{"id":"https://openalex.org/W4417004131","doi":"https://doi.org/10.1371/journal.pcbi.1013239","title":"Verification and reproducible curation of the BioModels repository","display_name":"Verification and reproducible curation of the BioModels repository","publication_year":2025,"publication_date":"2025-12-04","ids":{"openalex":"https://openalex.org/W4417004131","doi":"https://doi.org/10.1371/journal.pcbi.1013239","pmid":"https://pubmed.ncbi.nlm.nih.gov/41343683"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1013239","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013239","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1013239","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067339679","display_name":"Lucian P. Smith","orcid":"https://orcid.org/0000-0001-7002-6386"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lucian P. Smith","raw_affiliation_strings":["Department of Bioengineering, University of Washington, Seattle, Washington, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-7002-6386","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024795670","display_name":"Rahuman S. Malik\u2010Sheriff","orcid":"https://orcid.org/0000-0003-0705-9809"},"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":true,"raw_author_name":"Rahuman S. Malik-Sheriff","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028787682","display_name":"Tung V. N. Nguyen","orcid":"https://orcid.org/0000-0002-2876-6046"},"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":true,"raw_author_name":"Tung V. N. Nguyen","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom","institution_ids":["https://openalex.org/I1303153112"]}]},{"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":true,"raw_author_name":"Henning Hermjakob","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0001-8479-0262","affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016750554","display_name":"Jonathan R. Karr","orcid":"https://orcid.org/0000-0002-2605-5080"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jonathan Karr","raw_affiliation_strings":["Icahn School of Medicine at Mount Sinai, New York, New York, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-2605-5080","affiliations":[{"raw_affiliation_string":"Icahn School of Medicine at Mount Sinai, New York, New York, United States of America","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062432564","display_name":"Bilal Shaikh","orcid":"https://orcid.org/0000-0001-5801-5510"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bilal Shaikh","raw_affiliation_strings":["Icahn School of Medicine at Mount Sinai, New York, New York, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-5801-5510","affiliations":[{"raw_affiliation_string":"Icahn School of Medicine at Mount Sinai, New York, New York, United States of America","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115946809","display_name":"Logan Drescher","orcid":null},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Logan Drescher","raw_affiliation_strings":["University of Connecticut School of Medicine, Farmington, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Connecticut School of Medicine, Farmington, Connecticut, United States of America","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066544731","display_name":"Ion I. Moraru","orcid":"https://orcid.org/0000-0002-3746-9676"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ion I. Moraru","raw_affiliation_strings":["University of Connecticut School of Medicine, Farmington, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Connecticut School of Medicine, Farmington, Connecticut, United States of America","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027644564","display_name":"James C. Schaff","orcid":"https://orcid.org/0000-0003-3286-7736"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"James C. Schaff","raw_affiliation_strings":["University of Connecticut School of Medicine, Farmington, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Connecticut School of Medicine, Farmington, Connecticut, United States of America","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036760070","display_name":"Eran Agmon","orcid":"https://orcid.org/0000-0003-1279-2474"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Eran Agmon","raw_affiliation_strings":["University of Connecticut School of Medicine, Farmington, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Connecticut School of Medicine, Farmington, Connecticut, United States of America","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115946806","display_name":"Alexander A. Patrie","orcid":null},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Alexander A. Patrie","raw_affiliation_strings":["University of Connecticut School of Medicine, Farmington, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Connecticut School of Medicine, Farmington, Connecticut, United States of America","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107139754","display_name":"Michael L. Blinov","orcid":"https://orcid.org/0000-0002-9363-9705"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michael L. Blinov","raw_affiliation_strings":["University of Connecticut School of Medicine, Farmington, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Connecticut School of Medicine, Farmington, Connecticut, United States of America","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038863305","display_name":"Joseph L. Hellerstein","orcid":"https://orcid.org/0000-0003-0802-4069"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Joseph L. Hellerstein","raw_affiliation_strings":["eScience Institute, University of Washington, Seattle, Washington, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"eScience Institute, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112306313","display_name":"Elebeoba E. May","orcid":null},"institutions":[{"id":"https://openalex.org/I2802999273","display_name":"Wisconsin Institutes for Discovery","ror":"https://ror.org/05gbven85","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802999273"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Elebeoba E. May","raw_affiliation_strings":["Department of Medical Microbiology and Wisconsin Institute of Discovery, University of Wisconsin-Madison, Madison, Wisconsin, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Microbiology and Wisconsin Institute of Discovery, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I2802999273"]}]},{"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":true,"raw_author_name":"David P. Nickerson","raw_affiliation_strings":["Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand"],"raw_orcid":"https://orcid.org/0000-0003-4667-9779","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/A5010618664","display_name":"John H. Gennari","orcid":"https://orcid.org/0000-0001-8254-4957"},"institutions":[{"id":"https://openalex.org/I2801852214","display_name":"University of Washington Medical Center","ror":"https://ror.org/00wbzw723","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2801852214"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"John H. Gennari","raw_affiliation_strings":["Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I2801852214"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044484291","display_name":"Herbert M. Sauro","orcid":"https://orcid.org/0000-0002-3659-6817"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Herbert M. Sauro","raw_affiliation_strings":["Department of Bioengineering, University of Washington, Seattle, Washington, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-3659-6817","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5010618664","https://openalex.org/A5016750554","https://openalex.org/A5024795670","https://openalex.org/A5027644564","https://openalex.org/A5028787682","https://openalex.org/A5036760070","https://openalex.org/A5038863305","https://openalex.org/A5044484291","https://openalex.org/A5062432564","https://openalex.org/A5066544731","https://openalex.org/A5066783652","https://openalex.org/A5067339679","https://openalex.org/A5086460310","https://openalex.org/A5107139754","https://openalex.org/A5112306313","https://openalex.org/A5115946806","https://openalex.org/A5115946809"],"corresponding_institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I140172145","https://openalex.org/I154130895","https://openalex.org/I201448701","https://openalex.org/I2801852214","https://openalex.org/I2802999273","https://openalex.org/I98704320"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.3339702,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"21","issue":"12","first_page":"e1013239","last_page":"e1013239"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.5623000264167786,"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":0.5623000264167786,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.15320000052452087,"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/T13286","display_name":"Modeling and Simulation Systems","score":0.03970000147819519,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.9180999994277954},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.8371999859809875},{"id":"https://openalex.org/keywords/mistake","display_name":"Mistake","score":0.5879999995231628},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.4156000018119812},{"id":"https://openalex.org/keywords/exception-handling","display_name":"Exception handling","score":0.29179999232292175}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9180999994277954},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.8371999859809875},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.798799991607666},{"id":"https://openalex.org/C2777179996","wikidata":"https://www.wikidata.org/wiki/Q911222","display_name":"Mistake","level":2,"score":0.5879999995231628},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5376999974250793},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.43230000138282776},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.4156000018119812},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3149999976158142},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3147999942302704},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2955000102519989},{"id":"https://openalex.org/C145428669","wikidata":"https://www.wikidata.org/wiki/Q471748","display_name":"Exception handling","level":2,"score":0.29179999232292175},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.28760001063346863},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.2660999894142151},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.2648000121116638},{"id":"https://openalex.org/C153876917","wikidata":"https://www.wikidata.org/wiki/Q899704","display_name":"Traceability","level":2,"score":0.25619998574256897}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational 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":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1371/journal.pcbi.1013239","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013239","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:41343683","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41343683","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:a12979ba9e3241d481c616b4eb96a12c","is_oa":true,"landing_page_url":"https://doaj.org/article/a12979ba9e3241d481c616b4eb96a12c","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 21, Iss 12, p e1013239 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1013239","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013239","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1993729073","display_name":null,"funder_award_id":"R24GM137787","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G302012681","display_name":null,"funder_award_id":"116030","funder_id":"https://openalex.org/F4320314178","funder_display_name":"European Federation of Pharmaceutical Industries and Associations"},{"id":"https://openalex.org/G6618852487","display_name":null,"funder_award_id":"P41EB023912","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6632119201","display_name":null,"funder_award_id":"R24 GM137787","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8039369273","display_name":null,"funder_award_id":"P41 EB023912","funder_id":"https://openalex.org/F4320337363","funder_display_name":"National Institute of Biomedical Imaging and Bioengineering"}],"funders":[{"id":"https://openalex.org/F4320313288","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52"},{"id":"https://openalex.org/F4320314178","display_name":"European Federation of Pharmaceutical Industries and Associations","ror":"https://ror.org/00g1x4v36"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337363","display_name":"National Institute of Biomedical Imaging and Bioengineering","ror":"https://ror.org/00372qc85"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1569141053","https://openalex.org/W1754578874","https://openalex.org/W2020561965","https://openalex.org/W2024060242","https://openalex.org/W2032756564","https://openalex.org/W2062456307","https://openalex.org/W2075161553","https://openalex.org/W2100084634","https://openalex.org/W2102653059","https://openalex.org/W2123783513","https://openalex.org/W2150386276","https://openalex.org/W2157084984","https://openalex.org/W2170032647","https://openalex.org/W2187618037","https://openalex.org/W2406493898","https://openalex.org/W2525009482","https://openalex.org/W2790858109","https://openalex.org/W2859249641","https://openalex.org/W2884300959","https://openalex.org/W3035965352","https://openalex.org/W3080133182","https://openalex.org/W3091749330","https://openalex.org/W3132502413","https://openalex.org/W3142344196","https://openalex.org/W3168038426","https://openalex.org/W3206868055","https://openalex.org/W4226475868","https://openalex.org/W4321003856","https://openalex.org/W4367835104"],"related_works":[],"abstract_inverted_index":{"The":[0,64],"BioModels":[1,92,117,215,263],"Repository":[2],"contains":[3],"over":[4,102,208],"1000":[5],"manually":[6],"curated":[7,178],"mechanistic":[8,179],"models":[9,157,180,272,284],"from":[10,56],"published":[11],"literature,":[12],"most":[13],"often":[14],"encoded":[15],"in":[16,105,116,181,213,294],"the":[17,34,114,125,133,214,222,225,249,251,254,262,268],"Systems":[18],"Biology":[19],"Markup":[20,68],"Language":[21,69],"(SBML).":[22],"This":[23],"community-based":[24],"standard":[25,75],"formally":[26],"specifies":[27],"each":[28],"model,":[29],"but":[30],"does":[31],"not":[32],"describe":[33],"computational":[35],"experimental":[36],"conditions":[37],"to":[38,50,77,81,86,152,266],"run":[39,82],"a":[40,57,72,74,87,230],"simulation":[41,201],"and":[42,98,107,121,158,171,206,217,236,253,261,278,297],"collect":[43],"data.":[44],"Therefore,":[45],"it":[46,189],"can":[47,190],"be":[48,191],"challenging":[49],"reproduce":[51],"any":[52],"figure":[53,89],"or":[54,90],"result":[55],"publication":[58],"with":[59,259],"an":[60,83],"SBML":[61],"model":[62],"alone.":[63],"Simulation":[65],"Experiment":[66],"Description":[67],"(SED-ML)":[70],"provides":[71],"solution:":[73],"way":[76],"specify":[78],"exactly":[79],"how":[80],"experiment":[84],"corresponding":[85],"specific":[88],"result.":[91],"was":[93,130],"established":[94],"years":[95],"before":[96],"SED-ML,":[97,235],"both":[99,104],"systems":[100],"evolved":[101],"time,":[103],"content":[106],"acceptance.":[108],"Hence,":[109],"only":[110],"about":[111],"half":[112],"of":[113,127,138,224,270,300],"entries":[115],"contained":[118],"SED-ML":[119,128,140,174,186,211,260],"files,":[120],"these":[122,139,156,271,283],"files":[123,141,175,212,220],"reflected":[124],"version":[126],"that":[129,148,196],"available":[131],"at":[132,143],"time.":[134],"Additionally,":[135],"almost":[136],"all":[137],"had":[142],"least":[144],"one":[145],"minor":[146],"mistake":[147],"made":[149],"them":[150,275],"impossible":[151],"run.":[153],"To":[154],"make":[155],"their":[159],"results":[160,197,239],"more":[161,276,288],"reproducible,":[162],"we":[163,228],"report":[164,237],"here":[165],"on":[166],"our":[167],"work":[168,258],"updating,":[169],"correcting":[170],"generating":[172],"new":[173,295],"for":[176,193,221,233,290],"1055":[177],"BioModels.":[182],"In":[183],"addition,":[184],"because":[185],"is":[187],"implementation-independent,":[188],"used":[192,229],"verification,":[194],"demonstrating":[195],"hold":[198],"across":[199,240],"multiple":[200],"engines.":[202],"We":[203],"tested,":[204],"corrected,":[205],"improved":[207],"450":[209],"existing":[210],"database,":[216],"created":[218],"basic":[219],"rest":[223],"entries.":[226],"Then,":[227],"wrapper":[231],"architecture":[232],"interpreting":[234],"verification":[238],"five":[241],"different":[242],"ODE-based":[243],"biosimulation":[244],"engines,":[245],"after":[246],"further":[247],"improving":[248],"models,":[250],"wrappers,":[252],"engines":[255],"themselves.":[256],"Our":[257],"collection":[264],"aims":[265],"improve":[267],"utility":[269],"by":[273],"making":[274],"reproducible":[277],"credible.":[279],"Improved":[280],"reproducibility":[281],"means":[282],"are":[285],"now":[286],"even":[287],"fit":[289],"re-use,":[291],"such":[292],"as":[293,298],"investigations":[296],"components":[299],"multiscale":[301],"models.":[302]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-12-04T00:00:00"}
