EMBL-EBI Annual Scientific Report 2012

Henning HermjakobMSc Bioinformatics University of Bielefeld, Germany,1995. Research Assistant at the German NationalCentre for Biotechnology (GBF), 1996.At EMBL-EBI since 1997.to explore and refine models. We rose to the challenge ofintegrating these models into BioModels Database in 2012,increasing the number of available models by two orders ofmagnitude.Future plansFollowing the upgrade of the PRIDE submission system, wehave turned our attention to redeveloping the core databaseand web interface. This is essential for maintaining goodresponse times and helping users access increasingly largeand complex proteomics datasets. We will begin providingquality-controlled subsets and derived datasets from PRIDE,evolving this resource from a primary database into a systemsbiology source of protein expression data.IntAct will increasingly provide confidence-scored interactiondatasets derived from integration of individual publications.The same strategies will be applied, where possible, tointeraction data from multiple sources, which we accessthrough the PSICQUIC interface. This will ensure we canprovide integrated, up-to-date interaction datasets. We willredesign the IntAct website in 2013 to improve accessibility.In 2013 we will make IntAct datasets accessible throughReactome. This will enhance Reactome’s visualisation ofmolecular interactions in the context of molecular pathways.The next Reactome website release will include a newinteractive pathway viewer, and will feature improved overlayof external information such as expression data. Reactomecuration will focus on disease-induced modifications ofpathways, supported by improved visualisation toolsand close collaboration with disease-oriented researchcommunities.We will develop the new storage infrastructure for theBioModels Database so that the resource can cope with theinflux of computationally generated models. We will developnew features (e.g., full model versioning, support for moremodelling formats), update the user interface, enhance searchfacilities and improve overall performance.We will continue to work with journals, editors and dataproducers to make more data publicly available by utilisingcommunity-supported standards.Figure. Distribution of ProteomeXchange submissions in 20122012 EMBL-EBI Annual Scientific Report47