{"id":"https://openalex.org/W2107062718","doi":"https://doi.org/10.1093/nar/gkj092","title":"BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems","display_name":"BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems","publication_year":2005,"publication_date":"2005-12-28","ids":{"openalex":"https://openalex.org/W2107062718","doi":"https://doi.org/10.1093/nar/gkj092","mag":"2107062718","pmid":"https://pubmed.ncbi.nlm.nih.gov/16381960"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkj092","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj092","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D689/3925276/gkj092.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D689/3925276/gkj092.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5112438594","display_name":"Nicolas Le Nov\u00e8re","orcid":null},"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":"N. Le Novere","raw_affiliation_strings":["European Bioinformatics Institute EMBL, Wellcome-Trust Genome Campus, Hinxton, CB10 1SD, UK. lenov@ebi.ac.uk","European Bioinformatics Institute EMBL, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK"],"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute EMBL, Wellcome-Trust Genome Campus, Hinxton, CB10 1SD, UK. lenov@ebi.ac.uk","institution_ids":["https://openalex.org/I1303153112"]},{"raw_affiliation_string":"European Bioinformatics Institute EMBL, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5112438594"],"corresponding_institution_ids":["https://openalex.org/I1303153112"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":15.9988,"has_fulltext":true,"cited_by_count":783,"citation_normalized_percentile":{"value":0.9958342,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"34","issue":"90001","first_page":"D689","last_page":"D691"},"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":0.9983999729156494,"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/T13539","display_name":"thermodynamics and calorimetric analyses","score":0.974399983882904,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.9643360376358032},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.594141960144043},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.543799877166748},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4818171560764313},{"id":"https://openalex.org/keywords/controlled-vocabulary","display_name":"Controlled vocabulary","score":0.42462143301963806},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.32747066020965576},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32095867395401},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.28727278113365173},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.1685260832309723},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.08188280463218689}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9643360376358032},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.594141960144043},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.543799877166748},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4818171560764313},{"id":"https://openalex.org/C110615152","wikidata":"https://www.wikidata.org/wiki/Q1469824","display_name":"Controlled vocabulary","level":2,"score":0.42462143301963806},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.32747066020965576},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32095867395401},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.28727278113365173},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.1685260832309723},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.08188280463218689}],"mesh":[{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gkj092","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj092","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D689/3925276/gkj092.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:16381960","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16381960","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:europepmc.org:156897","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC1347454","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1347454","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1347454","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":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"},{"id":"pmh:oai:uhra.herts.ac.uk:2299/383","is_oa":true,"landing_page_url":"http://hdl.handle.net/2299/383","pdf_url":"http://hdl.handle.net/2299/383","source":{"id":"https://openalex.org/S4306400241","display_name":"University of Hertfordshire Research Archive (University of Hertfordshire)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I141584323","host_organization_name":"University of Hertfordshire","host_organization_lineage":["https://openalex.org/I141584323"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""}],"best_oa_location":{"id":"doi:10.1093/nar/gkj092","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj092","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D689/3925276/gkj092.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2107062718.pdf","grobid_xml":"https://content.openalex.org/works/W2107062718.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W2020561965","https://openalex.org/W2042880070","https://openalex.org/W2045115006","https://openalex.org/W2064354742","https://openalex.org/W2082621456","https://openalex.org/W2120679339","https://openalex.org/W2150908245","https://openalex.org/W2158691076","https://openalex.org/W2160751597","https://openalex.org/W2271430656"],"related_works":["https://openalex.org/W1833372769","https://openalex.org/W2128782793","https://openalex.org/W1994518768","https://openalex.org/W104010570","https://openalex.org/W2082621456","https://openalex.org/W2150908245","https://openalex.org/W3080133182","https://openalex.org/W2274214081","https://openalex.org/W2069107439","https://openalex.org/W266409346"],"abstract_inverted_index":{"BioModels":[0],"Database":[1],"(http://www.ebi.ac.uk/biomodels/),":[2],"part":[3],"of":[4,16,46,93],"the":[5,32,37,44,47,63,69,80,91,97],"international":[6],"initiative":[7],"BioModels.net,":[8],"provides":[9],"access":[10],"to":[11,26,31,56,65,89],"published,":[12],"peer-reviewed,":[13],"quantitative":[14],"models":[15,48,70,74],"biochemical":[17],"and":[18,35,54,83],"cellular":[19],"systems.":[20],"Each":[21],"model":[22],"is":[23],"carefully":[24],"curated":[25],"verify":[27],"that":[28],"it":[29],"corresponds":[30],"reference":[33],"publication":[34],"gives":[36],"proper":[38],"numerical":[39],"results.":[40],"Curators":[41],"also":[42],"annotate":[43],"components":[45],"with":[49],"terms":[50],"from":[51],"controlled":[52],"vocabularies":[53],"links":[55],"other":[57],"relevant":[58],"data":[59],"resources.":[60],"This":[61],"allows":[62],"users":[64],"search":[66],"accurately":[67],"for":[68],"they":[71],"need.":[72],"The":[73],"can":[75],"currently":[76],"be":[77],"retrieved":[78],"in":[79],"SBML":[81],"format,":[82],"import/export":[84],"facilities":[85],"are":[86],"being":[87],"developed":[88],"extend":[90],"spectrum":[92],"formats":[94],"supported":[95],"by":[96],"resource.":[98]},"counts_by_year":[{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":24},{"year":2023,"cited_by_count":22},{"year":2022,"cited_by_count":24},{"year":2021,"cited_by_count":29},{"year":2020,"cited_by_count":28},{"year":2019,"cited_by_count":28},{"year":2018,"cited_by_count":31},{"year":2017,"cited_by_count":34},{"year":2016,"cited_by_count":34},{"year":2015,"cited_by_count":46},{"year":2014,"cited_by_count":38},{"year":2013,"cited_by_count":60},{"year":2012,"cited_by_count":50}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
