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Functional genomics experiments present many challenges in data archiving, sharing and querying. As the size and complexity of data generated from such experiments grows, so does the requirement for standard data formats. To address these needs, the Functional Genomics Experiment [Object Model / Markup-Language] (FuGE-OM, FuGE-ML) has been created to facilitate the development of data standards.
FuGE is a model of the shared components in different functional genomics domains. FuGE facilitates the development of data standards in functional genomics in two ways:
1. FuGE provides a model of common components in functional genomics investigations, such as materials, data, protocols, equipment and software. These models can be extended to develop modular data formats with consistent structure.
2. FuGE provides a framework for capturing complete laboratory workflows, enabling the integration of pre-existing data formats. In this context, FuGE allows the capture of additional metadata that gives formats a context within the complete workflow.
FuGE is available as a UML model and an XML Schema (see development page)
See the FuGE wiki for discussion of extension guidelines and common design patterns
June 2009: FuGE extension guidelines published in OMICS
August 2008: The 1st version of the FuGE database STK has been released (Hibernate and EJB versions), see development page for more information.
14th February 2008: FuGE XML Schema software toolkit (XSD-STK) released as 1.0-SNAPSHOT (see Development page). Please test the toolkit, send us feedback on the documenation, and subscribe to the new SVN mailing list to keep updated with recent alterations.
24th January 2008: AndroMDA cartridges posted for XML Schema generation for FuGE v1 and extensions of FuGE (see Development page).
13th / 14th Decemeber 2007: Workshop in Manchester, UK to decide on best practice for building extensions of FuGE. The outcome of the meeting will be published in early/mid 2008
9th October 2007: The FuGE version 1 profile is now available to import into model extensions (see Development page).
5th October 2007: The main FuGE manuscript has now been published at Nature Biotech .
18th August 2007: FuGE has completed the PSI standadisation process, resulting in version 1 (final), see Development page.
FuGE is being used by the following organisations for data format development:
Other data formats planned to extend from FuGE:
FuGE implementations in software (in development):
If your model or software is using FuGE and you are not listed, please send us a mail.
FuGE is closely related to other efforts including:
See the UML models or documentation on the development page for more information