title: A systematic approach to modeling, capturing, and disseminating proteomics experimental data.
abstract: Both the generation and the analysis of proteome data are becoming increasingly widespread, and the field of proteomics is moving incrementally toward high-throughput approaches. Techniques are also increasing in complexity as the relevant technologies evolve. A standard representation of both the methods used and the data generated in proteomics experiments, analogous to that of the MIAME (minimum information about a microarray experiment) guidelines for transcriptomics, and the associated MAGE (microarray gene expression) object model and XML (extensible markup language) implementation, has yet to emerge. This hinders the handling, exchange, and dissemination of proteomics data. Here, we present a UML (unified modeling language) approach to proteomics experimental data, describe XML and SQL (structured query language) implementations of that model, and discuss capture, storage, and dissemination strategies. These make explicit what data might be most usefully captured about proteomics experiments and provide complementary routes toward the implementation of a proteome repository.
authors.affiliation: School of Biological Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK.
authors.forename: Chris F
authors.initials: CF
authors.lastname: Taylor
authors.forename: Norman W
authors.initials: NW
authors.lastname: Paton
authors.forename: Kevin L
authors.initials: KL
authors.lastname: Garwood
authors.forename: Paul D
authors.initials: PD
authors.lastname: Kirby
authors.forename: David A
authors.initials: DA
authors.lastname: Stead
authors.forename: Zhikang
authors.initials: Z
authors.lastname: Yin
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.forename: Laura
authors.initials: L
authors.lastname: Selway
authors.forename: Janet
authors.initials: J
authors.lastname: Walker
authors.forename: Isabel
authors.initials: I
authors.lastname: Riba-Garcia
authors.forename: Shabaz
authors.initials: S
authors.lastname: Mohammed
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Deery
authors.forename: Julie A
authors.initials: JA
authors.lastname: Howard
authors.forename: Tom
authors.initials: T
authors.lastname: Dunkley
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.forename: Douglas B
authors.initials: DB
authors.lastname: Kell
authors.forename: Kathryn S
authors.initials: KS
authors.lastname: Lilley
authors.forename: Peter
authors.initials: P
authors.lastname: Roepstorff
authors.forename: John R
authors.initials: JR
authors.lastname: Yates
authors.forename: Andy
authors.initials: A
authors.lastname: Brass
authors.forename: Alistair J P
authors.initials: AJ
authors.lastname: Brown
authors.forename: Phil
authors.initials: P
authors.lastname: Cash
authors.forename: Simon J
authors.initials: SJ
authors.lastname: Gaskell
authors.forename: Simon J
authors.initials: SJ
authors.lastname: Hubbard
authors.forename: Stephen G
authors.initials: SG
authors.lastname: Oliver
mesh_terms: D003628:Database Management Systems; D030562:Databases, Protein; D004282:Documentation / Q000379:methods; D019146:Hypermedia; D033181:Information Dissemination / Q000379:methods; D016247:Information Storage and Retrieval / Q000379:methods*; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods; D012984:Software; D012985:Software Design; D014584:User-Computer Interface
chemical_list: D011506:Proteins