{"id":"https://openalex.org/W3048575781","doi":"https://doi.org/10.1515/jib-2020-0021","title":"CellML 2.0","display_name":"CellML 2.0","publication_year":2020,"publication_date":"2020-06-01","ids":{"openalex":"https://openalex.org/W3048575781","doi":"https://doi.org/10.1515/jib-2020-0021","mag":"3048575781","pmid":"https://pubmed.ncbi.nlm.nih.gov/32759406"},"language":"en","primary_location":{"id":"doi:10.1515/jib-2020-0021","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2020-0021","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2020-0021/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://www.degruyter.com/document/doi/10.1515/jib-2020-0021/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085961856","display_name":"Michael Clerx","orcid":"https://orcid.org/0000-0003-4062-3061"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Michael Clerx","raw_affiliation_strings":["University of Oxford , Oxford , UK"],"affiliations":[{"raw_affiliation_string":"University of Oxford , Oxford , UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090837240","display_name":"Michael T. Cooling","orcid":"https://orcid.org/0000-0002-3417-0177"},"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":"Michael T. Cooling","raw_affiliation_strings":["University of Auckland , Auckland , New Zealand"],"affiliations":[{"raw_affiliation_string":"University of Auckland , Auckland , New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027917052","display_name":"Jonathan Cooper","orcid":"https://orcid.org/0000-0001-6009-3542"},"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":"Jonathan Cooper","raw_affiliation_strings":["University College London , London , UK"],"affiliations":[{"raw_affiliation_string":"University College London , London , UK","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073607042","display_name":"Alan Garny","orcid":"https://orcid.org/0000-0001-7606-5888"},"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":"Alan Garny","raw_affiliation_strings":["University of Auckland , Auckland , New Zealand"],"affiliations":[{"raw_affiliation_string":"University of Auckland , Auckland , New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071859477","display_name":"Keri Moyle","orcid":"https://orcid.org/0000-0002-7178-2631"},"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":"Keri Moyle","raw_affiliation_strings":["University of Auckland , Auckland , New Zealand"],"affiliations":[{"raw_affiliation_string":"University of Auckland , Auckland , New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"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":["University of Auckland , Auckland , New Zealand"],"affiliations":[{"raw_affiliation_string":"University of Auckland , Auckland , New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087987376","display_name":"Poul M. F. Nielsen","orcid":"https://orcid.org/0000-0002-4704-0179"},"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":"Poul M. F. Nielsen","raw_affiliation_strings":["University of Auckland , Auckland , New Zealand"],"affiliations":[{"raw_affiliation_string":"University of Auckland , Auckland , New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044859481","display_name":"Hugh Sorby","orcid":"https://orcid.org/0000-0001-8991-4703"},"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":"Hugh Sorby","raw_affiliation_strings":["University of Auckland , Auckland , New Zealand"],"affiliations":[{"raw_affiliation_string":"University of Auckland , Auckland , New Zealand","institution_ids":["https://openalex.org/I154130895"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5086460310"],"corresponding_institution_ids":["https://openalex.org/I154130895"],"apc_list":null,"apc_paid":null,"fwci":2.0024,"has_fulltext":false,"cited_by_count":45,"citation_normalized_percentile":{"value":0.87208688,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"17","issue":"2-3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.992900013923645,"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":0.992900013923645,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7803286910057068},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.6727280020713806},{"id":"https://openalex.org/keywords/syntax","display_name":"Syntax","score":0.49288463592529297},{"id":"https://openalex.org/keywords/formal-specification","display_name":"Formal specification","score":0.47839653491973877},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.44372284412384033},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.42027613520622253},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.36760810017585754},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3598514795303345},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.34847235679626465},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2963407635688782},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.11961290240287781}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7803286910057068},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.6727280020713806},{"id":"https://openalex.org/C60048249","wikidata":"https://www.wikidata.org/wiki/Q37437","display_name":"Syntax","level":2,"score":0.49288463592529297},{"id":"https://openalex.org/C116253237","wikidata":"https://www.wikidata.org/wiki/Q1437424","display_name":"Formal specification","level":2,"score":0.47839653491973877},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.44372284412384033},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.42027613520622253},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.36760810017585754},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3598514795303345},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.34847235679626465},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2963407635688782},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.11961290240287781}],"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":"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":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1515/jib-2020-0021","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2020-0021","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2020-0021/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32759406","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32759406","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":"Journal of integrative bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:f24b37efcdd446a495f6532302f62126","is_oa":true,"landing_page_url":"https://doaj.org/article/f24b37efcdd446a495f6532302f62126","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Integrative Bioinformatics, Vol 17, Iss 2-3 (2020)","raw_type":"article"},{"id":"pmh:oai:nottingham-repository.worktribe.com:25645691","is_oa":true,"landing_page_url":"https://nottingham-repository.worktribe.com/output/25645691","pdf_url":null,"source":{"id":"https://openalex.org/S4306402483","display_name":"Repository@Nottingham (University of Nottingham)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I142263535","host_organization_name":"University of Nottingham","host_organization_lineage":["https://openalex.org/I142263535"],"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":null,"raw_type":"publishedVersion"},{"id":"pmh:oai:pubmedcentral.nih.gov:7756617","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7756617","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":"J Integr Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1515/jib-2020-0021","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2020-0021","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2020-0021/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.4300000071525574,"display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G3474758542","display_name":null,"funder_award_id":"BB/P010008/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3048575781.pdf","grobid_xml":"https://content.openalex.org/works/W3048575781.grobid-xml"},"referenced_works_count":3,"referenced_works":["https://openalex.org/W1487338715","https://openalex.org/W1564944122","https://openalex.org/W1744779065"],"related_works":["https://openalex.org/W4388713123","https://openalex.org/W3194438104","https://openalex.org/W2570592793","https://openalex.org/W2753140600","https://openalex.org/W2354135050","https://openalex.org/W2592399342","https://openalex.org/W2125996595","https://openalex.org/W1559579193","https://openalex.org/W2069597759","https://openalex.org/W2620193245"],"abstract_inverted_index":{"We":[0],"present":[1],"here":[2],"CellML":[3,20,60,72,98,102],"2.0,":[4],"an":[5],"XML-based":[6],"language":[7],"for":[8,89],"describing":[9],"and":[10,42,74],"exchanging":[11],"mathematical":[12],"models":[13,53,103],"of":[14,29,33,36,57,92,101,111,122,128],"physiological":[15],"systems.":[16],"MathML":[17],"embedded":[18],"in":[19],"documents":[21],"is":[22,62,86],"used":[23],"to":[24,54,106],"define":[25],"the":[26,65,71,75,90,108,112,117,123],"underlying":[27],"mathematics":[28],"models.":[30],"Models":[31,49],"consist":[32],"a":[34],"network":[35],"reusable":[37],"components,":[38],"each":[39],"with":[40,120,126],"variables":[41],"equations":[43],"giving":[44],"relationships":[45],"between":[46],"those":[47],"variables.":[48],"may":[50,104],"import":[51],"other":[52],"create":[55],"systems":[56],"increasing":[58],"complexity.":[59],"2.0":[61],"defined":[63],"by":[64,77],"normative":[66,84,118],"specification":[67,85,113,119],"presented":[68],"here,":[69],"prescribing":[70],"syntax":[73],"rules":[76,124],"which":[78,95,115],"it":[79],"should":[80],"be":[81],"used.":[82],"The":[83],"intended":[87],"primarily":[88],"developers":[91],"software":[93],"tools":[94],"directly":[96],"consume":[97],"syntax.":[99],"Users":[100],"prefer":[105],"browse":[107],"informative":[109],"rendering":[110],"(https://cellml.org/specifications/cellml_2.0/)":[114],"extends":[116],"explanations":[121],"combined":[125],"examples":[127],"their":[129],"usage.":[130]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":1}],"updated_date":"2026-03-28T08:17:26.163206","created_date":"2020-08-18T00:00:00"}
