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Pathway content improvement. How to store an expert’s brain and use it to understand omics.

Pathway content improvement. How to store an expert’s brain and use it to understand omics. Chris Evelo NuGO WP7 BiGCaT Bioinformatics. Mapping. Annotation/ coupling. Scientist know GenMapp. Advantages: Easy to use, Reasonable visualisation Some pathway statistics Interesting content

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Pathway content improvement. How to store an expert’s brain and use it to understand omics.

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

  2. Mapping Annotation/coupling the European Nutrigenomics Organisation

  3. 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

  4. Proposed workflow Combine and forwardexisting mapsto limited group of experts Think of best way to storepathway information Text miningfrom key genes/metabolites Forward improved mapsto limited group of experts Develop storage format plus tools Collect back page info Forward new draft to alarger group of expertswithin NuGO Develop/adapt entry toolsplus converters Test resulting maps Make maps available the European Nutrigenomics Organisation

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

  6. Proposed at EBI Current 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 Expert data And…use in Reactome itself BioPax plus BioPAX Reactome ?? Layout data New GenMapp the European Nutrigenomics Organisation

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

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

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