title: PRIDE: Data submission and analysis.
abstract: The Proteomics Identifications database (PRIDE, http://www.ebi.ac.uk/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.
authors.affiliation: European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, United Kingdom.
authors.forename: Juan Antonio
authors.initials: JA
authors.lastname: Vizcaíno
authors.affiliation: European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, United Kingdom.
authors.forename: Florian
authors.initials: F
authors.lastname: Reisinger
authors.affiliation: European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, United Kingdom.
authors.forename: Richard
authors.initials: R
authors.lastname: Côté
authors.affiliation: European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, United Kingdom.
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
mesh_terms: D003628:Database Management Systems; D030562:Databases, Protein; D020407:Internet; D013058:Mass Spectrometry; D040901:Proteomics / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
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