{"id":"https://openalex.org/W2013011509","doi":"https://doi.org/10.1007/s00500-014-1467-6","title":"An integrative top-down and bottom-up qualitative model construction framework for exploration of biochemical systems","display_name":"An integrative top-down and bottom-up qualitative model construction framework for exploration of biochemical systems","publication_year":2014,"publication_date":"2014-09-29","ids":{"openalex":"https://openalex.org/W2013011509","doi":"https://doi.org/10.1007/s00500-014-1467-6","mag":"2013011509","pmid":"https://pubmed.ncbi.nlm.nih.gov/25999782"},"language":"en","primary_location":{"id":"doi:10.1007/s00500-014-1467-6","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s00500-014-1467-6","pdf_url":"https://link.springer.com/content/pdf/10.1007/s00500-014-1467-6.pdf","source":{"id":"https://openalex.org/S65753830","display_name":"Soft Computing","issn_l":"1432-7643","issn":["1432-7643","1433-7479"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"Soft Computing","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s00500-014-1467-6.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101911513","display_name":"Zujian Wu","orcid":"https://orcid.org/0000-0001-5937-0311"},"institutions":[{"id":"https://openalex.org/I159948400","display_name":"Jinan University","ror":"https://ror.org/02xe5ns62","country_code":"CN","type":"education","lineage":["https://openalex.org/I159948400"]},{"id":"https://openalex.org/I195460627","display_name":"University of Aberdeen","ror":"https://ror.org/016476m91","country_code":"GB","type":"education","lineage":["https://openalex.org/I195460627"]}],"countries":["CN","GB"],"is_corresponding":false,"raw_author_name":"Zujian Wu","raw_affiliation_strings":["College of Information Science and Technology, Jinan University, Guangzhou, 510632 People's Republic of China ; School of Natural and Computing Sciences, University of Aberdeen, Aberdeen, AB24 3UE Scotland, UK","College of Information Science and Technology, Jinan University, Guangzhou, 510632, People\u2019s Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Science and Technology, Jinan University, Guangzhou, 510632 People's Republic of China ; School of Natural and Computing Sciences, University of Aberdeen, Aberdeen, AB24 3UE Scotland, UK","institution_ids":["https://openalex.org/I195460627"]},{"raw_affiliation_string":"College of Information Science and Technology, Jinan University, Guangzhou, 510632, People\u2019s Republic of China","institution_ids":["https://openalex.org/I159948400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081644845","display_name":"Wei Pang","orcid":"https://orcid.org/0000-0002-1761-6659"},"institutions":[{"id":"https://openalex.org/I195460627","display_name":"University of Aberdeen","ror":"https://ror.org/016476m91","country_code":"GB","type":"education","lineage":["https://openalex.org/I195460627"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Wei Pang","raw_affiliation_strings":["School of Natural and Computing Sciences, University of Aberdeen, Aberdeen, AB24 3UE Scotland, UK","School of Natural and Computing Sciences, University of Aberdeen, Aberdeen, AB24 3UE, Scotland, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Natural and Computing Sciences, University of Aberdeen, Aberdeen, AB24 3UE Scotland, UK","institution_ids":["https://openalex.org/I195460627"]},{"raw_affiliation_string":"School of Natural and Computing Sciences, University of Aberdeen, Aberdeen, AB24 3UE, Scotland, UK","institution_ids":["https://openalex.org/I195460627"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082375941","display_name":"George M. Coghill","orcid":"https://orcid.org/0000-0002-2047-8277"},"institutions":[{"id":"https://openalex.org/I195460627","display_name":"University of Aberdeen","ror":"https://ror.org/016476m91","country_code":"GB","type":"education","lineage":["https://openalex.org/I195460627"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"George M. Coghill","raw_affiliation_strings":["School of Natural and Computing Sciences, University of Aberdeen, Aberdeen, AB24 3UE Scotland, UK","School of Natural and Computing Sciences, University of Aberdeen, Aberdeen, AB24 3UE, Scotland, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Natural and Computing Sciences, University of Aberdeen, Aberdeen, AB24 3UE Scotland, UK","institution_ids":["https://openalex.org/I195460627"]},{"raw_affiliation_string":"School of Natural and Computing Sciences, University of Aberdeen, Aberdeen, AB24 3UE, Scotland, UK","institution_ids":["https://openalex.org/I195460627"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5082375941"],"corresponding_institution_ids":["https://openalex.org/I195460627"],"apc_list":{"value":3190,"currency":"USD","value_usd":3190},"apc_paid":{"value":3190,"currency":"USD","value_usd":3190},"fwci":2.04,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.86435031,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"19","issue":"6","first_page":"1595","last_page":"1610"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11450","display_name":"Model-Driven Software Engineering Techniques","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/1712","display_name":"Software"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11450","display_name":"Model-Driven Software Engineering Techniques","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/1712","display_name":"Software"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9890999794006348,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.988099992275238,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/top-down-and-bottom-up-design","display_name":"Top-down and bottom-up design","score":0.8622700572013855},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.7218855023384094},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6708778142929077},{"id":"https://openalex.org/keywords/simulated-annealing","display_name":"Simulated annealing","score":0.5075063109397888},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4931130111217499},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.42287445068359375},{"id":"https://openalex.org/keywords/biochemical-engineering","display_name":"Biochemical engineering","score":0.3203011751174927},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.21255603432655334},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1623418927192688},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.1324566900730133},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08805534243583679}],"concepts":[{"id":"https://openalex.org/C135798126","wikidata":"https://www.wikidata.org/wiki/Q2167279","display_name":"Top-down and bottom-up design","level":2,"score":0.8622700572013855},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.7218855023384094},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6708778142929077},{"id":"https://openalex.org/C126980161","wikidata":"https://www.wikidata.org/wiki/Q863783","display_name":"Simulated annealing","level":2,"score":0.5075063109397888},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4931130111217499},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.42287445068359375},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.3203011751174927},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.21255603432655334},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1623418927192688},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.1324566900730133},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08805534243583679}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1007/s00500-014-1467-6","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s00500-014-1467-6","pdf_url":"https://link.springer.com/content/pdf/10.1007/s00500-014-1467-6.pdf","source":{"id":"https://openalex.org/S65753830","display_name":"Soft Computing","issn_l":"1432-7643","issn":["1432-7643","1433-7479"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"Soft Computing","raw_type":"journal-article"},{"id":"pmid:25999782","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25999782","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":"Soft computing","raw_type":"Journal Article"},{"id":"pmh:oai:aura.abdn.ac.uk:2164/4531","is_oa":true,"landing_page_url":"http://hdl.handle.net/2164/4531","pdf_url":"http://hdl.handle.net/2164/4531","source":{"id":"https://openalex.org/S4306400966","display_name":"Aberdeen University Research Archive (Aberdeen University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I195460627","host_organization_name":"University of Aberdeen","host_organization_lineage":["https://openalex.org/I195460627"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4433352","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4433352","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":"Soft comput","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1007/s00500-014-1467-6","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s00500-014-1467-6","pdf_url":"https://link.springer.com/content/pdf/10.1007/s00500-014-1467-6.pdf","source":{"id":"https://openalex.org/S65753830","display_name":"Soft Computing","issn_l":"1432-7643","issn":["1432-7643","1433-7479"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"Soft Computing","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3127346458","display_name":null,"funder_award_id":"BB/F00513X/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G5333611717","display_name":"Combinatorial responses of fungal pathogens to their human hosts: an Integrative Systems Biology approach","funder_award_id":"BB/F00513X/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2013011509.pdf","grobid_xml":"https://content.openalex.org/works/W2013011509.grobid-xml"},"referenced_works_count":58,"referenced_works":["https://openalex.org/W89094634","https://openalex.org/W118377870","https://openalex.org/W139884376","https://openalex.org/W154784516","https://openalex.org/W1496347746","https://openalex.org/W1508882373","https://openalex.org/W1530558387","https://openalex.org/W1551342597","https://openalex.org/W1576660662","https://openalex.org/W1587845087","https://openalex.org/W1594089636","https://openalex.org/W1840916145","https://openalex.org/W1896349060","https://openalex.org/W1963920034","https://openalex.org/W1967490380","https://openalex.org/W1976298319","https://openalex.org/W1979666113","https://openalex.org/W1983181251","https://openalex.org/W1994536159","https://openalex.org/W1996109622","https://openalex.org/W1997893082","https://openalex.org/W2001620484","https://openalex.org/W2004407704","https://openalex.org/W2013522363","https://openalex.org/W2013923357","https://openalex.org/W2020546096","https://openalex.org/W2021123893","https://openalex.org/W2024060531","https://openalex.org/W2028544289","https://openalex.org/W2029415078","https://openalex.org/W2033271549","https://openalex.org/W2056760934","https://openalex.org/W2062262077","https://openalex.org/W2069512297","https://openalex.org/W2078356881","https://openalex.org/W2085075090","https://openalex.org/W2086936470","https://openalex.org/W2090628795","https://openalex.org/W2090985740","https://openalex.org/W2103843797","https://openalex.org/W2107273065","https://openalex.org/W2114702809","https://openalex.org/W2124709868","https://openalex.org/W2126449841","https://openalex.org/W2127366503","https://openalex.org/W2136627244","https://openalex.org/W2137428110","https://openalex.org/W2139439234","https://openalex.org/W2148357359","https://openalex.org/W2156154713","https://openalex.org/W2165603655","https://openalex.org/W2169756968","https://openalex.org/W2178215137","https://openalex.org/W2912848477","https://openalex.org/W2913183991","https://openalex.org/W3003431618","https://openalex.org/W3023175778","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W1543048115","https://openalex.org/W2378076731","https://openalex.org/W4286888643","https://openalex.org/W3210795196","https://openalex.org/W2088988140","https://openalex.org/W2103019253","https://openalex.org/W22958017","https://openalex.org/W2951529875","https://openalex.org/W2391453316","https://openalex.org/W2297768894"],"abstract_inverted_index":{"Computational":[0],"modelling":[1,48,68,81,94,117],"of":[2,32,54,133,169,178],"biochemical":[3,59,126,136],"systems":[4],"based":[5,87],"on":[6,88],"top-down":[7,45,67,93,98],"and":[8,35,46,73,99,156],"bottom-up":[9,47,80,100],"approaches":[10,101],"has":[11],"been":[12],"well":[13],"studied":[14],"over":[15],"the":[16,66,79,92,97,109,123,134,179],"last":[17],"decade.":[18],"In":[19,129],"this":[20],"research,":[21],"after":[22],"illustrating":[23],"how":[24],"to":[25,65,70,83,121],"generate":[26],"atomic":[27],"components":[28],"by":[29,141,167],"a":[30,175],"set":[31],"given":[33],"reactants":[34,57,127,132,144,155],"two":[36],"user":[37],"pre-defined":[38],"component":[39],"patterns,":[40],"we":[41],"propose":[42],"an":[43],"integrative":[44],"approach":[49,69,82,118],"for":[50,108,162],"stepwise":[51,103],"qualitative":[52],"exploration":[53],"interactions":[55,86],"among":[56,125],"in":[58,78,145,174],"systems.":[60],"Evolution":[61],"strategy":[62],"is":[63,76,119],"applied":[64],"compose":[71],"models,":[72],"simulated":[74],"annealing":[75],"employed":[77],"explore":[84],"potential":[85],"models":[89,152],"constructed":[90],"from":[91],"process.":[95],"Both":[96],"support":[102],"modular":[104],"addition":[105],"or":[106],"subtraction":[107],"model":[110],"evolution.":[111],"Experimental":[112],"results":[113],"indicate":[114],"that":[115],"our":[116],"feasible":[120],"learn":[122],"relationships":[124],"qualitatively.":[128],"addition,":[130],"hidden":[131],"target":[135],"system":[137],"can":[138,159],"be":[139,160],"obtained":[140],"generating":[142],"complex":[143],"corresponding":[146],"composed":[147],"models.":[148],"Moreover,":[149],"qualitatively":[150],"learned":[151],"with":[153],"inferred":[154],"alternative":[157],"topologies":[158],"used":[161],"further":[163],"web-lab":[164],"experimental":[165],"investigations":[166],"biologists":[168],"interest,":[170],"which":[171],"may":[172],"result":[173],"better":[176],"understanding":[177],"system.":[180]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
