{"id":"https://openalex.org/W2144143904","doi":"https://doi.org/10.1186/2041-1480-4-24","title":"Function of dynamic models in systems biology: linking structure to behaviour","display_name":"Function of dynamic models in systems biology: linking structure to behaviour","publication_year":2013,"publication_date":"2013-01-01","ids":{"openalex":"https://openalex.org/W2144143904","doi":"https://doi.org/10.1186/2041-1480-4-24","mag":"2144143904","pmid":"https://pubmed.ncbi.nlm.nih.gov/24103739"},"language":"en","primary_location":{"id":"doi:10.1186/2041-1480-4-24","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-4-24","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-24","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"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 Biomedical Semantics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-24","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5107856156","display_name":"Christian Kn\u00fcpfer","orcid":null},"institutions":[{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Christian Kn\u00fcpfer","raw_affiliation_strings":["Artificial Intelligence Group, University of Jena, Jena, Germany. christian.knuepfer@uni-jena.de","Artificial Intelligence Group, University of Jena, Jena, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Artificial Intelligence Group, University of Jena, Jena, Germany. christian.knuepfer@uni-jena.de","institution_ids":["https://openalex.org/I76198965"]},{"raw_affiliation_string":"Artificial Intelligence Group, University of Jena, Jena, Germany","institution_ids":["https://openalex.org/I76198965"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068049841","display_name":"Clemens Beckstein","orcid":null},"institutions":[{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Clemens Beckstein","raw_affiliation_strings":["Artificial Intelligence Group, University of Jena, Jena, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Artificial Intelligence Group, University of Jena, Jena, Germany","institution_ids":["https://openalex.org/I76198965"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5107856156"],"corresponding_institution_ids":["https://openalex.org/I76198965"],"apc_list":{"value":1190,"currency":"GBP","value_usd":1459},"apc_paid":{"value":1190,"currency":"GBP","value_usd":1459},"fwci":0.0,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.11012811,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"4","issue":"1","first_page":"24","last_page":"24"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.3734000027179718,"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":0.3734000027179718,"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/T10778","display_name":"Philosophy and History of Science","score":0.1525000035762787,"subfield":{"id":"https://openalex.org/subfields/1207","display_name":"History and Philosophy of Science"},"field":{"id":"https://openalex.org/fields/12","display_name":"Arts and Humanities"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11445","display_name":"Origins and Evolution of Life","score":0.10220000147819519,"subfield":{"id":"https://openalex.org/subfields/3103","display_name":"Astronomy and Astrophysics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7666469812393188},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.6764301657676697},{"id":"https://openalex.org/keywords/teleology","display_name":"Teleology","score":0.6725621223449707},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.5740706920623779},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5016589164733887},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4649592339992523},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.41402146220207214},{"id":"https://openalex.org/keywords/cognitive-science","display_name":"Cognitive science","score":0.34044602513313293},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33209165930747986},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1180504560470581},{"id":"https://openalex.org/keywords/epistemology","display_name":"Epistemology","score":0.10826000571250916}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7666469812393188},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.6764301657676697},{"id":"https://openalex.org/C80038905","wikidata":"https://www.wikidata.org/wiki/Q192121","display_name":"Teleology","level":2,"score":0.6725621223449707},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.5740706920623779},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5016589164733887},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4649592339992523},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.41402146220207214},{"id":"https://openalex.org/C188147891","wikidata":"https://www.wikidata.org/wiki/Q147638","display_name":"Cognitive science","level":1,"score":0.34044602513313293},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33209165930747986},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1180504560470581},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.10826000571250916},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/2041-1480-4-24","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-4-24","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-24","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"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 Biomedical Semantics","raw_type":"journal-article"},{"id":"pmid:24103739","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24103739","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 biomedical semantics","raw_type":null},{"id":"pmh:oai:europepmc.org:2840208","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3853929","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3853929","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3853929","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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 Biomed Semantics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/2041-1480-4-24","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-4-24","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-24","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"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 Biomedical Semantics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6399999856948853,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2144143904.pdf","grobid_xml":"https://content.openalex.org/works/W2144143904.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W3608534","https://openalex.org/W1518364836","https://openalex.org/W1544923801","https://openalex.org/W1548849615","https://openalex.org/W1553811868","https://openalex.org/W1566102697","https://openalex.org/W1608590154","https://openalex.org/W1963654627","https://openalex.org/W1989263028","https://openalex.org/W2001598892","https://openalex.org/W2049302531","https://openalex.org/W2049696674","https://openalex.org/W2050554833","https://openalex.org/W2053798630","https://openalex.org/W2073061263","https://openalex.org/W2080573473","https://openalex.org/W2084998011","https://openalex.org/W2091579301","https://openalex.org/W2097971625","https://openalex.org/W2103017472","https://openalex.org/W2105941683","https://openalex.org/W2108723074","https://openalex.org/W2113777491","https://openalex.org/W2123783513","https://openalex.org/W2137665890","https://openalex.org/W2143784594","https://openalex.org/W2145435867","https://openalex.org/W2150908245","https://openalex.org/W2156094678","https://openalex.org/W2158004435","https://openalex.org/W2187364252","https://openalex.org/W2280255230","https://openalex.org/W2293871408","https://openalex.org/W2399869838","https://openalex.org/W2757307321"],"related_works":["https://openalex.org/W2384294123","https://openalex.org/W1583619997","https://openalex.org/W1693849728","https://openalex.org/W1470012352","https://openalex.org/W2810208651","https://openalex.org/W4378831103","https://openalex.org/W207829213","https://openalex.org/W4238967417","https://openalex.org/W2315680351","https://openalex.org/W2577456850"],"abstract_inverted_index":{"BACKGROUND:":[0],"Dynamic":[1],"models":[2,31,85,169,204,213,264,276],"in":[3,8,40,74,86,114,136,214,265,292,300,304,311],"Systems":[4,41,215,266,312],"Biology":[5],"are":[6],"used":[7,135],"computational":[9],"simulation":[10,39,137,142,174,296,310],"experiments":[11,138],"for":[12,33,36,121,199,209,230,248,272],"addressing":[13],"biological":[14,21,183],"questions.":[15],"The":[16,268],"complexity":[17],"of":[18,29,53,66,83,104,118,153,167,202,212,232,241,252,263,275,287],"the":[19,24,30,81,99,102,115,154,157,165,173,182,187,195,200,233,249,259,273,288,293],"modelled":[20,158],"systems":[22],"and":[23,27,38,89,101,150,156,181,221,261,295,309],"growing":[25],"number":[26],"size":[28],"calls":[32],"computer":[34,44],"support":[35,45],"modelling":[37,294,308],"Biology.":[42,267,313],"This":[43,69],"has":[46,132],"to":[47,126,133,146,171,205,238],"be":[48,134],"based":[49],"on":[50,95],"formal":[51,207,222,228,285],"representations":[52],"relevant":[54],"knowledge":[55,290],"fragments.":[56],"RESULTS:":[57],"In":[58,124,236],"this":[59,128,301],"paper":[60],"we":[61,93,225,244],"describe":[62],"different":[63],"functional":[64,88,210,234,289],"aspects":[65,211],"dynamic":[67,84,122,168,203],"models.":[68,253],"description":[70],"is":[71,277],"conceptually":[72],"embedded":[73],"our":[75],"\"meaning":[76],"facets\"":[77],"framework":[78,198,271],"which":[79,185],"systematises":[80],"interpretation":[82],"structural,":[87],"behavioural":[90],"facets.":[91],"Here":[92],"focus":[94],"how":[96],"function":[97,166,201,251,274],"links":[98],"structure":[100],"behaviour":[103],"a":[105,109,130,147,151,283],"model.":[106],"Models":[107],"play":[108],"specific":[110,148],"role":[111,129,260],"(teleological":[112],"function)":[113,180],"scientific":[116],"process":[117],"finding":[119],"explanations":[120],"phenomena.":[123],"order":[125,237],"fulfil":[127],"model":[131,155],"(pragmatical":[139],"function).":[140,161,192],"A":[141],"experiment":[143,175,184],"always":[144],"refers":[145,170],"situation":[149],"state":[152],"system":[159],"(conditional":[160],"We":[162,193,255],"claim":[163],"that":[164],"both":[172],"executed":[176],"by":[177],"software":[178],"(intrinsic":[179],"produces":[186],"phenomena":[188],"under":[189],"investigation":[190],"(extrinsic":[191],"use":[194,262],"presented":[196],"conceptual":[197,270],"review":[206],"accounts":[208,229],"Biology,":[216],"such":[217],"as":[218],"checklists,":[219],"ontologies,":[220],"languages.":[223],"Furthermore,":[224],"identify":[226],"missing":[227],"some":[231],"aspects.":[235],"fill":[239],"one":[240],"these":[242],"gaps":[243],"propose":[245],"an":[246,278],"ontology":[247],"teleological":[250],"CONCLUSION:":[254],"have":[256],"thoroughly":[257],"analysed":[258],"resulting":[269],"important":[279],"first":[280],"step":[281],"towards":[282],"comprehensive":[284],"representation":[286],"involved":[291],"process.":[297],"Any":[298],"progress":[299],"area":[302],"will":[303],"turn":[305],"improve":[306],"computer-supported":[307]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
