Database proteomics data repository
title A guide to the Proteomics Identifications Database proteomics data repository
title_full A guide to the Proteomics Identifications Database proteomics data repository
title_fullStr A guide to the Proteomics Identifications Database proteomics data repository
title_full_unstemmed A guide to the Proteomics Identifications Database proteomics data repository
title_short A guide to the Proteomics Identifications Database proteomics data repository
title_sort guide to the proteomics identifications database proteomics data repository
topic Standardisation & Guidelines
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970915/
https://www.ncbi.nlm.nih.gov/pubmed/19662629
http://dx.doi.org/10.1002/pmic.200900402
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