Functional Genomics Experiment (FuGE) Documents

Documents:

• Andrew R. Jones, Allyson L. Lister, Leandro Hermida, Peter Wilkinson, Martin Eisenacher, Khalid Belhajjame, Frank Gibson, Phil Lord, Matthew Pocock, Heiko Rosenfelder, Javier Santoyo-Lopez, Anil Wipat, Norman W. Paton. Modeling and Managing Experimental Data Using FuGE OMICS: A Journal of Integrative Biology. June 2009, 13(3): 239-251. doi:10.1089/omi.2008.0080.
• Khalid Belhajjame, Andrew R. Jones, and Norman W. Paton A toolkit for capturing and sharing FuGE experiments Bioinformatics, 15 November 2008; 24: 2647 - 2649.
• Jones, A.R., Miller, M., Aebersold, R., Apweiler, R., Ball, C.A., Brazma, A., DeGreef, J., Hardy, N., Hermjakob, H., Hubbard, S.J., Hussey, P., Igra, M., Jenkins, H., Julian, R.K. Jr, Laursen, K., Oliver, S.G., Paton, N.W., Sansone, S-A, Sarkans, U., Stoeckert, C.J. Jr, Taylor, C.F., Whetzel, P.L., White, J.A., Spellman, P. and Pizarro, A., The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics, Nature Biotech , October;25(10), 1127-1133, 2007.
• Ontology usage guide: word doc, XML example (describes best practice for encoding ontology terms in FuGE version 1)
• Draft guide describing rules for building extensions of FuGE: word doc
• A guide describing how to install FuGE, AndroMDA, Maven etc and create a first XML Schema for extensions (developed by Josef Spidlen and Olga Tchuvatkina)
• Jones AR, Pizarro A, Spellman P, Miller M; FuGE Working Group. FuGE: Functional Genomics Experiment Object Model, OMICS: A Journal of Integrative Biology, 2006 10:2 p179-184
• "FuGE in plain English" (Milestone 1, Sept 2005), (Milestone 2, Dec 2005), (Milestone 3, June 2006)
• Guide to extending FuGE (Milestone 2), (Milestone 3)
• UML Primer (guide to UML structures used in FuGE)
• Integrating FuGE and PSI models. - Andrew Jones, April 2005 - A report on how one would go about extending the FuGE model for PSI concepts.
• Bio.Material use case - Angel Pizarro - A small textual use case used for modeling the FuGE.Bio.Material package

Posters:

• Poster for Metabomeeting 1.0

Presentations:

• PSI meeting in San Francisco, April 2006: Meeting site, FuGE Update - Angel Pizarro - FuGE: A framework for developing standards for functional genomics
• Metabomeeting 2.0 Cambridge, Jan 2006: Meeting site, FuGE Update - Andrew Jones - Update on FuGE milestone 2 for the metabolomics community
• Metabomeeting 1.0 Cambridge, July 2005: Meeting site, FuGE - Andrew Jones - Update on FuGE for the metabolomics community
• PSI meeting in Geneva, August 2005: Meeting report, Experiments extending FuGE for Mass Spectrometry and Gels - Andrew Jones - Some early examples of how FuGE couple accomodate different kinds of data such as mass spec and gels.
• PSI meeting in Siena, Italy, April 2005: Meeting report, "FuGE in plain English" PPT - Angel Pizarro - some background needed to understand FuGE and some simple english descriptions of the UML model.
• PSI meeting in Siena, Italy, April 2005: Meeting report, "Evaluation of PSI constructs and use cases within FuGE" (PPT) - Andrew Jones - Several proteomics use cases are covered, with details as where to extend FuGE to handle proteomics data, and when to rely on central FuGE concepts.