{"id":"https://openalex.org/W2114211768","doi":"https://doi.org/10.1093/bioinformatics/btp495","title":"A method for visualizing CellML models","display_name":"A method for visualizing CellML models","publication_year":2009,"publication_date":"2009-08-24","ids":{"openalex":"https://openalex.org/W2114211768","doi":"https://doi.org/10.1093/bioinformatics/btp495","mag":"2114211768","pmid":"https://pubmed.ncbi.nlm.nih.gov/19703920"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp495","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp495","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/22/3012/48998106/bioinformatics_25_22_3012.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/25/22/3012/48998106/bioinformatics_25_22_3012.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034436640","display_name":"Sarala Wimalaratne","orcid":"https://orcid.org/0000-0002-5355-2576"},"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":"S. M. Wimalaratne","raw_affiliation_strings":["1 Auckland Bioengineering Institute and 2Department of Engineering Science, The University of Auckland, 70 Symonds St, Auckland, New Zealand"],"affiliations":[{"raw_affiliation_string":"1 Auckland Bioengineering Institute and 2Department of Engineering Science, The University of Auckland, 70 Symonds St, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038702774","display_name":"Matt Halstead","orcid":null},"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":"M. D. B. Halstead","raw_affiliation_strings":["1 Auckland Bioengineering Institute and 2Department of Engineering Science, The University of Auckland, 70 Symonds St, Auckland, New Zealand"],"affiliations":[{"raw_affiliation_string":"1 Auckland Bioengineering Institute and 2Department of Engineering Science, The University of Auckland, 70 Symonds St, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105570389","display_name":"Catherine M. Lloyd","orcid":null},"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":"C. M. Lloyd","raw_affiliation_strings":["1 Auckland Bioengineering Institute and 2Department of Engineering Science, The University of Auckland, 70 Symonds St, Auckland, New Zealand"],"affiliations":[{"raw_affiliation_string":"1 Auckland Bioengineering Institute and 2Department of Engineering Science, The University of Auckland, 70 Symonds St, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"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":"M. T. Cooling","raw_affiliation_strings":["1 Auckland Bioengineering Institute and 2Department of Engineering Science, The University of Auckland, 70 Symonds St, Auckland, New Zealand"],"affiliations":[{"raw_affiliation_string":"1 Auckland Bioengineering Institute and 2Department of Engineering Science, The University of Auckland, 70 Symonds St, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083478373","display_name":"Edmund J. Crampin","orcid":"https://orcid.org/0000-0001-6569-9543"},"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":"E. J. Crampin","raw_affiliation_strings":["1 Auckland Bioengineering Institute and 2Department of Engineering Science, The University of Auckland, 70 Symonds St, Auckland, New Zealand"],"affiliations":[{"raw_affiliation_string":"1 Auckland Bioengineering Institute and 2Department of Engineering Science, The University of Auckland, 70 Symonds St, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113689138","display_name":"Poul Nielsen","orcid":null},"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":"P. F. Nielsen","raw_affiliation_strings":["1 Auckland Bioengineering Institute and 2Department of Engineering Science, The University of Auckland, 70 Symonds St, Auckland, New Zealand"],"affiliations":[{"raw_affiliation_string":"1 Auckland Bioengineering Institute and 2Department of Engineering Science, The University of Auckland, 70 Symonds St, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5034436640"],"corresponding_institution_ids":["https://openalex.org/I154130895"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6714,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.69788155,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"25","issue":"22","first_page":"3012","last_page":"3019"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9987999796867371,"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":0.9987999796867371,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9805999994277954,"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":0.8013018369674683},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6858633756637573},{"id":"https://openalex.org/keywords/interpretation","display_name":"Interpretation (philosophy)","score":0.4635331928730011},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4503334164619446},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3681265711784363},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.35369110107421875},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3376674950122833}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8013018369674683},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6858633756637573},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.4635331928730011},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4503334164619446},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3681265711784363},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35369110107421875},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3376674950122833}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","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":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btp495","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp495","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/22/3012/48998106/bioinformatics_25_22_3012.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19703920","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19703920","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:researchspace.auckland.ac.nz:2292/7553","is_oa":false,"landing_page_url":"http://hdl.handle.net/2292/7553","pdf_url":null,"source":{"id":"https://openalex.org/S7407055463","display_name":"ResearchSpace (University of Auckland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I154130895","host_organization_name":"University of Auckland","host_organization_lineage":["https://openalex.org/I154130895"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp495","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp495","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/22/3012/48998106/bioinformatics_25_22_3012.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.550000011920929}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2114211768.pdf","grobid_xml":"https://content.openalex.org/works/W2114211768.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1489737525","https://openalex.org/W1499796720","https://openalex.org/W1541343226","https://openalex.org/W1702766678","https://openalex.org/W1985940938","https://openalex.org/W2028307228","https://openalex.org/W2031631803","https://openalex.org/W2042880070","https://openalex.org/W2045478141","https://openalex.org/W2069157810","https://openalex.org/W2087308849","https://openalex.org/W2099007946","https://openalex.org/W2108036176","https://openalex.org/W2110728169","https://openalex.org/W2121905803","https://openalex.org/W2133429395","https://openalex.org/W2133938042","https://openalex.org/W2139383813","https://openalex.org/W2147990117","https://openalex.org/W2148329459","https://openalex.org/W2149991291","https://openalex.org/W2161749893","https://openalex.org/W2170122529","https://openalex.org/W4249884416","https://openalex.org/W6676198171","https://openalex.org/W6680602640","https://openalex.org/W6681881340"],"related_works":["https://openalex.org/W2166247150","https://openalex.org/W4243252198","https://openalex.org/W2118300983","https://openalex.org/W2112962394","https://openalex.org/W3137189469","https://openalex.org/W4235530921","https://openalex.org/W2104078272","https://openalex.org/W2382501300","https://openalex.org/W3162240892","https://openalex.org/W4245713008"],"abstract_inverted_index":{"To":[0],"address":[1],"this":[2],"issue":[3],"a":[4,24,28],"set":[5],"of":[6,39,67],"ontologies":[7],"was":[8],"developed":[9],"to":[10,35],"explicitly":[11],"annotate":[12],"the":[13,18,37,40,48,56,65],"biophysical":[14],"concepts":[15,45,69],"represented":[16],"in":[17,64],"CellML":[19,33,57,60],"models.":[20],"This":[21],"article":[22],"presents":[23],"framework":[25],"that":[26],"combines":[27],"visual":[29],"language,":[30],"together":[31],"with":[32,55],"ontologies,":[34],"support":[36],"visualization":[38,62],"underlying":[41],"physical":[42],"and":[43,51,70,74],"biological":[44],"described":[46],"by":[47],"mathematical":[49],"model":[50,61,68,72],"also":[52],"their":[53],"relationships":[54],"model.":[58],"Automated":[59],"assists":[63],"interpretation":[66],"facilitates":[71],"communication":[73],"exchange":[75],"between":[76],"different":[77],"communities.":[78]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":1}],"updated_date":"2026-03-18T14:38:29.013473","created_date":"2025-10-10T00:00:00"}
