BioModels Database, a curated resource of annotated published models Nicolas Le Novère, EMBL-EBI http://www.ebi.ac.uk/biomodels/ What is BioModels Database? Store and serve quantitative models of biomedical interest Only models described in the peer-reviewed scientific literature. Models are curated: computer software check the syntax, while human curators check the semantics. Models are simulated to check the reference correspondence Model components are annotated, to improve identification and retrieval. BioModels DB native format is SBML but models are accepted in several formats, and served in several others. Where are the models coming from I) Individuals Authors (prior to grant application, before publication etc.) Members of the SBML community (developers+modellers) II) Existing model repositories SBML repository, JWS Online, The Virtual Cell, Database Of Quantitative Cell Signalling, CellML repository III) Journals (> 200 journals advise deposition, including all PloS journals, all BMC journals, Nature Molecular Systems Biology) IV) BioModels DB curators encode new models from literature Increase of content models reactions 800 700 35000 models 600 reactions (x50) 30000 500 25000 400 20000 300 15000 200 10000 100 5000 0 Apr2005 March2009 Production pipeline Submission Curation Annotation Public Non-curated Non-curated Models Models Consistency Check distribution MIRIAM Curated Curated Curation Models Models Perfect pipeline: model unchanged SBML compare model submission consistency with original check publication non curated branch curated branch compare annotation gets BIOMD ID simulation results still not public with publication curated branch public 7 Model manually correct changed SBML Re: Submission SBML compare model submission consistency with original check publication beautify and correct non curated SBML, enter units branch change IDs and names curated branch compare annotation gets BIOMD ID simulation results still not public with publication curated branch public 8 contact: Model manually correct submitter, creator changed SBML or finally authors add notes of Re: Publications changes SBML compare model submission consistency with original check publication beautify and correct non curated SBML, enter units branch change IDs and names curated branch compare annotation gets BIOMD ID simulation results still not public with publication add notes of changes contact: curated branch submitter, creator public or finally authors 9 BioModels DB supported format Level 2 Version 1 Level 2 Version 3 all Levels and Versions Version 1.1 XPP-Aut NeuroML VCML VCML BioPAX Version 1.0 PDF Version 1.1 BioModels DB Infrastructure (1) Users . Application Servers Cluster biomodels.caltech.edu Node 1 Node 2 computing-intensive tasks, external formats' conversions and some user-driven tasks will be running on clusters www.ebi.ac.uk/biomodels ... BioModels DB Infrastructure (2) external resources MIRIAM annotations models in SBML export (all versions) text indices files direct search in BioModels DB retrieval of IDs from 3rd party eg. in notes, SBML elements, resources by search terms → specific annotations by ID then search specific annotations 15 Explore taxonomy for relevant models fungi Homo sapiens fungi/metazoa mammalia Rattus norvegicus metazoa arthropoda fungi/metazoa Homo sapiens Rattus norvegicus Different views of a model http://www.ebi.ac.uk/biomodels/webservices.html Model of Month (RSS) Usage increase hitsper day (averagedper month) Funding structure Nicolas Le Novère PI Camille Laibe developer Chen Li Lukas Endler (MIRIAM, developer curator SBO) Nick Juty curator (MIRIAM, SBO) Melanie Stefan (model of the month) Nicolas Vijayalakshmi Rodriguez Chelliah Michael Hucka developer curator PI (50%).