title: PRIDE: the proteomics identifications database.
abstract: The advent of high-throughput proteomics has enabled the identification of ever increasing numbers of proteins. Correspondingly, the number of publications centered on these protein identifications has increased dramatically. With the first results of the HUPO Plasma Proteome Project being analyzed and many other large-scale proteomics projects about to disseminate their data, this trend is not likely to flatten out any time soon. However, the publication mechanism of these identified proteins has lagged behind in technical terms. Often very long lists of identifications are either published directly with the article, resulting in both a voluminous and rather tedious read, or are included on the publisher's website as supplementary information. In either case, these lists are typically only provided as portable document format documents with a custom-made layout, making it practically impossible for computer programs to interpret them, let alone efficiently query them. Here we propose the proteomics identifications (PRIDE) database (http://www.ebi.ac.uk/pride) as a means to finally turn publicly available data into publicly accessible data. PRIDE offers a web-based query interface, a user-friendly data upload facility, and a documented application programming interface for direct computational access. The complete PRIDE database, source code, data, and support tools are freely available for web access or download and local installation.
authors.affiliation: Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
authors.forename: Henning
authors.initials: H
authors.lastname: Hermjakob
authors.forename: Philip
authors.initials: P
authors.lastname: Jones
authors.forename: Marcin
authors.initials: M
authors.lastname: Adamski
authors.forename: Chris
authors.initials: C
authors.lastname: Taylor
authors.forename: David
authors.initials: D
authors.lastname: States
authors.forename: Kris
authors.initials: K
authors.lastname: Gevaert
authors.forename: Joël
authors.initials: J
authors.lastname: Vandekerckhove
authors.forename: Rolf
authors.initials: R
authors.lastname: Apweiler
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003628:Database Management Systems; D016206:Databases, Bibliographic; D030541:Databases, Genetic; D030562:Databases, Protein; D006801:Humans; D016247:Information Storage and Retrieval; D020407:Internet; D011381:Programming Languages; D040081:Protein Array Analysis; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D011642:Publications; D012984:Software; D013997:Time Factors
chemical_list: D020543:Proteome