PRIDE: Data submission and analysis.
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.
Vizcaíno
Juan Antonio
JA
European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, United Kingdom.
Reisinger
Florian
F
European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, United Kingdom.
Côté
Richard
R
European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, United Kingdom.
Martens
Lennart
L
European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, United Kingdom.
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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