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Nu GO Pathway content improvement. How to store an expert’s brain and use it to understand omics. Chris Evelo NuGO WP7 BiGCaT Bioinformatics the European Nutrigenomics Organisation Nu GO Mapping Annotation/ coupling the European Nutrigenomics Organisation Nu GO Scientist know GenMapp Advantages: • Easy to use, • Reasonable visualisation • Some pathway statistics • Interesting content Disadvantages: • Small academic initiative, uncertain lifespan • No info on reactions, metabolites, location • No change (e.g. time course) visualisation the European Nutrigenomics Organisation Nu GO Proposed workflow Combine and forward existing maps to limited group of experts Text mining from key genes/metabolites Forward improved maps to limited group of experts Think of best way to store pathway information Develop storage format plus tools Collect back page info Forward new draft to a larger group of experts within NuGO Develop/adapt entry tools plus converters Test resulting maps Make maps available the European Nutrigenomics Organisation Nu GO GenMapp/BioPAX Current GenMapp Not a very elegant solution... BioPAX And a lot of format specific work… BioPAX plus editor Layout data But it does store extra information about interactions, reactions metabolites, localizations etc in BioPAX format. New GenMapp Expert data the European Nutrigenomics Organisation Nu GO Proposed at EBI Using Reactome Current GenMapp could allow us to: • store everything • use high quality entry tools Expert data • ad an extra round of curation And… (referees) use in Reactome • develop Reactome – BioPAX itself BioPAX converters together Reactome • convince BioPAX about BioPax “plus” plus ?? Layout data • to work with GenMapp on a more general problem New GenMapp the European Nutrigenomics Organisation Adaptation EBI Nu GO Current GenMapp Expert data BioPAX Reactome BioPax plus ?? Layout data New GenMapp the European Nutrigenomics Organisation Adaptation MDP/GenMapp Rachel van Haaften Nu GO(BiGCaT/NuGO) and Marjan van Erk Rachel van Haaften (TNO/NuGO) will test This step hasand not (BiGCaT/NuGO) GMML (GenMapp Markup this and give user been taken Marjan van care Erk off Language) is a superset of Current GenMapp feedback as of yet… (TNO/NuGO) will BioPAX 1. BioPAX could visitviews. EBI early 2005 contain graphical toBiGCaT learn doing this Expert data 2 = BioPAX2). (GMML students BioPAX will create GenMapp Philippe Rocca and But, how doe we make 2 – GMML Imre Vastrik BioPAX Plus/GMML 2 that happen? NUGO/EBI converters with help (EBI/Reactome) will from Lynn Ferrante define a way to get (GenMapp.org) Reactome views andGMML Reactome export them to GenMapp2 EBI MDP4/GenMapp GenMapp 2 the European Nutrigenomics Organisation