{"id":"https://openalex.org/W3134460489","doi":"https://doi.org/10.1371/journal.pcbi.1008859","title":"Hierarchical semantic composition of biosimulation models using bond graphs","display_name":"Hierarchical semantic composition of biosimulation models using bond graphs","publication_year":2021,"publication_date":"2021-05-13","ids":{"openalex":"https://openalex.org/W3134460489","doi":"https://doi.org/10.1371/journal.pcbi.1008859","mag":"3134460489","pmid":"https://pubmed.ncbi.nlm.nih.gov/33983945"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1008859","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008859","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.1008859","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022410605","display_name":"Niloofar Shahidi","orcid":"https://orcid.org/0000-0001-5532-1651"},"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":"Niloofar Shahidi","raw_affiliation_strings":["Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand"],"affiliations":[{"raw_affiliation_string":"Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059730193","display_name":"Michael Pan","orcid":"https://orcid.org/0000-0002-8978-7350"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Michael Pan","raw_affiliation_strings":["ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Faculty of Engineering and Information Technology, University of Melbourne, Melbourne, Victoria, Australia","Systems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne, Melbourne, Victoria, Australia"],"affiliations":[{"raw_affiliation_string":"ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Faculty of Engineering and Information Technology, University of Melbourne, Melbourne, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Systems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne, Melbourne, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042815545","display_name":"Soroush Safaei","orcid":"https://orcid.org/0000-0001-5734-243X"},"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":"Soroush Safaei","raw_affiliation_strings":["Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand"],"affiliations":[{"raw_affiliation_string":"Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029429630","display_name":"Kenneth Tran","orcid":"https://orcid.org/0000-0002-8651-3557"},"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":"Kenneth Tran","raw_affiliation_strings":["Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand"],"affiliations":[{"raw_affiliation_string":"Auckland Bioengineering Institute, The University of Auckland, 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/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Edmund J. Crampin","raw_affiliation_strings":["ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Faculty of Engineering and Information Technology, University of Melbourne, Melbourne, Victoria, Australia","Systems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne, Melbourne, Victoria, Australia"],"affiliations":[{"raw_affiliation_string":"ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Faculty of Engineering and Information Technology, University of Melbourne, Melbourne, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Systems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne, Melbourne, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086460310","display_name":"David Nickerson","orcid":"https://orcid.org/0000-0003-4667-9779"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"David P. Nickerson","raw_affiliation_strings":["Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand"],"affiliations":[{"raw_affiliation_string":"Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5022410605"],"corresponding_institution_ids":["https://openalex.org/I154130895"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.4637,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.81823107,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"17","issue":"5","first_page":"e1008859","last_page":"e1008859"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9952999949455261,"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":0.9952999949455261,"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/T11195","display_name":"Simulation Techniques and Applications","score":0.9801999926567078,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"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/T13286","display_name":"Modeling and Simulation Systems","score":0.9715999960899353,"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/computer-science","display_name":"Computer science","score":0.7104799747467041},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.6593989133834839},{"id":"https://openalex.org/keywords/bond-graph","display_name":"Bond graph","score":0.5989489555358887},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.5596259236335754},{"id":"https://openalex.org/keywords/composition","display_name":"Composition (language)","score":0.5002670288085938},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4922129213809967},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4883386790752411},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4496031403541565},{"id":"https://openalex.org/keywords/complex-system","display_name":"Complex system","score":0.4475114643573761},{"id":"https://openalex.org/keywords/cognitive-science","display_name":"Cognitive science","score":0.3594605326652527},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.195118248462677},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.18322870135307312},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18172448873519897},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1036447286605835}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7104799747467041},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.6593989133834839},{"id":"https://openalex.org/C187593909","wikidata":"https://www.wikidata.org/wiki/Q838024","display_name":"Bond graph","level":2,"score":0.5989489555358887},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.5596259236335754},{"id":"https://openalex.org/C40231798","wikidata":"https://www.wikidata.org/wiki/Q1333743","display_name":"Composition (language)","level":2,"score":0.5002670288085938},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4922129213809967},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4883386790752411},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4496031403541565},{"id":"https://openalex.org/C47822265","wikidata":"https://www.wikidata.org/wiki/Q854457","display_name":"Complex system","level":2,"score":0.4475114643573761},{"id":"https://openalex.org/C188147891","wikidata":"https://www.wikidata.org/wiki/Q147638","display_name":"Cognitive science","level":1,"score":0.3594605326652527},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.195118248462677},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.18322870135307312},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18172448873519897},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1036447286605835},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001158","descriptor_name":"Arteries","qualifier_ui":"Q000033","qualifier_name":"anatomy & histology","is_major_topic":false},{"descriptor_ui":"D001158","descriptor_name":"Arteries","qualifier_ui":"Q000033","qualifier_name":"anatomy & histology","is_major_topic":false},{"descriptor_ui":"D001158","descriptor_name":"Arteries","qualifier_ui":"Q000033","qualifier_name":"anatomy & histology","is_major_topic":false},{"descriptor_ui":"D001158","descriptor_name":"Arteries","qualifier_ui":"Q000033","qualifier_name":"anatomy & histology","is_major_topic":false},{"descriptor_ui":"D001158","descriptor_name":"Arteries","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001158","descriptor_name":"Arteries","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001158","descriptor_name":"Arteries","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001158","descriptor_name":"Arteries","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001775","descriptor_name":"Blood Circulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001775","descriptor_name":"Blood Circulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001775","descriptor_name":"Blood Circulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001775","descriptor_name":"Blood Circulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D008955","descriptor_name":"Models, Cardiovascular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008955","descriptor_name":"Models, Cardiovascular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008955","descriptor_name":"Models, Cardiovascular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008955","descriptor_name":"Models, Cardiovascular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1008859","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008859","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:33983945","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33983945","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:jupiter.its.unimelb.edu.au:11343/278350","is_oa":true,"landing_page_url":"http://hdl.handle.net/11343/278350","pdf_url":"http://hdl.handle.net/11343/278350","source":{"id":"https://openalex.org/S4377196259","display_name":"Minerva Access (University of Melbourne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165779595","host_organization_name":"The University of Melbourne","host_organization_lineage":["https://openalex.org/I165779595"],"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":"","raw_type":"Journal Article"},{"id":"pmh:oai:RePEc:plo:pcbi00:1008859","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008859","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:4bfb9cc489314474b6711a5498360cc7","is_oa":true,"landing_page_url":"https://doaj.org/article/4bfb9cc489314474b6711a5498360cc7","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":"PLoS Computational Biology, Vol 17, Iss 5, p e1008859 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8148364","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8148364","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":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:researchspace.auckland.ac.nz:2292/60000","is_oa":true,"landing_page_url":"https://hdl.handle.net/2292/60000","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1008859","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008859","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":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.8100000023841858}],"awards":[{"id":"https://openalex.org/G1013137589","display_name":null,"funder_award_id":"Marsden","funder_id":"https://openalex.org/F4320320774","funder_display_name":"Royal Society Te Ap\u0101rangi"},{"id":"https://openalex.org/G114059409","display_name":null,"funder_award_id":"P41EB023912","funder_id":"https://openalex.org/F4320337363","funder_display_name":"National Institute of Biomedical Imaging and Bioengineering"},{"id":"https://openalex.org/G1363728023","display_name":null,"funder_award_id":"P41EB02391","funder_id":"https://openalex.org/F4320337363","funder_display_name":"National Institute of Biomedical Imaging and Bioengineering"},{"id":"https://openalex.org/G1504221976","display_name":null,"funder_award_id":"CE14010003","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"},{"id":"https://openalex.org/G2674840903","display_name":null,"funder_award_id":"Fellowship","funder_id":"https://openalex.org/F4320320006","funder_display_name":"Royal Society"},{"id":"https://openalex.org/G3354284890","display_name":null,"funder_award_id":"NIBIB","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4277741201","display_name":null,"funder_award_id":"21/116","funder_id":"https://openalex.org/F4320334749","funder_display_name":"Health Research Council of New Zealand"},{"id":"https://openalex.org/G5714184577","display_name":null,"funder_award_id":"Fellowship","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"},{"id":"https://openalex.org/G5980719551","display_name":null,"funder_award_id":"project number CE140100036","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"},{"id":"https://openalex.org/G611870384","display_name":null,"funder_award_id":"grant","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"},{"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/G6732895847","display_name":null,"funder_award_id":"EB023912","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7792449127","display_name":null,"funder_award_id":"P41 E","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8235486229","display_name":null,"funder_award_id":"UOA1703","funder_id":"https://openalex.org/F4320320774","funder_display_name":"Royal Society Te Ap\u0101rangi"},{"id":"https://openalex.org/G8470230451","display_name":null,"funder_award_id":"CE140100036","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"},{"id":"https://openalex.org/G8877730500","display_name":null,"funder_award_id":"P41 EB023912","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320320006","display_name":"Royal Society","ror":"https://ror.org/03wnrjx87"},{"id":"https://openalex.org/F4320320774","display_name":"Royal Society Te Ap\u0101rangi","ror":"https://ror.org/04tajb587"},{"id":"https://openalex.org/F4320331449","display_name":"Aotearoa Foundation","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334704","display_name":"Australian Research Council","ror":"https://ror.org/05mmh0f86"},{"id":"https://openalex.org/F4320334749","display_name":"Health Research Council of New Zealand","ror":"https://ror.org/00zbf3d93"},{"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":60,"referenced_works":["https://openalex.org/W59902744","https://openalex.org/W115724341","https://openalex.org/W256241826","https://openalex.org/W589302049","https://openalex.org/W1965368971","https://openalex.org/W2001114982","https://openalex.org/W2003251032","https://openalex.org/W2016462601","https://openalex.org/W2021380963","https://openalex.org/W2024580333","https://openalex.org/W2027082381","https://openalex.org/W2066061549","https://openalex.org/W2081684301","https://openalex.org/W2085224783","https://openalex.org/W2087308849","https://openalex.org/W2087789886","https://openalex.org/W2106055118","https://openalex.org/W2110726849","https://openalex.org/W2128647811","https://openalex.org/W2131294353","https://openalex.org/W2146437022","https://openalex.org/W2150908245","https://openalex.org/W2151019661","https://openalex.org/W2168618155","https://openalex.org/W2169038227","https://openalex.org/W2170122529","https://openalex.org/W2219048344","https://openalex.org/W2328108594","https://openalex.org/W2462447859","https://openalex.org/W2490209367","https://openalex.org/W2553698069","https://openalex.org/W2605614966","https://openalex.org/W2750262575","https://openalex.org/W2771570772","https://openalex.org/W2779506242","https://openalex.org/W2786877773","https://openalex.org/W2788254992","https://openalex.org/W2792485946","https://openalex.org/W2807737529","https://openalex.org/W2892906004","https://openalex.org/W2902365877","https://openalex.org/W2903541311","https://openalex.org/W2972248834","https://openalex.org/W2996168077","https://openalex.org/W2996366821","https://openalex.org/W2996893734","https://openalex.org/W3006461037","https://openalex.org/W3008956387","https://openalex.org/W3009513829","https://openalex.org/W3091832416","https://openalex.org/W3099142114","https://openalex.org/W3102051271","https://openalex.org/W3103086489","https://openalex.org/W3104064088","https://openalex.org/W3105704522","https://openalex.org/W3137329076","https://openalex.org/W3165695615","https://openalex.org/W4225477695","https://openalex.org/W4241440178","https://openalex.org/W4246991885"],"related_works":["https://openalex.org/W3009669764","https://openalex.org/W1958094387","https://openalex.org/W2032170356","https://openalex.org/W2371731813","https://openalex.org/W2358330211","https://openalex.org/W2628002430","https://openalex.org/W2570127249","https://openalex.org/W2614520266","https://openalex.org/W2367105195","https://openalex.org/W2391669314"],"abstract_inverted_index":{"Simulating":[0],"complex":[1,146],"biological":[2,147],"and":[3,6,19,31,39,45,104,148,151],"physiological":[4,76,149],"systems":[5,16,150],"predicting":[7],"their":[8],"behaviours":[9],"under":[10],"different":[11],"conditions":[12],"remains":[13],"challenging.":[14],"Breaking":[15],"into":[17,50],"smaller":[18],"more":[20,139],"manageable":[21],"modules":[22],"can":[23,137],"address":[24],"this":[25,55,118],"challenge,":[26],"assisting":[27],"both":[28],"model":[29,60,102,109,122,126,156],"development":[30],"simulation.":[32],"Nevertheless,":[33],"existing":[34],"computational":[35],"models":[36],"in":[37],"biology":[38],"physiology":[40],"are":[41],"often":[42],"not":[43,62],"modular":[44],"therefore":[46],"difficult":[47],"to":[48,66,120],"assemble":[49],"larger":[51],"models.":[52],"Even":[53],"when":[54],"is":[56,110,134],"possible,":[57],"the":[58,70,75,79,91,143],"resulting":[59],"may":[61],"be":[63],"useful":[64],"due":[65],"inconsistencies":[67],"either":[68],"with":[69,96,155],"laws":[71],"of":[72,78,127,145],"physics":[73],"or":[74],"behaviour":[77,144],"system.":[80],"Here,":[81],"we":[82,116],"propose":[83],"a":[84,107,125],"general":[85],"methodology":[86],"for":[87],"composing":[88],"models,":[89],"combining":[90],"energy-based":[92],"bond":[93],"graph":[94],"approach":[95,100,119],"semantics-based":[97],"annotations.":[98],"This":[99],"improves":[101],"composition":[103,123],"ensures":[105],"that":[106,135],"composite":[108],"physically":[111],"plausible.":[112],"As":[113],"an":[114],"example,":[115],"demonstrate":[117],"automated":[121],"using":[124],"human":[128],"arterial":[129],"circulation.":[130],"The":[131],"major":[132],"benefit":[133],"modellers":[136],"spend":[138],"time":[140,153],"on":[141],"understanding":[142],"less":[152],"wrangling":[154],"composition.":[157]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
