FuGE Update
12
An update on the Functional Genomics Experiment (FuGE) model Frank Gibson 1 and Andy Jones 2 1 University of Newcastle and 2 University of Liverpool
-
Upload
guest469de8 -
Category
Technology
-
view
745 -
download
1
description
An update on the FuGE project and a database implementation called SyMBA presented at the first MIBBI workshop
Transcript of FuGE Update
An update on the Functional Genomics Experiment (FuGE) model
Frank Gibson1 and Andy Jones2
1University of Newcastle and 2University of Liverpool
License
• This document is licensed to the public under the Creative Commons Attribution 3.0 License
FuGE model
• Model of common components in science investigations, such as sample description, Experiment variables and design, data, protocols, equipment and software.
FuGE model• Three main uses:
1. Capture description / data for techniques that do not require a specific format
2. Additional metadata for existing data formats3. Framework to be extended for creating new data formats
• Aims: – bring about convergence of data formats across the omics– develop open-source toolkits for simplifying the
integration of data and submission to public repositories
FuGE Availability• http://fuge.sourceforge.net/
• FuGE version 1 released Aug 2007
• First version of toolkit released in Jan 2008
• Jones et al. Nature Biotech 25, 1127 - 1133 (2007) PMID: 17921998
FuGE Implementation - Extension
• Can be extended to cover the specifics of a particular experiment
• Dec 2007 - workshop bringing together groups developing extensions on FuGE: – proteomics (GelML, spML, analysisXML), – flow cytometry, – RNAi, – e-Neuroscience
• Also being used in various ways for modelling microarray data, metabolomics, genetical genomics, immunohistochemistry...
Tools and software• Tooling– Toolkit now available for generating XML Schema from
model– Toolkits for generating database back-end and XML
input/output released in beta versions
• Software implementations– On-going projects to develop converters between FuGE-
ML and tab formats (EBI), generic XML data input and dissemination (Manchester)
– Symba (Newcastle), SystemX (Basel), CPAS (Fred Hutch), Genologics
Getting involved...
• See the FuGE website http://fuge.sourceforge.net/• Read the documentation:
– FuGE version 1 (http://fuge.sf.net/dev/V1Final/FuGE-v1-SpecDoc.doc)– Nature Biotech paper (
http://www.nature.com/nbt/journal/v25/n10/full/nbt1347.html) – Workshop report (coming soon)– Toolkit documentation
(http://fuge.sourceforge.net/stks/xsd-stk/index.html)
• Contact FuGE mailing list: [email protected]#
• Look at an implementation Symba: http://symba.sourceforge.net/
