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Biomodels Database BioModels Database Camille Laibe HARMONY 2012, 21-25th May 2012, Maastricht EBI is an Outstation of the European Molecular Biology Laboratory. What is BioModelsWho Database? are we? BioModels.net team Technology part of the Computational Systems Neurobiology group (Nicolas Le Novère) at EMBL-EBI Standards: Minimal Information Required In the Annotation of Models (MIRIAM), Minimal Information About a Simulation Experiment (MIASE), Systems Biology Graphical Notation (SBGN), ¼ Formats: Systems Biology Markup Language (SBML), Simulation Experiment Description Markup Language (SED-ML), ... Ontologies: Systems Biology Ontology (SBO), Kinetic Simulation Algorithm Ontology (KiSAO), TErminology for the Description of DYnamics (TEDDY), ¼ Services: BioModels Database, MIRIAM Registry, Identifiers.org, ... Tools: libSBML, JSBML, SBFC, SBMLeditor, ¼ 2 Basic (biochemical)What is BioModels model Database? example k k A+B 1 A_B 3 Ap+B k2 d[A]/dt = - k1[B][A] + k2[A_B] d[Ap]/dt = + k3[A_B] d[B]/dt = - k1[B][A] + k2[A_B] + k3[A_B] d[A_B]/dt = + k1[B][A] - k2[A_B] - k3[A_B] [x] 3 t How to build a model? biological model mathematical model simulation computational model4 Tyson et al (1991) PNAS 88(1):7328-32 What Whyis BioModels are models Database? useful? quantitative / dynamic understanding of biological systems integration of data from various scales make clear the current state of knowledge effective way of highlighting gaps in the knowledge prediction of the behaviour of systems under certain conditions sometimes the only tool available design novel experiments ¼ Models are significant tools in Systems Biology 5 RequirementsStorage for and storage exchange and ofexchange models Modellers need to: find understand reuse combine existing models 6 RequirementsStorage for and storage exchange and ofexchange models Modellers need to: find understand reuse combine existing models This requires: standard formats access to published models provision of reliable models: curated and annotated 7 http://www.ebi.ac.uk/biomodels/ 8 Examples of modelsWhat is in BioModels BioModels Database? Database Biochemical models interactions between molecules in multiple cellular compartments Pharmacometrics models tumor growth and treatment response Single-compartment neurons membrane voltage, current flow, concentrations of various ions intra- and extracellularly Spread of infectious diseases outbreak of zombie infection Ecosystem models interaction of living organisms in a given environment ... 9 What Curatedis BioModels branch Database? content 10 Production pipeline 11 Model submission 12 SupportModels for provenance deposition From authors prior to publication Supported (listed in instructions for authors) by > 300 journals, including: ● Molecular Systems Biology ● All PLoS journals ● All BioMedCentral journals ● ¼ Submitted by curators implemented from literature imported from journal supplementary materials exchanged with other repositories (DOQCS, CellML Model Repository, JWS Online, ...) 13 Provided by other people curating models out of interest Model submission (step 1) 14 Model submission (step 2) 15 Curation 16 MIRIAM The Minimum Information Required In the Annotation of a Model http://biomodels.net/miriam/ MIRIAMMIRIAM STANDARD Guidelines set of guidelines for the curation and annotation of quantitative models about encoding and annotation applicable to any structured model format cf. Nicolas Le Novère et al. Minimum Information Requested in the Annotation of biochemical Models (MIRIAM). Nature Biotechnology, 2005 MIRIAM Compliance Models must (among other things): be encoded in a public machine-readable format be clearly linked to a single publication reflect the structure of the biological processes described in the reference paper (list of reactions, ...) be instantiable in a simulation (possess initial conditions, ...) be able to reproduce the results given in the reference paper contain creator's contact details annotated: each model constituent must be unambiguously identified Annotation 20 Curated andSupport non-curated for deposition branches Curated branch MIRIAM compliant models Non-curated branch valid SBML but not curated or annotated not MIRIAM compliant models cannot reproduce published results different model structure non kinetic model (FBA, stoichiometric maps, ...) MIRIAM compliant models models contain kinetic that we cannot curate up to now work in progress, will be moved to curated branch in the near future 21 Why are annotations important? Annotations, and generally metadata, are essential for: understanding data reusing data comparing data integrating data converting data providing efficient search strategies ... 22 Why are annotations important? Annotations, and generally metadata, are essential for: understanding data reusing data comparing data integrating data converting data providing efficient search strategies ... → true for any kind of data! 23 Identifiers for annotations Unique and unambiguous an identifier must never be assigned to two different objects Perennial the identifier is constant and its lifetime is permanent Standards compliant must conform on existing standards, such as URI Resolvable identifiers must be able to be transformed into locations of online resources storing the object or information about the object Free of use everybody should be able to use and create identifiers, freely and at no cost Towards globally unique identifiers Entity Namespace identifier Identifies a Identifies a data data collection entry within the data collection provided by the from a shared list of data collection namespaces unique within the data collection format defined by the data collection 25 Provision of URIs for annotations MIRIAM Registry catalogue of data collections and their associated namespace provides perennial identifiers for annotation and cross- referencing purposes Human calmodulin: P62158 in UniProt urn:miriam:uniprot:P62158 Alcohol dehydrogenase: 1.1.1.1 in Enzyme Nomenclature urn:miriam:ec-code:1.1.1.1 Activation of MAPKK activity: GO:0000186 in Gene Ontology 26 urn:miriam:obo.go:GO%3A0000186 Provision of URIs for annotations MIRIAM Registry catalogue of data collections and their associated namespace provides perennial identifiers for annotation and cross- referencing purposes Identifiers.org ● built on the information stored in the Registry ● provides directly resolvable URIs Human calmodulin: P62158 in UniProt http://identifiers.org/uniprot/P62158 Alcohol dehydrogenase: 1.1.1.1 in Enzyme Nomenclature http://identifiers.org/ec-code/1.1.1.1 Activation of MAPKK activity: GO:0000186 in Gene Ontology 27 http://identifiers.org/obo.go/GO:0000186 Qualified annotation Current BioModels.netBioModels.net Qualifiersqualifiers bqmodel:is bqbiol:isPropertyOf bqmodel:isDerivedFrom bqbiol:isVersionOf bqmodel:isDescribedBy bqbiol:hasVersion bqbiol:isHomologTo bqbiol:is bqbiol:isDescribedBy bqbiol:isDescribedBy bqbiol:encodes bqbiol:hasPart bqbiol:isEncodedBy bqbiol:hasProperty bqbiol:occursIn bqbiol:isPartOf [...] http://biomodels.net/qualifiers/ 29 Annotations in SBML 30 Publication 31 List of models 32 Model browsing via GO terms 33 Model browsing via GO terms 34 Model browsing via Taxonomy 35 Model search 36 Advanced model search 37 SearchBioModels.net strategy 38 Taxonomic search Searching for mammalia retrieves all models fitting mammals both up and down the phylogenetic tree Fungi Homo sapiens Fungi / Metazoa Mammalia Rattus norvegicus Metazoa Arthropoda 39 Taxonomic search metazoa/fungi homo sapiens rattus rattus norvegicus mammalia 40 41 42 43 44 User interface 45 User interface 46 Curation information 47 Graphical export 48 Online simulation 49 JWS Online 50 Sub-model creation 51 Sub-model creation 52 Sub-model creation 53 Sub-model creation 54 Sub-model creation 55 Model of the month 56 Report issues 57 Web Services 58 Supported formats XPP-Aut Octave VCML (Vcell) 59 Converter framework System Biology Format Converter generic framework that potentially allows any conversion between two formats aims to be easily extended currently supported: conversion from SBML to SBGN-ML, BioPAX Level 2 and Level 3, XPP, Octave, Dot, ... allows the combination of several existing converters (conversion pipeline) collaborative project developed in Java online conversion service: http://www.ebi.ac.uk/compneur-srv/converters/ (beta) http://sourceforge.net/projects/sbfc Path2Models large scale generation of quantitative models form pathways initial pathways coming from databases (such as KEGG) completed with information coming from other resources (BioCarta, MetaCyc, ...) converted into SBML enriched with cross-references mathematical models are generated (using common modular rate law for the metabolic networks and logical models for the signalling pathways) whole genome metabolism models are reconstructed using flux balance constraint methods http://www.ebi.ac.uk/biomodels-main/path2models Path2Models 62 Path2Models: browsing 63 Path2Models: display 64 Path2Models acknowledgements Finja Büchel Claudine Chaouiya Andreas Dräger Sarah Keating Camille Laibe Julio Saez-Rodriguez Nicolas Le Novère Martijn Van Iersel Florian Mittag Tobias Czauderna Nicolas Rodriguez Michael Hucka Michael Schubert Roland Keller Niel Swainston Falk Schreiber Clemens Wrzodek 65 What isDatabase BioModels content Database? (r21) 160000 1000 M s o n d o 900 i 140000 e t l s a l 800 e 120000 R 700 100000 600 80000 500 400 60000 300 40000 200 20000 100 0 0 04/2005 04/2006 04/2007 04/2008 04/2009 04/2010 04/2011 04/2012 Evolution of the content of BioModels
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