{"id":"https://openalex.org/W2119375092","doi":"https://doi.org/10.1093/bioinformatics/btv013","title":"Cooperative development of logical modelling standards and tools with CoLoMoTo","display_name":"Cooperative development of logical modelling standards and tools with CoLoMoTo","publication_year":2015,"publication_date":"2015-01-25","ids":{"openalex":"https://openalex.org/W2119375092","doi":"https://doi.org/10.1093/bioinformatics/btv013","mag":"2119375092","pmid":"https://pubmed.ncbi.nlm.nih.gov/25619997"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv013","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv013","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/7/1154/438964/btv013.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"letter","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/7/1154/438964/btv013.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054156724","display_name":"Aur\u00e9lien Naldi","orcid":"https://orcid.org/0000-0002-6495-2655"},"institutions":[{"id":"https://openalex.org/I4210125590","display_name":"Institute for Systems Engineering and Computers","ror":"https://ror.org/033wn8m60","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"funder","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]},{"id":"https://openalex.org/I48057805","display_name":"Instituto Gulbenkian de Ci\u00eancia","ror":"https://ror.org/04b08hq31","country_code":"PT","type":"education","lineage":["https://openalex.org/I48057805"]}],"countries":["CH","DE","FR","GB","PT"],"is_corresponding":true,"raw_author_name":"Aur\u00e9lien Naldi","raw_affiliation_strings":["1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA"],"affiliations":[{"raw_affiliation_string":"1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA","institution_ids":["https://openalex.org/I4210125590","https://openalex.org/I97565354","https://openalex.org/I121345201","https://openalex.org/I76198965","https://openalex.org/I12708293","https://openalex.org/I48057805","https://openalex.org/I1303153112","https://openalex.org/I154526488","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025560387","display_name":"Pedro T. Monteiro","orcid":"https://orcid.org/0000-0002-7934-5495"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]},{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]},{"id":"https://openalex.org/I48057805","display_name":"Instituto Gulbenkian de Ci\u00eancia","ror":"https://ror.org/04b08hq31","country_code":"PT","type":"education","lineage":["https://openalex.org/I48057805"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"funder","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I4210125590","display_name":"Institute for Systems Engineering and Computers","ror":"https://ror.org/033wn8m60","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210125590"]}],"countries":["CH","DE","FR","GB","PT"],"is_corresponding":false,"raw_author_name":"Pedro T. Monteiro","raw_affiliation_strings":["1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA"],"affiliations":[{"raw_affiliation_string":"1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA","institution_ids":["https://openalex.org/I4210125590","https://openalex.org/I97565354","https://openalex.org/I121345201","https://openalex.org/I76198965","https://openalex.org/I12708293","https://openalex.org/I48057805","https://openalex.org/I1303153112","https://openalex.org/I154526488","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033625762","display_name":"Christoph M\u00fcssel","orcid":null},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I4210125590","display_name":"Institute for Systems Engineering and Computers","ror":"https://ror.org/033wn8m60","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]},{"id":"https://openalex.org/I48057805","display_name":"Instituto Gulbenkian de Ci\u00eancia","ror":"https://ror.org/04b08hq31","country_code":"PT","type":"education","lineage":["https://openalex.org/I48057805"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"funder","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["CH","DE","FR","GB","PT"],"is_corresponding":false,"raw_author_name":"Christoph M\u00fcssel","raw_affiliation_strings":["1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA"],"affiliations":[{"raw_affiliation_string":"1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA","institution_ids":["https://openalex.org/I4210125590","https://openalex.org/I97565354","https://openalex.org/I121345201","https://openalex.org/I76198965","https://openalex.org/I12708293","https://openalex.org/I48057805","https://openalex.org/I1303153112","https://openalex.org/I154526488","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023316486","display_name":"Hans A. Kestler","orcid":"https://orcid.org/0000-0002-4759-5254"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]},{"id":"https://openalex.org/I48057805","display_name":"Instituto Gulbenkian de Ci\u00eancia","ror":"https://ror.org/04b08hq31","country_code":"PT","type":"education","lineage":["https://openalex.org/I48057805"]},{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"funder","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I4210125590","display_name":"Institute for Systems Engineering and Computers","ror":"https://ror.org/033wn8m60","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["CH","DE","FR","GB","PT"],"is_corresponding":false,"raw_author_name":"Hans A. Kestler","raw_affiliation_strings":["1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA"],"affiliations":[{"raw_affiliation_string":"1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA","institution_ids":["https://openalex.org/I4210125590","https://openalex.org/I97565354","https://openalex.org/I121345201","https://openalex.org/I76198965","https://openalex.org/I12708293","https://openalex.org/I48057805","https://openalex.org/I1303153112","https://openalex.org/I154526488","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081933836","display_name":"Denis Thieffry","orcid":"https://orcid.org/0000-0003-0271-1757"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]},{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I48057805","display_name":"Instituto Gulbenkian de Ci\u00eancia","ror":"https://ror.org/04b08hq31","country_code":"PT","type":"education","lineage":["https://openalex.org/I48057805"]},{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"funder","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I4210125590","display_name":"Institute for Systems Engineering and Computers","ror":"https://ror.org/033wn8m60","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]}],"countries":["CH","DE","FR","GB","PT"],"is_corresponding":false,"raw_author_name":"Denis Thieffry","raw_affiliation_strings":["1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA","1Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland"],"affiliations":[{"raw_affiliation_string":"1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA","institution_ids":["https://openalex.org/I4210125590","https://openalex.org/I97565354","https://openalex.org/I121345201","https://openalex.org/I76198965","https://openalex.org/I12708293","https://openalex.org/I48057805","https://openalex.org/I1303153112","https://openalex.org/I154526488","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"1Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I97565354"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065825020","display_name":"Ioannis X\u00e9narios","orcid":"https://orcid.org/0000-0002-3413-6841"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"funder","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]},{"id":"https://openalex.org/I48057805","display_name":"Instituto Gulbenkian de Ci\u00eancia","ror":"https://ror.org/04b08hq31","country_code":"PT","type":"education","lineage":["https://openalex.org/I48057805"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]},{"id":"https://openalex.org/I4210125590","display_name":"Institute for Systems Engineering and Computers","ror":"https://ror.org/033wn8m60","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210125590"]}],"countries":["CH","DE","FR","GB","PT"],"is_corresponding":false,"raw_author_name":"Ioannis Xenarios","raw_affiliation_strings":["1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA"],"affiliations":[{"raw_affiliation_string":"1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA","institution_ids":["https://openalex.org/I4210125590","https://openalex.org/I97565354","https://openalex.org/I121345201","https://openalex.org/I76198965","https://openalex.org/I12708293","https://openalex.org/I48057805","https://openalex.org/I1303153112","https://openalex.org/I154526488","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005499510","display_name":"Julio S\u00e1ez-Rodr\u00edguez","orcid":"https://orcid.org/0000-0002-8552-8976"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]},{"id":"https://openalex.org/I4210125590","display_name":"Institute for Systems Engineering and Computers","ror":"https://ror.org/033wn8m60","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I48057805","display_name":"Instituto Gulbenkian de Ci\u00eancia","ror":"https://ror.org/04b08hq31","country_code":"PT","type":"education","lineage":["https://openalex.org/I48057805"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"funder","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]}],"countries":["CH","DE","FR","GB","PT"],"is_corresponding":false,"raw_author_name":"Julio Saez-Rodriguez","raw_affiliation_strings":["1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA"],"affiliations":[{"raw_affiliation_string":"1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA","institution_ids":["https://openalex.org/I4210125590","https://openalex.org/I97565354","https://openalex.org/I121345201","https://openalex.org/I76198965","https://openalex.org/I12708293","https://openalex.org/I48057805","https://openalex.org/I1303153112","https://openalex.org/I154526488","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073371703","display_name":"Tom\u00e1\u0161 Helikar","orcid":"https://orcid.org/0000-0003-3653-1906"},"institutions":[{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]},{"id":"https://openalex.org/I48057805","display_name":"Instituto Gulbenkian de Ci\u00eancia","ror":"https://ror.org/04b08hq31","country_code":"PT","type":"education","lineage":["https://openalex.org/I48057805"]},{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"funder","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]},{"id":"https://openalex.org/I4210125590","display_name":"Institute for Systems Engineering and Computers","ror":"https://ror.org/033wn8m60","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210125590"]}],"countries":["CH","DE","FR","GB","PT"],"is_corresponding":false,"raw_author_name":"Tomas Helikar","raw_affiliation_strings":["1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA"],"affiliations":[{"raw_affiliation_string":"1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA","institution_ids":["https://openalex.org/I4210125590","https://openalex.org/I97565354","https://openalex.org/I121345201","https://openalex.org/I76198965","https://openalex.org/I12708293","https://openalex.org/I48057805","https://openalex.org/I1303153112","https://openalex.org/I154526488","https://openalex.org/I1294671590"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038231285","display_name":"Claudine Chaouiya","orcid":"https://orcid.org/0000-0003-2350-0756"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"funder","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I48057805","display_name":"Instituto Gulbenkian de Ci\u00eancia","ror":"https://ror.org/04b08hq31","country_code":"PT","type":"education","lineage":["https://openalex.org/I48057805"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]},{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I4210125590","display_name":"Institute for Systems Engineering and Computers","ror":"https://ror.org/033wn8m60","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]}],"countries":["CH","DE","FR","GB","PT"],"is_corresponding":false,"raw_author_name":"Claudine Chaouiya","raw_affiliation_strings":["1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA"],"affiliations":[{"raw_affiliation_string":"1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA","institution_ids":["https://openalex.org/I4210125590","https://openalex.org/I97565354","https://openalex.org/I121345201","https://openalex.org/I76198965","https://openalex.org/I12708293","https://openalex.org/I48057805","https://openalex.org/I1303153112","https://openalex.org/I154526488","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":5,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5054156724"],"corresponding_institution_ids":["https://openalex.org/I121345201","https://openalex.org/I12708293","https://openalex.org/I1294671590","https://openalex.org/I1303153112","https://openalex.org/I154526488","https://openalex.org/I4210125590","https://openalex.org/I48057805","https://openalex.org/I76198965","https://openalex.org/I97565354"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":5.8854,"has_fulltext":true,"cited_by_count":103,"citation_normalized_percentile":{"value":0.96917042,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":100},"biblio":{"volume":"31","issue":"7","first_page":"1154","last_page":"1159"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9847999811172485,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7225273847579956},{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.7098738551139832},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6308590173721313},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.563986599445343},{"id":"https://openalex.org/keywords/reusability","display_name":"Reusability","score":0.5582658648490906},{"id":"https://openalex.org/keywords/logical-data-model","display_name":"Logical data model","score":0.4907172918319702},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.48800864815711975},{"id":"https://openalex.org/keywords/management-science","display_name":"Management science","score":0.4579024314880371},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.45126110315322876},{"id":"https://openalex.org/keywords/logical-conjunction","display_name":"Logical conjunction","score":0.435702919960022},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4213058054447174},{"id":"https://openalex.org/keywords/data-modeling","display_name":"Data modeling","score":0.19074228405952454},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.142225980758667},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.12343376874923706},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11591887474060059}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7225273847579956},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.7098738551139832},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6308590173721313},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.563986599445343},{"id":"https://openalex.org/C137981799","wikidata":"https://www.wikidata.org/wiki/Q1369184","display_name":"Reusability","level":3,"score":0.5582658648490906},{"id":"https://openalex.org/C203702819","wikidata":"https://www.wikidata.org/wiki/Q17146953","display_name":"Logical data model","level":3,"score":0.4907172918319702},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.48800864815711975},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.4579024314880371},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.45126110315322876},{"id":"https://openalex.org/C21847791","wikidata":"https://www.wikidata.org/wiki/Q191081","display_name":"Logical conjunction","level":2,"score":0.435702919960022},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4213058054447174},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.19074228405952454},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.142225980758667},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.12343376874923706},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11591887474060059},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002477","descriptor_name":"Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002477","descriptor_name":"Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002477","descriptor_name":"Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012958","descriptor_name":"Societies, Scientific","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012958","descriptor_name":"Societies, Scientific","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012958","descriptor_name":"Societies, Scientific","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1093/bioinformatics/btv013","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv013","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/7/1154/438964/btv013.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25619997","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25619997","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:serval.unil.ch:BIB_918E26626992","is_oa":true,"landing_page_url":"https://serval.unil.ch/notice/serval:BIB_918E26626992","pdf_url":null,"source":{"id":"https://openalex.org/S4306401797","display_name":"SERVAL (Universit\u00e9 de Lausanne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210093590","host_organization_name":"Swiss School of Archaeology in Greece","host_organization_lineage":["https://openalex.org/I4210093590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics, vol. 31, no. 7, pp. 1154-1159","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:iris.unil.ch:iris/215293","is_oa":true,"landing_page_url":"https://iris.unil.ch/handle/iris/215293","pdf_url":"https://iris.unil.ch/bitstreams/9c0dc54d-252a-4dae-ab2c-963951cfb5c7/download","source":{"id":"https://openalex.org/S7407055444","display_name":"IRIS","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"review article"},{"id":"pmh:oai:dare.uva.nl:openaire_cris_publications/43d151e0-a1fd-409f-ac3c-d1129d2263fd","is_oa":false,"landing_page_url":"https://hdl.handle.net/11245.1/43d151e0-a1fd-409f-ac3c-d1129d2263fd","pdf_url":null,"source":{"id":"https://openalex.org/S4306400088","display_name":"UvA-DARE (University of Amsterdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I887064364","host_organization_name":"University of Amsterdam","host_organization_lineage":["https://openalex.org/I887064364"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Naldi, A, Monteiro, P T, M\u00fcssel, C, Kestler, H A, Thieffry, D, Xenarios, I, Saez-Rodriguez, J, Helikar, T, Chaouiya, C, Albert, R, Barberis, M, Calzone, L, Chasapi, A, Cokelaer, T, Crespo, I, Dorier, J, Dr\u00e4ger, A, Hernandez, C, Hucka, M, de Jong, H, Keating, S M, Klamt, S, Klarner, H, Laubenbacher, R, Le Nov\u00e8re, N, Niknejad, A, Rodriguez, N, Siebert, H & Stoll, G & Za\u00f1udo, J G T 2015, 'Cooperative development of logical modelling standards and tools with CoLoMoTo', Bioinformatics, vol. 31, no. 7, pp. 1154-1159. https://doi.org/10.1093/bioinformatics/btv013","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doc.rero.ch:304576","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400148","display_name":"reroDoc Digital Library","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:epubs.surrey.ac.uk:851012","is_oa":false,"landing_page_url":"http://epubs.surrey.ac.uk/851012/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400680","display_name":"Surrey Research Insight Open Access (The University of Surrey)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28290843","host_organization_name":"University of Surrey","host_organization_lineage":["https://openalex.org/I28290843"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:uvapub:oai:dare.uva.nl:publications/43d151e0-a1fd-409f-ac3c-d1129d2263fd","is_oa":false,"landing_page_url":"https://dare.uva.nl/personal/pure/en/publications/cooperative-development-of-logical-modelling-standards-and-tools-with-colomoto(43d151e0-a1fd-409f-ac3c-d1129d2263fd).html","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 31(7), 1154 - 1159. Oxford University Press","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv013","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv013","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/7/1154/438964/btv013.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.4099999964237213,"display_name":"Industry, innovation and infrastructure"},{"id":"https://metadata.un.org/sdg/17","score":0.4000000059604645,"display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G2240538154","display_name":null,"funder_award_id":"LSHG-CT-2005-518254","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G2277000059","display_name":null,"funder_award_id":"305299","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G3157282430","display_name":null,"funder_award_id":"FP7-KBBE-2011-5","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G3394992377","display_name":null,"funder_award_id":"KBBE-2011-5","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5326042306","display_name":null,"funder_award_id":"SystemsX","funder_id":"https://openalex.org/F4320327577","funder_display_name":"SystemsX.ch"},{"id":"https://openalex.org/G7216406532","display_name":"From Data to Models: New Bioinformatics Methods and Tools for Data-Driven Predictive Dynamic Modelling in Biotechnological Applications","funder_award_id":"289434","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7582053920","display_name":null,"funder_award_id":"FP7-KBBE","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320313288","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320327577","display_name":"SystemsX.ch","ror":"https://ror.org/02s09gf16"},{"id":"https://openalex.org/F4320338366","display_name":"FP7 Food, Agriculture and Fisheries, Biotechnology","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2119375092.pdf","grobid_xml":"https://content.openalex.org/works/W2119375092.grobid-xml"},"referenced_works_count":85,"referenced_works":["https://openalex.org/W72928827","https://openalex.org/W100617303","https://openalex.org/W174102300","https://openalex.org/W177374653","https://openalex.org/W344332445","https://openalex.org/W649201746","https://openalex.org/W1493523706","https://openalex.org/W1508878545","https://openalex.org/W1556027180","https://openalex.org/W1677575702","https://openalex.org/W1968519358","https://openalex.org/W1971144865","https://openalex.org/W1971224531","https://openalex.org/W1975054980","https://openalex.org/W1989284002","https://openalex.org/W1998356614","https://openalex.org/W2000982470","https://openalex.org/W2004073264","https://openalex.org/W2009437679","https://openalex.org/W2011220908","https://openalex.org/W2018519939","https://openalex.org/W2031000707","https://openalex.org/W2031369606","https://openalex.org/W2035036685","https://openalex.org/W2041289840","https://openalex.org/W2046538693","https://openalex.org/W2048013262","https://openalex.org/W2049047355","https://openalex.org/W2053961182","https://openalex.org/W2058221907","https://openalex.org/W2059110753","https://openalex.org/W2061391666","https://openalex.org/W2062029454","https://openalex.org/W2067088953","https://openalex.org/W2069233518","https://openalex.org/W2069947940","https://openalex.org/W2073903631","https://openalex.org/W2076935369","https://openalex.org/W2078734575","https://openalex.org/W2080721009","https://openalex.org/W2084251771","https://openalex.org/W2085885352","https://openalex.org/W2090020814","https://openalex.org/W2092755129","https://openalex.org/W2095433609","https://openalex.org/W2098739408","https://openalex.org/W2102141778","https://openalex.org/W2103454055","https://openalex.org/W2104130992","https://openalex.org/W2105841205","https://openalex.org/W2108020239","https://openalex.org/W2111123076","https://openalex.org/W2114518254","https://openalex.org/W2115782725","https://openalex.org/W2121149194","https://openalex.org/W2122792487","https://openalex.org/W2122902176","https://openalex.org/W2123125245","https://openalex.org/W2123783513","https://openalex.org/W2124419982","https://openalex.org/W2125886217","https://openalex.org/W2127020923","https://openalex.org/W2129325583","https://openalex.org/W2129388048","https://openalex.org/W2131463591","https://openalex.org/W2132935366","https://openalex.org/W2134221731","https://openalex.org/W2134978629","https://openalex.org/W2136559804","https://openalex.org/W2142400903","https://openalex.org/W2145435867","https://openalex.org/W2147450898","https://openalex.org/W2150908245","https://openalex.org/W2151852639","https://openalex.org/W2157947216","https://openalex.org/W2158973107","https://openalex.org/W2160533336","https://openalex.org/W2161636210","https://openalex.org/W2162144833","https://openalex.org/W2166214692","https://openalex.org/W2340735175","https://openalex.org/W2913459036","https://openalex.org/W3099614534","https://openalex.org/W4251606455","https://openalex.org/W4388252848"],"related_works":["https://openalex.org/W2129965124","https://openalex.org/W2076363549","https://openalex.org/W1711240648","https://openalex.org/W245582143","https://openalex.org/W4253240495","https://openalex.org/W2030738422","https://openalex.org/W2359308925","https://openalex.org/W2387527048","https://openalex.org/W2373769979","https://openalex.org/W2500395615"],"abstract_inverted_index":{"The":[0],"identification":[1],"of":[2,12,27,59,88,99],"large":[3],"regulatory":[4],"and":[5,33,66,81,105,133],"signalling":[6],"networks":[7],"involved":[8],"in":[9,39,126,130],"the":[10,89,95,100],"control":[11],"crucial":[13],"cellular":[14],"processes":[15],"calls":[16],"for":[17,102],"proper":[18],"modelling":[19,91,128],"approaches.":[20],"Indeed,":[21],"models":[22],"can":[23],"help":[24],"elucidate":[25],"properties":[26],"these":[28],"networks,":[29],"understand":[30],"their":[31],"behaviour":[32],"provide":[34],"(testable)":[35],"predictions":[36],"by":[37,55],"performing":[38],"silico":[40],"experiments.":[41],"In":[42],"this":[43,116],"context,":[44],"qualitative,":[45],"logical":[46,90,127],"frameworks":[47],"have":[48],"emerged":[49],"as":[50,53],"relevant":[51],"approaches,":[52],"demonstrated":[54],"a":[56,74],"growing":[57],"number":[58],"published":[60],"models,":[61],"along":[62,107],"with":[63,108],"new":[64],"methodologies":[65],"software":[67],"tools.":[68,84],"This":[69],"productive":[70],"activity":[71],"now":[72],"requires":[73],"concerted":[75],"effort":[76],"to":[77,114],"ensure":[78],"model":[79],"reusability":[80],"interoperability":[82],"between":[83],"Following":[85],"an":[86],"outline":[87],"framework,":[92],"we":[93],"present":[94],"most":[96],"important":[97],"achievements":[98],"Consortium":[101],"Logical":[103],"Models":[104],"Tools,":[106],"future":[109],"objectives.":[110],"Our":[111],"aim":[112],"is":[113],"advertise":[115],"open":[117],"community,":[118],"which":[119],"welcomes":[120],"contributions":[121],"from":[122],"all":[123],"researchers":[124],"interested":[125],"or":[129],"related":[131],"mathematical":[132],"computational":[134],"developments.":[135]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":15},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":12},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":18},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":6}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}