{"database":"BioModels","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000562?filename=curation_notes.txt"],"Pdf":["https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000562?filename=BIOMD0000000562.pdf"],"Owl":["https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000562?filename=BIOMD0000000562-biopax2.owl","https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000562?filename=BIOMD0000000562-biopax3.owl"],"Svg":["https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000562?filename=BIOMD0000000562.svg"],"Xml":["https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000562?filename=BIOMD0000000562_url.xml","https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000562?filename=manifest.xml"],"Other":["https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000562?filename=metadata.rdf","https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000562?filename=BIOMD0000000562.png","https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000562?filename=BIOMD0000000561-notebook.ipynb","https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000562?filename=curation_image.png"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"submitter":["Thomas Cokelaer"],"curationStatus":["Manually curated"],"modellingApproach":["logical model"],"levelVersion":["L3V1"],"full_dataset_link":["https://www.ebi.ac.uk/biomodels/BIOMD0000000562"],"publication_pubmed":["24321545"],"isPrivate":["false"],"repository":["BioModels"],"modelFormat":["SBML"],"omics_type":["Models"],"tokenised_name":["Chaouiya2013   EGF and TNFalpha mediated signalling pathway"],"publication_year":["2013"],"submissionId":["MODEL1411240000"],"publication_authors":["Claudine Chaouiya, Duncan Bérenguier, Sarah M Keating, Aurélien Naldi, Martijn P van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel Gonçalves, Julien Dorier, Michel Page, Pedro T Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomáš Helikar"],"first_author":["Claudine Chaouiya"],"publication":["24321545,\n                            <h4>Background</h4>Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific computational tools that provide original methods to analyse qualitative models, a standard format to exchange qualitative models has been missing.<h4>Results</h4>We present the Systems Biology Markup Language (SBML) Qualitative Models Package (\"qual\"), an extension of the SBML Level 3 standard designed for computer representation of qualitative models of biological networks. We demonstrate the interoperability of models via SBML qual through the analysis of a specific signalling network by three independent software tools. Furthermore, the collective effort to define the SBML qual format paved the way for the development of LogicalModel, an open-source model library, which will facilitate the adoption of the format as well as the collaborative development of algorithms to analyse qualitative models.<h4>Conclusions</h4>SBML qual allows the exchange of qualitative models among a number of complementary software tools. SBML qual has the potential to promote collaborative work on the development of novel computational approaches, as well as on the specification and the analysis of comprehensive qualitative models of regulatory and signalling networks.. null, 7.\n                            Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal. chaouiya@igc.gulbenkian.pt."],"submitter_mail":["cokelaer@ebi.ac.uk"],"submitter_affiliation":["EMBL-EBI"],"publicationId":["BIOMD0000000562"],"pubmed_abstract":["<h4>Background</h4>Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific computational tools that provide original methods to analyse qualitative models, a standard format to exchange qualitative models has been missing.<h4>Results</h4>We present the Systems Biology Markup Language (SBML) Qualitative Models Package (\"qual\"), an extension of the SBML Level 3 standard designed for computer representation of qualitative models of biological networks. We demonstrate the interoperability of models via SBML qual through the analysis of a specific signalling network by three independent software tools. Furthermore, the collective effort to define the SBML qual format paved the way for the development of LogicalModel, an open-source model library, which will facilitate the adoption of the format as well as the collaborative development of algorithms to analyse qualitative models.<h4>Conclusions</h4>SBML qual allows the exchange of qualitative models among a number of complementary software tools. SBML qual has the potential to promote collaborative work on the development of novel computational approaches, as well as on the specification and the analysis of comprehensive qualitative models of regulatory and signalling networks."],"pubmed_title":["SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools."],"pubmed_authors":["Chaouiya Claudine C, Bérenguier Duncan D, Keating Sarah M SM, Naldi Aurélien A, van Iersel Martijn P MP, Rodriguez Nicolas N, Dräger Andreas A, Büchel Finja F, Cokelaer Thomas T, Kowal Bryan B, Wicks Benjamin B, Gonçalves Emanuel E, Dorier Julien J, Page Michel M, Monteiro Pedro T PT, von Kamp Axel A, Xenarios Ioannis I, de Jong Hidde H, Hucka Michael M, Klamt Steffen S, Thieffry Denis D, Le Novère Nicolas N, Saez-Rodriguez Julio J, Helikar Tomáš T"],"additional_accession":[]},"is_claimable":false,"name":"Chaouiya2013 - EGF and TNFalpha mediated signalling pathway","description":"\n      \n    Chaouiya2013 - EGF and TNFalpha mediated signalling pathway\n\n  This model is described in the article:\n  \n    SBML qualitative models: a\n    model representation format and infrastructure to foster\n    interactions between qualitative modelling formalisms and\n    tools.\n  \n  Chaouiya C, Bérenguier D,\n  Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A,\n  Büchel F, Cokelaer T, Kowal B, Wicks B, Gonçalves E,\n  Dorier J, Page M, Monteiro PT, von Kamp A, Xenarios I, de Jong H,\n  Hucka M, Klamt S, Thieffry D, Le Novère N, Saez-Rodriguez J,\n  Helikar T.\n  BMC Syst Biol 2013; 7: 135\n  Abstract:\n  \n    BACKGROUND: Qualitative frameworks, especially those based\n    on the logical discrete formalism, are increasingly used to\n    model regulatory and signalling networks. A major advantage of\n    these frameworks is that they do not require precise\n    quantitative data, and that they are well-suited for studies of\n    large networks. While numerous groups have developed specific\n    computational tools that provide original methods to analyse\n    qualitative models, a standard format to exchange qualitative\n    models has been missing. RESULTS: We present the Systems\n    Biology Markup Language (SBML) Qualitative Models Package\n    (\"qual\"), an extension of the SBML Level 3 standard designed\n    for computer representation of qualitative models of biological\n    networks. We demonstrate the interoperability of models via\n    SBML qual through the analysis of a specific signalling network\n    by three independent software tools. Furthermore, the\n    collective effort to define the SBML qual format paved the way\n    for the development of LogicalModel, an open-source model\n    library, which will facilitate the adoption of the format as\n    well as the collaborative development of algorithms to analyse\n    qualitative models. CONCLUSIONS: SBML qual allows the exchange\n    of qualitative models among a number of complementary software\n    tools. SBML qual has the potential to promote collaborative\n    work on the development of novel computational approaches, as\n    well as on the specification and the analysis of comprehensive\n    qualitative models of regulatory and signalling networks.\n  \n\n\n  This model is hosted on \n  BioModels Database\n  and identified by: \n  BIOMD0000000562.\n  To cite BioModels Database, please use: \n  BioModels Database:\n  An enhanced, curated and annotated resource for published\n  quantitative kinetic models.\n\n\n  To the extent possible under law, all copyright and related or\n  neighbouring rights to this encoded model have been dedicated to\n  the public domain worldwide. Please refer to \n  CC0\n  Public Domain Dedication for more information.\n\n\n    ","dates":{"last_modification":"2024-08-21","publication":"2024-09-02","submission":"2014-11-24"},"accession":"BIOMD0000000562","cross_references":{"pubmed":["24321545"],"biomodels__db":["MODEL1411240000","BIOMD0000000562"],"go":["GO:0007173","GO:0033209"],"taxonomy":["9606"]}}