title: The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
abstract: The Functional Genomics Experiment data model (FuGE) has been developed to facilitate convergence of data standards for high-throughput, comprehensive analyses in biology. FuGE models the components of an experimental activity that are common across different technologies, including protocols, samples and data. FuGE provides a foundation for describing entire laboratory workflows and for the development of new data formats. The Microarray Gene Expression Data society and the Proteomics Standards Initiative have committed to using FuGE as the basis for defining their respective standards, and other standards groups, including the Metabolomics Standards Initiative, are evaluating FuGE in their development efforts. Adoption of FuGE by multiple standards bodies will enable uniform reporting of common parts of functional genomics workflows, simplify data-integration efforts and ease the burden on researchers seeking to fulfill multiple minimum reporting requirements. Such advances are important for transparent data management and mining in functional genomics and systems biology.
authors.affiliation: School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Jones
authors.forename: Michael
authors.initials: M
authors.lastname: Miller
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.forename: Rolf
authors.initials: R
authors.lastname: Apweiler
authors.forename: Catherine A
authors.initials: CA
authors.lastname: Ball
authors.forename: Alvis
authors.initials: A
authors.lastname: Brazma
authors.forename: James
authors.initials: J
authors.lastname: Degreef
authors.forename: Nigel
authors.initials: N
authors.lastname: Hardy
authors.forename: Henning
authors.initials: H
authors.lastname: Hermjakob
authors.forename: Simon J
authors.initials: SJ
authors.lastname: Hubbard
authors.forename: Peter
authors.initials: P
authors.lastname: Hussey
authors.forename: Mark
authors.initials: M
authors.lastname: Igra
authors.forename: Helen
authors.initials: H
authors.lastname: Jenkins
authors.forename: Randall K
authors.initials: RK
authors.lastname: Julian
authors.forename: Kent
authors.initials: K
authors.lastname: Laursen
authors.forename: Stephen G
authors.initials: SG
authors.lastname: Oliver
authors.forename: Norman W
authors.initials: NW
authors.lastname: Paton
authors.forename: Susanna-Assunta
authors.initials: SA
authors.lastname: Sansone
authors.forename: Ugis
authors.initials: U
authors.lastname: Sarkans
authors.forename: Christian J
authors.initials: CJ
authors.lastname: Stoeckert
authors.forename: Chris F
authors.initials: CF
authors.lastname: Taylor
authors.forename: Patricia L
authors.initials: PL
authors.lastname: Whetzel
authors.forename: Joseph A
authors.initials: JA
authors.lastname: White
authors.forename: Paul
authors.initials: P
authors.lastname: Spellman
authors.forename: Angel
authors.initials: A
authors.lastname: Pizarro
mesh_terms: D019295:Computational Biology; D003198:Computer Simulation / Q000592:standards*; D016208:Databases, Factual; D023281:Genomics / Q000592:standards*; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis / Q000592:standards*; D040901:Proteomics / Q000592:standards*