PRIDE: Data Submission and Analysis

Juan Antonio Vizcaíno1, Florian Reisinger1, Richard Côté1, Lennart Martens1

1 European Molecular Biology Laboratory–European Bioinformatics Institute (EMBL‐EBI), Hinxton, Cambridge, United Kingdom
Publication Name:  Current Protocols in Protein Science
Unit Number:  Unit 25.4
DOI:  10.1002/0471140864.ps2504s60
Online Posting Date:  April, 2010
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The Proteomics Identifications database (PRIDE, is one of the main repositories designed to store, disseminate, and analyze mass spectrometry–based proteomics datasets. In this unit, an overview of the PRIDE system is given, including its key satellite tools: the Ontology Lookup Service (OLS), the Protein Identifier Cross‐Referencing Service (PICR), and Database on Demand (DoD). Also described in detail are procedures for submitting data to PRIDE, and accessing data stored in PRIDE using the BioMart interface. Finally, to demonstrate the potential of PRIDE as a source for data mining, an example protocol is provided to showcase the powerful cross‐domain query capabilities available through a combination of BioMarts. Curr. Protoc. Protein Sci. 60:25.4.1‐25.4.11. © 2010 by John Wiley & Sons, Inc.

Keywords: PRIDE; proteomics; ontologies; data mining; BioMart

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Table of Contents

  • Introduction
  • Pride and Satellite Tools: OLS, PICR, and DoD
  • Data Submission to Pride
  • The Pride BioMart Interface
  • Conclusions
  • Basic Protocol 1: Cross‐Resource Data Retrieval Between Pride and Ensembl Using the Biomart Interface
  • Literature Cited
  • Figures
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Literature Cited

Literature Cited
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