FuGE statistics

Tool stats & trends

Looking to identify usage trends or leading experts?


FuGE specifications


Unique identifier OMICS_27713
Name FuGE
Alternative name Functional Genomics Experiment
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Angel Pizarro
  • person_outline Andrew Jones
  • person_outline Michael Miller
  • person_outline Paul Spellman

Publications for Functional Genomics Experiment

FuGE citations


Proteomics Standards Initiative: Fifteen Years of Progress and Future Work

J Proteome Res
PMCID: 5715286
PMID: 28849660
DOI: 10.1021/acs.jproteome.7b00370

[…] ons group designed formats in the past to represent data derived from gel-based workflows and generically describe separations performed in proteomics workflows, called sepML—both built on top of the FuGE framework. GelML and sepML have not been widely implemented, however, and as such they have become deprecated by PSI. […]


A digital repository with an extensible data model for biobanking and genomic analysis management

BMC Genomics
PMCID: 4083403
PMID: 25077808
DOI: 10.1186/1471-2164-15-S3-S3

[…] udies, visits and acquisitions and allows to track patients clinical history. XCEDE is more suitable to exchange documents and protocols about research projects than to share the data themselves. The Functional Genomics Experiment data model (FuGE) [] aims to develop a standard for data sharing. It is used to describe complete experimental workflows and it relies heavily on inheritance and ontolog […]


Semantic integration of gene expression analysis tools and data sources using software connectors

BMC Genomics
PMCID: 3908368
PMID: 24341380
DOI: 10.1186/1471-2164-14-S6-S2

[…] rimental processes has lead to development of different (standard) formats for the representation and exchange of gene expression data, such as MAGE-ML [], MAGE-TAB [], SOFT [], MINiML [], SAM [] and FuGE-ML [,]. However, the availability of a standard data representation format is not enough to guarantee semantic integration of heterogenous tools because not all tools comply with these formats, d […]


LabTrove: A Lightweight, Web Based, Laboratory “Blog” as a Route towards a Marked Up Record of Work in a Bioscience Research Laboratory

PLoS One
PMCID: 3720848
PMID: 23935832
DOI: 10.1371/journal.pone.0067460

[…] bTrove offers the polar opposite of structured experimental descriptions and semantic tools such as the MyTea electronic laboratory notebook . We have avoided experimental description formats such as FuGE (http://fuge.sourceforge.net/), or more widely the range of ontologies designed to describe biological systems and biological science .Our experience is that freedom, and the ability arbitrarily […]


A repository based on a dynamically extensible data model supporting multidisciplinary research in neuroscience

BMC Med Inform Decis Mak
PMCID: 3560115
PMID: 23043673
DOI: 10.1186/1472-6947-12-115

[…] acquisitions) have been extracted and further developed in our work together with some data and metadata hierarchies used by the BIRN (Biomedical Informatics Research Network) initiative [,].Also the Functional Genomics Experiment (FuGE) object model is aimed at providing a framework for the development of standards in life science. As such, FuGE provides a solid foundation for other technology-sp […]


File Formats Commonly Used in Mass Spectrometry Proteomics*

PMCID: 3518119
PMID: 22956731
DOI: 10.1074/mcp.R112.019695

[…] sing sepML have emerged.A few other very general formats are not specific to pre-MS sample processing metadata but do include components to encode at least some sample information. One example is the Functional Genomics Experiment (FuGE) () format, which attempts to provide components for information common to most experiments, as well as a framework for building components specific to a particula […]


Looking to check out a full list of citations?

FuGE institution(s)
School of Computer Science, University of Manchester, Manchester, UK; Faculty of Life Sciences, University of Manchester, Manchester, UK; Rosetta Biosoftware, Seattle, WA, USA; Institute of Molecular Systems Biology, Zurich, Switzerland; Faculty of Science, University of Zurich, Switzerland; Center for Systems Physiology and Metabolic Disease at ETH Zurich, Zurich, Switzerland; The Institute for Systems Biology, Seattle, WA, USA; European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Microarray and Genome Informatics, Department of Biochemistry, Stanford School of Medicine, CCSR, Stanford, CA, USA; GenoLogics Life Sciences Software, Victoria, BC, Canada; Department of Computer Science, Aberystwyth University, Ceredigion, Wales, UK; LabKey Software, Seattle, WA, USA; Indigo BioSystems, Inc., Carmel, IN, USA; Department of Genetics, University of Pennsylvania, Center for Bioinformatics, Philadelphia, PA, USA; Dana-Farber Cancer Institute, Boston, MA, USA; Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, USA; Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
FuGE funding source(s)
Supported by a grant from the BBSRC, and by the National Institutes of Health grant 1P41HG003619.

FuGE reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review FuGE