1. the European Nutrigenomics Organisation Pathway content improvement. How to store an expert’s brain and use it to understand omics. Chris Evelo NuGO WP7 BiGCaT Bioinformatics

2. the European Nutrigenomics Organisation Mapping Annotation/ coupling

3. the European Nutrigenomics Organisation 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

4. the European Nutrigenomics Organisation 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 Collect back page info Forward new draft to a larger group of experts within NuGO Develop storage format plus tools Think of best way to store pathway information Develop/adapt entry tools plus converters Test resulting maps Make maps available

5. the European Nutrigenomics Organisation GenMapp/BioPAX Expert data Current GenMapp BioPAX Layout data BioPAX plus editor New GenMapp Not a very elegant solution... And a lot of format specific work… But it does store extra information about interactions, reactions metabolites, localizations etc in BioPAX format.

6. the European Nutrigenomics Organisation BioPax plus Proposed at EBI Expert data Reactome BioPAX Layout data Current GenMapp New GenMapp ?? Using Reactome could allow us to: store everything use high quality entry tools ad an extra round of curation (referees) develop Reactome – BioPAX converters together convince BioPAX about “plus” to work with GenMapp on a more general problem And… use in Reactome itself

7. the European Nutrigenomics Organisation BioPax plus Adaptation EBI Expert data Reactome BioPAX Layout data Current GenMapp New GenMapp ??

8. the European Nutrigenomics Organisation BioPAX Plus/GMML 2 Adaptation MDP/GenMapp Expert data Reactome BioPAX GMML Current GenMapp GenMapp 2 NUGO/EBI EBI MDP4/GenMapp Rachel van Haaften (BiGCaT/NuGO) and Marjan van Erk (TNO/NuGO) will visit EBI early 2005 to learn doing this Philippe Rocca and Imre Vastrik (EBI/Reactome) will define a way to get Reactome views and export them to GenMapp2 Rachel van Haaften (BiGCaT/NuGO) and Marjan van Erk (TNO/NuGO) will test this and give user feedback BiGCaT students will create GenMapp 2 – GMML converters with help from Lynn Ferrante (GenMapp.org) This step has not been taken care off as of yet… GMML (GenMapp Markup Language) is a superset of BioPAX 1. BioPAX could contain graphical views. (GMML 2 = BioPAX2). But, how doe we make that happen?