The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
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.
Jones
Andrew R
AR
School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
Miller
Michael
M
Aebersold
Ruedi
R
Apweiler
Rolf
R
Ball
Catherine A
CA
Brazma
Alvis
A
Degreef
James
J
Hardy
Nigel
N
Hermjakob
Henning
H
Hubbard
Simon J
SJ
Hussey
Peter
P
Igra
Mark
M
Jenkins
Helen
H
Julian
Randall K
RK
Laursen
Kent
K
Oliver
Stephen G
SG
Paton
Norman W
NW
Sansone
Susanna-Assunta
SA
Sarkans
Ugis
U
Stoeckert
Christian J
CJ
Taylor
Chris F
CF
Whetzel
Patricia L
PL
White
Joseph A
JA
Spellman
Paul
P
Pizarro
Angel
A
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*