{"id":"https://openalex.org/W2135752912","doi":"https://doi.org/10.1093/bib/bbp003","title":"Exploring autonomy through computational biomodelling","display_name":"Exploring autonomy through computational biomodelling","publication_year":2009,"publication_date":"2009-03-10","ids":{"openalex":"https://openalex.org/W2135752912","doi":"https://doi.org/10.1093/bib/bbp003","mag":"2135752912","pmid":"https://pubmed.ncbi.nlm.nih.gov/19276201"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbp003","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbp003","pdf_url":"https://academic.oup.com/bib/article-pdf/10/4/462/837539/bbp003.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/10/4/462/837539/bbp003.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031724144","display_name":"Niall Palfreyman","orcid":"https://orcid.org/0000-0001-7033-2391"},"institutions":[{"id":"https://openalex.org/I309496635","display_name":"Weihenstephan-Triesdorf University of Applied Sciences","ror":"https://ror.org/00gzkxz88","country_code":"DE","type":"education","lineage":["https://openalex.org/I309496635"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"N. Palfreyman","raw_affiliation_strings":["Department of Biotechnology and Bioinformatics, Weihenstephan University of Applied Sciences, 85350 Freising, Germany. niall.palfreyman@fh-weihenstephan.de","Dept, of Biotechnology & Bioinformatics, Weihenstephan University of Applied Sciences, 85350 Freising, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Biotechnology and Bioinformatics, Weihenstephan University of Applied Sciences, 85350 Freising, Germany. niall.palfreyman@fh-weihenstephan.de","institution_ids":["https://openalex.org/I309496635"]},{"raw_affiliation_string":"Dept, of Biotechnology & Bioinformatics, Weihenstephan University of Applied Sciences, 85350 Freising, Germany","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5031724144"],"corresponding_institution_ids":["https://openalex.org/I309496635"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.13361006,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"10","issue":"4","first_page":"462","last_page":"474"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13811","display_name":"Earth Systems and Cosmic Evolution","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1902","display_name":"Atmospheric Science"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T13811","display_name":"Earth Systems and Cosmic Evolution","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1902","display_name":"Atmospheric Science"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11445","display_name":"Origins and Evolution of Life","score":0.9959999918937683,"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"}},{"id":"https://openalex.org/T10778","display_name":"Philosophy and History of Science","score":0.9833999872207642,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.8300849795341492},{"id":"https://openalex.org/keywords/ambiguity","display_name":"Ambiguity","score":0.6435053944587708},{"id":"https://openalex.org/keywords/causality","display_name":"Causality (physics)","score":0.6359597444534302},{"id":"https://openalex.org/keywords/autonomy","display_name":"Autonomy","score":0.6140748858451843},{"id":"https://openalex.org/keywords/trace","display_name":"TRACE (psycholinguistics)","score":0.5910314321517944},{"id":"https://openalex.org/keywords/epistemology","display_name":"Epistemology","score":0.5731532573699951},{"id":"https://openalex.org/keywords/action","display_name":"Action (physics)","score":0.559165894985199},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5215941667556763},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5177609324455261},{"id":"https://openalex.org/keywords/philosophy-of-biology","display_name":"Philosophy of biology","score":0.471443772315979},{"id":"https://openalex.org/keywords/living-systems","display_name":"Living systems","score":0.4648538827896118},{"id":"https://openalex.org/keywords/cognitive-science","display_name":"Cognitive science","score":0.45292580127716064},{"id":"https://openalex.org/keywords/biological-organism","display_name":"Biological organism","score":0.44980350136756897},{"id":"https://openalex.org/keywords/philosophy-of-science","display_name":"Philosophy of science","score":0.4330296814441681},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4239901304244995},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.36735427379608154},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.2946058511734009},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.2746641933917999},{"id":"https://openalex.org/keywords/political-science","display_name":"Political science","score":0.13026750087738037},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1233101487159729},{"id":"https://openalex.org/keywords/philosophy","display_name":"Philosophy","score":0.11762017011642456},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.10715600848197937}],"concepts":[{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.8300849795341492},{"id":"https://openalex.org/C2780522230","wikidata":"https://www.wikidata.org/wiki/Q1140419","display_name":"Ambiguity","level":2,"score":0.6435053944587708},{"id":"https://openalex.org/C64357122","wikidata":"https://www.wikidata.org/wiki/Q1149766","display_name":"Causality (physics)","level":2,"score":0.6359597444534302},{"id":"https://openalex.org/C65414064","wikidata":"https://www.wikidata.org/wiki/Q484105","display_name":"Autonomy","level":2,"score":0.6140748858451843},{"id":"https://openalex.org/C75291252","wikidata":"https://www.wikidata.org/wiki/Q1315756","display_name":"TRACE (psycholinguistics)","level":2,"score":0.5910314321517944},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.5731532573699951},{"id":"https://openalex.org/C2780791683","wikidata":"https://www.wikidata.org/wiki/Q846785","display_name":"Action (physics)","level":2,"score":0.559165894985199},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5215941667556763},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5177609324455261},{"id":"https://openalex.org/C180182882","wikidata":"https://www.wikidata.org/wiki/Q1028964","display_name":"Philosophy of biology","level":3,"score":0.471443772315979},{"id":"https://openalex.org/C2776184637","wikidata":"https://www.wikidata.org/wiki/Q6506039","display_name":"Living systems","level":2,"score":0.4648538827896118},{"id":"https://openalex.org/C188147891","wikidata":"https://www.wikidata.org/wiki/Q147638","display_name":"Cognitive science","level":1,"score":0.45292580127716064},{"id":"https://openalex.org/C2992918937","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Biological organism","level":3,"score":0.44980350136756897},{"id":"https://openalex.org/C110099512","wikidata":"https://www.wikidata.org/wiki/Q59115","display_name":"Philosophy of science","level":2,"score":0.4330296814441681},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4239901304244995},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.36735427379608154},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.2946058511734009},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.2746641933917999},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.13026750087738037},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1233101487159729},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.11762017011642456},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.10715600848197937},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C2984787389","wikidata":"https://www.wikidata.org/wiki/Q4915000","display_name":"Biological materials","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","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":"D010684","descriptor_name":"Philosophy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010684","descriptor_name":"Philosophy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010684","descriptor_name":"Philosophy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":2,"locations":[{"id":"doi:10.1093/bib/bbp003","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbp003","pdf_url":"https://academic.oup.com/bib/article-pdf/10/4/462/837539/bbp003.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19276201","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19276201","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbp003","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbp003","pdf_url":"https://academic.oup.com/bib/article-pdf/10/4/462/837539/bbp003.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4699999988079071,"id":"https://metadata.un.org/sdg/12","display_name":"Responsible consumption and production"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2135752912.pdf","grobid_xml":"https://content.openalex.org/works/W2135752912.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W67623166","https://openalex.org/W139062680","https://openalex.org/W143373625","https://openalex.org/W199313025","https://openalex.org/W636632878","https://openalex.org/W643863419","https://openalex.org/W1495873555","https://openalex.org/W1506888295","https://openalex.org/W1509643880","https://openalex.org/W1515814298","https://openalex.org/W1551374748","https://openalex.org/W1557693421","https://openalex.org/W1557926810","https://openalex.org/W1562393358","https://openalex.org/W1571649231","https://openalex.org/W1581574738","https://openalex.org/W1606208442","https://openalex.org/W1629051378","https://openalex.org/W1729777349","https://openalex.org/W1751769270","https://openalex.org/W1765868291","https://openalex.org/W1934703699","https://openalex.org/W1938688953","https://openalex.org/W1974839532","https://openalex.org/W2003316767","https://openalex.org/W2031751756","https://openalex.org/W2031970520","https://openalex.org/W2035791902","https://openalex.org/W2043576402","https://openalex.org/W2049218516","https://openalex.org/W2074397232","https://openalex.org/W2105291362","https://openalex.org/W2148300948","https://openalex.org/W2148358401","https://openalex.org/W2150281203","https://openalex.org/W2160904769","https://openalex.org/W2167061037","https://openalex.org/W2251026370","https://openalex.org/W2487249630","https://openalex.org/W2487722770","https://openalex.org/W2501807371","https://openalex.org/W2610191465","https://openalex.org/W2798374369","https://openalex.org/W2885015663","https://openalex.org/W3139934447","https://openalex.org/W4236892381"],"related_works":["https://openalex.org/W2345318432","https://openalex.org/W2809030615","https://openalex.org/W1607576957","https://openalex.org/W2204280986","https://openalex.org/W2592523828","https://openalex.org/W2132876278","https://openalex.org/W2084818160","https://openalex.org/W134242285","https://openalex.org/W2073808674","https://openalex.org/W1925475638"],"abstract_inverted_index":{"The":[0,60,118],"question":[1],"of":[2,8,16,22,49,63,66,103,120,168,210,217,227],"whether":[3],"living":[4],"organisms":[5,23],"possess":[6,108],"autonomy":[7],"action":[9],"is":[10,24],"tied":[11],"up":[12],"with":[13],"the":[14,20,34,38,58,74,85,100,143,155,165,215,221],"nature":[15,21],"causal":[17,31],"efficacy.":[18],"Yet":[19],"such":[25,124],"that":[26,199],"they":[27,147],"frequently":[28],"defy":[29],"conventional":[30],"language.":[32],"Did":[33],"fig":[35],"wasp":[36],"select":[37],"fig,":[39],"or":[40,53,129],"vice":[41],"versa?":[42],"Is":[43],"this":[44,151],"an":[45,106,136],"epithelial":[46],"cell":[47],"because":[48,54],"its":[50,112],"genetic":[51],"structure,":[52],"it":[55],"develops":[56],"within":[57,88],"epithelium?":[59],"intimate":[61],"coupling":[62],"biological":[64,75,121,188,228],"levels":[65],"organisation":[67],"leads":[68],"developmental":[69,91],"systems":[70],"theory":[71],"to":[72,127,139,180,186,190],"deconstruct":[73],"organism":[76,107],"into":[77],"a":[78,89,191,203,208,224],"life-cycle":[79],"process":[80],"which":[81,146],"constitutes":[82],"itself":[83],"from":[84,111,174,177],"resources":[86],"available":[87],"complete":[90],"system.":[92],"This":[93],"radical":[94],"proposal":[95],"necessarily":[96],"raises":[97],"questions":[98,125],"regarding":[99],"ontological":[101,166],"status":[102,167],"organisms:":[104],"Does":[105],"existence":[109],"distinguishable":[110],"molecular":[113,178],"composition":[114],"and":[115,132,183,193,219],"social":[116],"environment?":[117],"ambiguity":[119],"causality":[122],"makes":[123],"difficult":[126],"answer":[128],"even":[130],"formulate,":[131],"computational":[133,159,200],"biology":[134],"has":[135],"important":[137],"role":[138,156,205],"play":[140],"in":[141,145,161,206,214],"operationalising":[142],"language":[144],"are":[148,172],"framed.":[149],"In":[150],"article":[152],"we":[153],"review":[154],"played":[157],"by":[158],"biomodels":[160],"shedding":[162],"light":[163],"on":[164],"organisms.":[169],"These":[170],"models":[171],"drawn":[173],"backgrounds":[175],"ranging":[176],"kinetics":[179],"niche":[181],"construction,":[182],"all":[184],"attempt":[185],"trace":[187],"processes":[189],"causal,":[192],"therefore":[194],"existent,":[195],"source.":[196],"We":[197],"conclude":[198],"biomodelling":[201],"plays":[202],"fertile":[204],"furnishing":[207],"proof":[209],"concept":[211],"for":[212,223],"conjectures":[213],"philosophy":[216],"biology,":[218],"suggests":[220],"need":[222],"process-based":[225],"ontology":[226],"systems.":[229]},"counts_by_year":[],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
