TY - JOUR
T1 - The Functional Genomics Experiment model (FuGE)
T2 - An extensible framework for standards in functional genomics
AU - Jones, Andrew R.
AU - Miller, Michael
AU - Aebersold, Ruedi
AU - Apweiler, Rolf
AU - Ball, Catherine A.
AU - Brazma, Alvis
AU - DeGreef, James
AU - Hardy, Nigel
AU - Hermjakob, Henning
AU - Hubbard, Simon J.
AU - Hussey, Peter
AU - Igra, Mark
AU - Jenkins, Helen
AU - Julian, Randall K.
AU - Laursen, Kent
AU - Oliver, Stephen G.
AU - Paton, Norman W.
AU - Sansone, Susanna Assunta
AU - Sarkans, Ugis
AU - Stoeckert, Christian J.
AU - Taylor, Chris F.
AU - Whetzel, Patricia L.
AU - White, Joseph A.
AU - Spellman, Paul
AU - Pizarro, Angel
N1 - Funding Information:
We would like to thank MGED and PSI for their support of the FuGE project. We would also like to thank FuGO members, RSBI, the CPAS group at the Fred Hutchinson Cancer Research Center and Genologics for their input into the model, testing and supplying use cases. Work on FuGE in Manchester has been supported by a grant from the BBSRC to S.G.O., N.W.P., S.J.H. and Andy Brass. MGED is funded by the National Institutes of Health grant 1P41HG003619, which has provided financial support for development meetings. The FuGE initiative is endorsed by Oliver Fiehn, chair of the Metabolomics Standards Initiative oversight committee.
PY - 2007/10
Y1 - 2007/10
N2 - 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.
AB - 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.
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U2 - 10.1038/nbt1347
DO - 10.1038/nbt1347
M3 - Review article
C2 - 17921998
AN - SCOPUS:35148889036
SN - 1087-0156
VL - 25
SP - 1127
EP - 1133
JO - Nature biotechnology
JF - Nature biotechnology
IS - 10
ER -