{"id":"https://openalex.org/W4281655261","doi":"https://doi.org/10.1093/bib/bbac212","title":"Addressing <i>barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology</i>","display_name":"Addressing <i>barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology</i>","publication_year":2022,"publication_date":"2022-06-07","ids":{"openalex":"https://openalex.org/W4281655261","doi":"https://doi.org/10.1093/bib/bbac212"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac212","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac212","pdf_url":"https://academic.oup.com/bib/article-pdf/23/4/bbac212/45016803/bbac212.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/23/4/bbac212/45016803/bbac212.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050740875","display_name":"Anna Niarakis","orcid":"https://orcid.org/0000-0002-9687-7426"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210126360","display_name":"Centre Inria de Saclay","ror":"https://ror.org/0315e5x55","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210126360"]},{"id":"https://openalex.org/I88467170","display_name":"Universit\u00e9 d'\u00c9vry Val-d'Essonne","ror":"https://ror.org/00e96v939","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954","https://openalex.org/I88467170"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Anna Niarakis","raw_affiliation_strings":["Lifeware Group, Inria, Saclay-\u00eele de France , 91120 Palaiseau, France","Universit\u00e9 Paris-Saclay, Laboratoire Europ\u00e9en de Recherche pour la Polyarthrite rhumato\u00efde - Genhotel , Univ Evry, Evry, France"],"affiliations":[{"raw_affiliation_string":"Lifeware Group, Inria, Saclay-\u00eele de France , 91120 Palaiseau, France","institution_ids":["https://openalex.org/I4210126360"]},{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, Laboratoire Europ\u00e9en de Recherche pour la Polyarthrite rhumato\u00efde - Genhotel , Univ Evry, Evry, France","institution_ids":["https://openalex.org/I88467170","https://openalex.org/I277688954"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103188993","display_name":"Dagmar Waltemath","orcid":"https://orcid.org/0000-0002-5886-5563"},"institutions":[{"id":"https://openalex.org/I2799318839","display_name":"Universit\u00e4tsmedizin Greifswald","ror":"https://ror.org/025vngs54","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2799318839"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Dagmar Waltemath","raw_affiliation_strings":["Department of Medical Informatics, University Medicine Greifswald , Greifswald, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Medical Informatics, University Medicine Greifswald , Greifswald, Germany","institution_ids":["https://openalex.org/I2799318839"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032161283","display_name":"James A. Glazier","orcid":"https://orcid.org/0000-0003-3634-190X"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]},{"id":"https://openalex.org/I4210151352","display_name":"Biocom","ror":"https://ror.org/03ymdxs56","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210151352"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Glazier","raw_affiliation_strings":["Biocomplexity Institute and Department of Intelligent Systems Engineering, Indiana University , Bloomington, IN, USA"],"affiliations":[{"raw_affiliation_string":"Biocomplexity Institute and Department of Intelligent Systems Engineering, Indiana University , Bloomington, IN, USA","institution_ids":["https://openalex.org/I4210119109","https://openalex.org/I4210151352"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003441276","display_name":"Falk Schreiber","orcid":"https://orcid.org/0000-0002-9307-3254"},"institutions":[{"id":"https://openalex.org/I189712700","display_name":"University of Konstanz","ror":"https://ror.org/0546hnb39","country_code":"DE","type":"education","lineage":["https://openalex.org/I189712700"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU","DE"],"is_corresponding":false,"raw_author_name":"Falk Schreiber","raw_affiliation_strings":["Department of Computer and Information Science, University of Konstanz , Konstanz, Germany","Faculty of Information Technology, Monash University , Clayton, Australia"],"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science, University of Konstanz , Konstanz, Germany","institution_ids":["https://openalex.org/I189712700"]},{"raw_affiliation_string":"Faculty of Information Technology, Monash University , Clayton, Australia","institution_ids":["https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049649026","display_name":"Sarah Keating","orcid":"https://orcid.org/0000-0002-3356-3542"},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sarah M Keating","raw_affiliation_strings":["University College London , London, United Kingdom"],"affiliations":[{"raw_affiliation_string":"University College London , London, United Kingdom","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086460310","display_name":"David Nickerson","orcid":"https://orcid.org/0000-0003-4667-9779"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"David Nickerson","raw_affiliation_strings":["Auckland Bioengineering Institute, University of Auckland , Auckland, New Zealand"],"affiliations":[{"raw_affiliation_string":"Auckland Bioengineering Institute, University of Auckland , Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038231285","display_name":"Claudine Chaouiya","orcid":"https://orcid.org/0000-0003-2350-0756"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I21491767","display_name":"Aix-Marseille Universit\u00e9","ror":"https://ror.org/035xkbk20","country_code":"FR","type":"education","lineage":["https://openalex.org/I21491767"]},{"id":"https://openalex.org/I4210160189","display_name":"Institut Polytechnique de Bordeaux","ror":"https://ror.org/054qv7y42","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210160189"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Claudine Chaouiya","raw_affiliation_strings":["Aix Marseille Univ, CNRS , I2M, Marseille, France"],"affiliations":[{"raw_affiliation_string":"Aix Marseille Univ, CNRS , I2M, Marseille, France","institution_ids":["https://openalex.org/I4210160189","https://openalex.org/I1294671590","https://openalex.org/I21491767"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063755415","display_name":"Anne Siegel","orcid":"https://orcid.org/0000-0001-6542-1568"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I2802519937","display_name":"Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires","ror":"https://ror.org/00myn0z94","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210159245","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I56067802","display_name":"Universit\u00e9 de Rennes","ror":"https://ror.org/015m7wh34","country_code":"FR","type":"education","lineage":["https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Anne Siegel","raw_affiliation_strings":["Univ Rennes, CNRS, Inria - IRISA lab. Rennes"],"affiliations":[{"raw_affiliation_string":"Univ Rennes, CNRS, Inria - IRISA lab. Rennes","institution_ids":["https://openalex.org/I2802519937","https://openalex.org/I56067802","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085105326","display_name":"Vincent No\u00ebl","orcid":"https://orcid.org/0000-0003-3448-291X"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I190752583","display_name":"ParisTech","ror":"https://ror.org/05c2qg481","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Vincent No\u00ebl","raw_affiliation_strings":["INSERM , U900, Paris, France","Institut Curie, PSL Research University , Paris, France","MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology , Paris, France"],"affiliations":[{"raw_affiliation_string":"INSERM , U900, Paris, France","institution_ids":["https://openalex.org/I154526488"]},{"raw_affiliation_string":"Institut Curie, PSL Research University , Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I80043"]},{"raw_affiliation_string":"MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology , Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I190752583"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066783652","display_name":"Henning Hermjakob","orcid":"https://orcid.org/0000-0001-8479-0262"},"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"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Henning Hermjakob","raw_affiliation_strings":["EMBL-European Bioinformatics Institute, Wellcome Genome Campus , Cambridge, UK"],"affiliations":[{"raw_affiliation_string":"EMBL-European Bioinformatics Institute, Wellcome Genome Campus , Cambridge, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"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/I114395901","display_name":"University of Nebraska\u2013Lincoln","ror":"https://ror.org/043mer456","country_code":"US","type":"education","lineage":["https://openalex.org/I114395901"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tom\u00e1\u0161 Helikar","raw_affiliation_strings":["Department of Biochemistry, University of Nebraska-Lincoln , Lincoln, NE, 68588, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Nebraska-Lincoln , Lincoln, NE, 68588, USA","institution_ids":["https://openalex.org/I114395901"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003525513","display_name":"Sylvain Soliman","orcid":"https://orcid.org/0000-0001-5525-7418"},"institutions":[{"id":"https://openalex.org/I4210126360","display_name":"Centre Inria de Saclay","ror":"https://ror.org/0315e5x55","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210126360"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Sylvain Soliman","raw_affiliation_strings":["Lifeware Group, Inria, Saclay-\u00eele de France , 91120 Palaiseau, France"],"affiliations":[{"raw_affiliation_string":"Lifeware Group, Inria, Saclay-\u00eele de France , 91120 Palaiseau, France","institution_ids":["https://openalex.org/I4210126360"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061154457","display_name":"Laurence Calzone","orcid":"https://orcid.org/0000-0002-7835-1148"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I190752583","display_name":"ParisTech","ror":"https://ror.org/05c2qg481","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Laurence Calzone","raw_affiliation_strings":["INSERM , U900, Paris, France","Institut Curie, PSL Research University , Paris, France","MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology , Paris, France"],"affiliations":[{"raw_affiliation_string":"INSERM , U900, Paris, France","institution_ids":["https://openalex.org/I154526488"]},{"raw_affiliation_string":"Institut Curie, PSL Research University , Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I80043"]},{"raw_affiliation_string":"MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology , Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I190752583"]}]}],"institutions":[],"countries_distinct_count":6,"institutions_distinct_count":13,"corresponding_author_ids":["https://openalex.org/A5050740875"],"corresponding_institution_ids":["https://openalex.org/I277688954","https://openalex.org/I4210126360","https://openalex.org/I88467170"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":11.5643,"has_fulltext":true,"cited_by_count":29,"citation_normalized_percentile":{"value":0.97829785,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"23","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9979000091552734,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9979000091552734,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9922999739646912,"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":0.9908999800682068,"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/interoperability","display_name":"Interoperability","score":0.9104505777359009},{"id":"https://openalex.org/keywords/reusability","display_name":"Reusability","score":0.8942147493362427},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6281535029411316},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.41405177116394043},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.35195618867874146},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.328860878944397},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22877293825149536},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.22495469450950623},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13235226273536682},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.05967402458190918}],"concepts":[{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.9104505777359009},{"id":"https://openalex.org/C137981799","wikidata":"https://www.wikidata.org/wiki/Q1369184","display_name":"Reusability","level":3,"score":0.8942147493362427},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6281535029411316},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.41405177116394043},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.35195618867874146},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.328860878944397},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22877293825149536},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.22495469450950623},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13235226273536682},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.05967402458190918}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1093/bib/bbac212","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac212","pdf_url":"https://academic.oup.com/bib/article-pdf/23/4/bbac212/45016803/bbac212.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:digitalcommons.unl.edu:biochemfacpub-1550","is_oa":true,"landing_page_url":"https://digitalcommons.unl.edu/biochemfacpub/549","pdf_url":null,"source":{"id":"https://openalex.org/S4306513441","display_name":"Insecta mundi","issn_l":"0749-6737","issn":["0749-6737","1942-1354","1942-1362"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310316217","host_organization_name":"Center for Systematic Entomology","host_organization_lineage":["https://openalex.org/P4310316217"],"host_organization_lineage_names":["Center for Systematic Entomology"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Department of Biochemistry: Faculty Publications","raw_type":"text"},{"id":"pmh:oai:HAL:hal-03690604v1","is_oa":true,"landing_page_url":"https://inria.hal.science/hal-03690604","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Briefings in Bioinformatics, 2022, 23 (4), pp.1-11. &#x27E8;10.1093/bib/bbac212&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:10158980","is_oa":false,"landing_page_url":"https://discovery.ucl.ac.uk/id/eprint/10158980/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"   Briefings in Bioinformatics , 23  (4)    , Article bbac212. (2022)      ","raw_type":"Article"},{"id":"pmh:oai:kops.uni-konstanz.de:123456789/57769","is_oa":true,"landing_page_url":"http://nbn-resolving.de/urn:nbn:de:bsz:352-2-glgemut7d62v3","pdf_url":null,"source":{"id":"https://openalex.org/S4306401487","display_name":"KOPS (University of Konstanz)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I189712700","host_organization_name":"University of Konstanz","host_organization_lineage":["https://openalex.org/I189712700"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9294410","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9294410","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbac212","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac212","pdf_url":"https://academic.oup.com/bib/article-pdf/23/4/bbac212/45016803/bbac212.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G114059409","display_name":null,"funder_award_id":"P41EB023912","funder_id":"https://openalex.org/F4320337363","funder_display_name":"National Institute of Biomedical Imaging and Bioengineering"},{"id":"https://openalex.org/G14263084","display_name":null,"funder_award_id":"NSF1720625","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1539972074","display_name":null,"funder_award_id":"BB/N019482/1","funder_id":"https://openalex.org/F4320326631","funder_display_name":"Innovative Medicines Initiative"},{"id":"https://openalex.org/G2295339731","display_name":null,"funder_award_id":"2020/0766","funder_id":"https://openalex.org/F4320307781","funder_display_name":"Sanofi"},{"id":"https://openalex.org/G2649193276","display_name":null,"funder_award_id":"2117-422037984","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G442535691","display_name":null,"funder_award_id":"DFG-391322026","funder_id":"https://openalex.org/F4320307781","funder_display_name":"Sanofi"},{"id":"https://openalex.org/G4563450687","display_name":null,"funder_award_id":"BB/N019474/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G5171689093","display_name":null,"funder_award_id":"U24 EB028887","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5278229474","display_name":null,"funder_award_id":"116030","funder_id":"https://openalex.org/F4320326631","funder_display_name":"Innovative Medicines Initiative"},{"id":"https://openalex.org/G6401459825","display_name":null,"funder_award_id":"251654672","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G678639578","display_name":null,"funder_award_id":"NSF188553","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6926376750","display_name":null,"funder_award_id":"R01 GM122424","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7731648302","display_name":null,"funder_award_id":"R35GM119770","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7837880268","display_name":null,"funder_award_id":"ANR-17-CE40-0036","funder_id":"https://openalex.org/F4320307781","funder_display_name":"Sanofi"},{"id":"https://openalex.org/G8774603174","display_name":null,"funder_award_id":"BB/N019482/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G970836562","display_name":null,"funder_award_id":"BB/N019474/1","funder_id":"https://openalex.org/F4320326631","funder_display_name":"Innovative Medicines Initiative"}],"funders":[{"id":"https://openalex.org/F4320307781","display_name":"Sanofi","ror":"https://ror.org/027vj4x92"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320326631","display_name":"Innovative Medicines Initiative","ror":"https://ror.org/019af4n30"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"},{"id":"https://openalex.org/F4320337363","display_name":"National Institute of Biomedical Imaging and Bioengineering","ror":"https://ror.org/00372qc85"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4281655261.pdf","grobid_xml":"https://content.openalex.org/works/W4281655261.grobid-xml"},"referenced_works_count":82,"referenced_works":["https://openalex.org/W58125149","https://openalex.org/W60164658","https://openalex.org/W96334552","https://openalex.org/W115452890","https://openalex.org/W1514256992","https://openalex.org/W1977643020","https://openalex.org/W1992154841","https://openalex.org/W2000982470","https://openalex.org/W2035438595","https://openalex.org/W2036493602","https://openalex.org/W2068109876","https://openalex.org/W2069157810","https://openalex.org/W2096328440","https://openalex.org/W2096951208","https://openalex.org/W2100058250","https://openalex.org/W2100108891","https://openalex.org/W2103454055","https://openalex.org/W2119375092","https://openalex.org/W2122902176","https://openalex.org/W2123125245","https://openalex.org/W2123783513","https://openalex.org/W2129325583","https://openalex.org/W2137700068","https://openalex.org/W2138793275","https://openalex.org/W2146055051","https://openalex.org/W2146958900","https://openalex.org/W2153947402","https://openalex.org/W2154268795","https://openalex.org/W2154601808","https://openalex.org/W2161749893","https://openalex.org/W2163415630","https://openalex.org/W2163993275","https://openalex.org/W2188979829","https://openalex.org/W2272546316","https://openalex.org/W2302501749","https://openalex.org/W2345275877","https://openalex.org/W2404737222","https://openalex.org/W2416349955","https://openalex.org/W2558342853","https://openalex.org/W2593809500","https://openalex.org/W2788254992","https://openalex.org/W2790950219","https://openalex.org/W2792322849","https://openalex.org/W2796191283","https://openalex.org/W2804977648","https://openalex.org/W2892906004","https://openalex.org/W2926692152","https://openalex.org/W2949797623","https://openalex.org/W2950329335","https://openalex.org/W2972248834","https://openalex.org/W2988361147","https://openalex.org/W3013993136","https://openalex.org/W3016336210","https://openalex.org/W3021219695","https://openalex.org/W3025361835","https://openalex.org/W3040579653","https://openalex.org/W3048575781","https://openalex.org/W3080133182","https://openalex.org/W3091749330","https://openalex.org/W3092520281","https://openalex.org/W3110795479","https://openalex.org/W3117326807","https://openalex.org/W3117470460","https://openalex.org/W3132502413","https://openalex.org/W3135261648","https://openalex.org/W3164409030","https://openalex.org/W3169349611","https://openalex.org/W3174278278","https://openalex.org/W3201211850","https://openalex.org/W3205620409","https://openalex.org/W3211402536","https://openalex.org/W3214094975","https://openalex.org/W4226475868","https://openalex.org/W4242902282","https://openalex.org/W4254464710","https://openalex.org/W6602409066","https://openalex.org/W6659946796","https://openalex.org/W6682879297","https://openalex.org/W6683800640","https://openalex.org/W6694229850","https://openalex.org/W6770460946","https://openalex.org/W6796124448"],"related_works":["https://openalex.org/W4282938614","https://openalex.org/W2906929912","https://openalex.org/W2350686889","https://openalex.org/W1965839502","https://openalex.org/W2099755394","https://openalex.org/W2129965124","https://openalex.org/W2155486208","https://openalex.org/W2111589395","https://openalex.org/W2753086708","https://openalex.org/W2157191986"],"abstract_inverted_index":{"Abstract":[0],"Computational":[1],"models":[2,34,75],"are":[3],"often":[4],"employed":[5],"in":[6,20,49,76],"systems":[7],"biology":[8],"to":[9,28,38],"study":[10],"the":[11,18,21,30,83],"dynamic":[12],"behaviours":[13],"of":[14,23,32,82],"complex":[15],"systems.":[16],"With":[17],"rise":[19],"number":[22],"computational":[24,74],"models,":[25],"finding":[26],"ways":[27],"improve":[29],"reusability":[31],"these":[33],"and":[35,45,51,72,78],"their":[36],"ability":[37],"reproduce":[39],"virtual":[40],"experiments":[41],"becomes":[42],"critical.":[43],"Correct":[44],"effective":[46],"model":[47],"annotation":[48],"community-supported":[50],"standardised":[52],"formats":[53],"is":[54],"necessary":[55],"for":[56,68],"this":[57],"improvement.":[58],"Here,":[59],"we":[60],"present":[61],"recent":[62],"efforts":[63],"toward":[64],"a":[65],"common":[66],"framework":[67],"annotated,":[69],"accessible,":[70],"reproducible":[71],"interoperable":[73],"biology,":[77],"discuss":[79],"key":[80],"challenges":[81],"field.":[84]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":1}],"updated_date":"2026-03-28T08:17:26.163206","created_date":"2022-06-13T00:00:00"}
