The Functional Genomics Experiment model (FuGE): An extensible framework for standards in functional genomics

Andrew R. Jones, Michael Miller, Ruedi Aebersold, Rolf Apweiler, Catherine A. Ball, Alvis Brazma, James DeGreef, Nigel Hardy, Henning Hermjakob, Simon J. Hubbard, Peter Hussey, Mark Igra, Helen Jenkins, Randall K. Julian, Kent Laursen, Stephen G. Oliver, Norman W. Paton, Susanna Assunta Sansone, Ugis Sarkans, Christian J. StoeckertChris F. Taylor, Patricia L. Whetzel, Joseph A. White, Paul Spellman, Angel Pizarro

Research output: Contribution to journalArticle

75 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1127-1133
Number of pages7
JournalNature Biotechnology
Volume25
Issue number10
DOIs
StatePublished - Oct 2007
Externally publishedYes

Fingerprint

Genomics
Experiments
Workflow
Metabolomics
Systems Biology
Data Mining
Data integration
Microarrays
Gene expression
Proteomics
Information management
Data mining
Data structures
Theoretical Models
Research Personnel
Throughput
Technology
Gene Expression

ASJC Scopus subject areas

  • Microbiology

Cite this

Jones, A. R., Miller, M., Aebersold, R., Apweiler, R., Ball, C. A., Brazma, A., ... Pizarro, A. (2007). The Functional Genomics Experiment model (FuGE): An extensible framework for standards in functional genomics. Nature Biotechnology, 25(10), 1127-1133. https://doi.org/10.1038/nbt1347

The Functional Genomics Experiment model (FuGE) : An extensible framework for standards in functional genomics. / Jones, Andrew R.; Miller, Michael; Aebersold, Ruedi; Apweiler, Rolf; Ball, Catherine A.; Brazma, Alvis; DeGreef, James; Hardy, Nigel; Hermjakob, Henning; Hubbard, Simon J.; Hussey, Peter; Igra, Mark; Jenkins, Helen; Julian, Randall K.; Laursen, Kent; Oliver, Stephen G.; Paton, Norman W.; Sansone, Susanna Assunta; Sarkans, Ugis; Stoeckert, Christian J.; Taylor, Chris F.; Whetzel, Patricia L.; White, Joseph A.; Spellman, Paul; Pizarro, Angel.

In: Nature Biotechnology, Vol. 25, No. 10, 10.2007, p. 1127-1133.

Research output: Contribution to journalArticle

Jones, AR, Miller, M, Aebersold, R, Apweiler, R, Ball, CA, Brazma, A, DeGreef, J, Hardy, N, Hermjakob, H, Hubbard, SJ, Hussey, P, Igra, M, Jenkins, H, Julian, RK, Laursen, K, Oliver, SG, Paton, NW, Sansone, SA, Sarkans, U, Stoeckert, CJ, Taylor, CF, Whetzel, PL, White, JA, Spellman, P & Pizarro, A 2007, 'The Functional Genomics Experiment model (FuGE): An extensible framework for standards in functional genomics', Nature Biotechnology, vol. 25, no. 10, pp. 1127-1133. https://doi.org/10.1038/nbt1347
Jones, Andrew R. ; Miller, Michael ; Aebersold, Ruedi ; Apweiler, Rolf ; Ball, Catherine A. ; Brazma, Alvis ; DeGreef, James ; Hardy, Nigel ; Hermjakob, Henning ; Hubbard, Simon J. ; Hussey, Peter ; Igra, Mark ; Jenkins, Helen ; Julian, Randall K. ; Laursen, Kent ; Oliver, Stephen G. ; Paton, Norman W. ; Sansone, Susanna Assunta ; Sarkans, Ugis ; Stoeckert, Christian J. ; Taylor, Chris F. ; Whetzel, Patricia L. ; White, Joseph A. ; Spellman, Paul ; Pizarro, Angel. / The Functional Genomics Experiment model (FuGE) : An extensible framework for standards in functional genomics. In: Nature Biotechnology. 2007 ; Vol. 25, No. 10. pp. 1127-1133.
@article{41db1fb69bf4437599a3523c2c37bbcb,
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.",
author = "Jones, {Andrew R.} and Michael Miller and Ruedi Aebersold and Rolf Apweiler and Ball, {Catherine A.} and Alvis Brazma and James DeGreef and Nigel Hardy and Henning Hermjakob and Hubbard, {Simon J.} and Peter Hussey and Mark Igra and Helen Jenkins and Julian, {Randall K.} and Kent Laursen and Oliver, {Stephen G.} and Paton, {Norman W.} and Sansone, {Susanna Assunta} and Ugis Sarkans and Stoeckert, {Christian J.} and Taylor, {Chris F.} and Whetzel, {Patricia L.} and White, {Joseph A.} and Paul Spellman and Angel Pizarro",
year = "2007",
month = "10",
doi = "10.1038/nbt1347",
language = "English (US)",
volume = "25",
pages = "1127--1133",
journal = "Biotechnology",
issn = "1087-0156",
publisher = "Nature Publishing Group",
number = "10",

}

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

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.

UR - http://www.scopus.com/inward/record.url?scp=35148889036&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=35148889036&partnerID=8YFLogxK

U2 - 10.1038/nbt1347

DO - 10.1038/nbt1347

M3 - Article

C2 - 17921998

AN - SCOPUS:35148889036

VL - 25

SP - 1127

EP - 1133

JO - Biotechnology

JF - Biotechnology

SN - 1087-0156

IS - 10

ER -