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 journalArticlepeer-review

    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. © 2007 Nature Publishing Group.
    Original languageEnglish
    Pages (from-to)1127-1133
    Number of pages6
    JournalNature biotechnology
    Volume25
    Issue number10
    DOIs
    Publication statusPublished - Oct 2007

    Keywords

    • PROTEIN ABUNDANCE
    • MESSENGER-RNA
    • OBJECT MODEL
    • PROTEOMICS
    • REPRESENTATION
    • COMMUNITY
    • ONTOLOGY
    • SCALE

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