{"id":"https://openalex.org/W2100481137","doi":"https://doi.org/10.2390/biecoll-jib-2007-80","title":"Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models","display_name":"Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models","publication_year":2008,"publication_date":"2008-01-01","ids":{"openalex":"https://openalex.org/W2100481137","doi":"https://doi.org/10.2390/biecoll-jib-2007-80","mag":"2100481137"},"language":"en","primary_location":{"id":"doi:10.2390/biecoll-jib-2007-80","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2007-80","pdf_url":null,"source":{"id":"https://openalex.org/S4306401670","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"},"type":"article","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.2390/biecoll-jib-2007-80","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087271600","display_name":"Allyson Lister","orcid":"https://orcid.org/0000-0002-7702-4495"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Lister, Allyson L.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109242321","display_name":"Matthew Pocock","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pocock, Matthew","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5089978830","display_name":"Anil Wipat","orcid":"https://orcid.org/0000-0001-7310-4191"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Wipat, Anil","raw_affiliation_strings":["Newcastle University"],"affiliations":[{"raw_affiliation_string":"Newcastle University","institution_ids":["https://openalex.org/I84884186"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5087271600"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.6733,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.69466141,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9975000023841858,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9975000023841858,"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":0.9954000115394592,"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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9912999868392944,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.9800169467926025},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8712663650512695},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.7825429439544678},{"id":"https://openalex.org/keywords/schema","display_name":"Schema (genetic algorithms)","score":0.557970404624939},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.554904580116272},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5535120964050293},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4643322229385376},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4179916977882385},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3238414525985718},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.2809198498725891},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.25099456310272217},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.20065617561340332},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.1563827395439148}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9800169467926025},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8712663650512695},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.7825429439544678},{"id":"https://openalex.org/C52146309","wikidata":"https://www.wikidata.org/wiki/Q7431116","display_name":"Schema (genetic algorithms)","level":2,"score":0.557970404624939},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.554904580116272},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5535120964050293},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4643322229385376},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4179916977882385},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3238414525985718},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.2809198498725891},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.25099456310272217},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.20065617561340332},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.1563827395439148},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.2390/biecoll-jib-2007-80","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2007-80","pdf_url":null,"source":{"id":"https://openalex.org/S4306401670","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.2390/biecoll-jib-2007-80","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2007-80","pdf_url":null,"source":{"id":"https://openalex.org/S4306401670","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":9,"referenced_works":["https://openalex.org/W1748928863","https://openalex.org/W1917591099","https://openalex.org/W1978465163","https://openalex.org/W1990890881","https://openalex.org/W2050355460","https://openalex.org/W2135290856","https://openalex.org/W2150908245","https://openalex.org/W2154829072","https://openalex.org/W2583688014"],"related_works":["https://openalex.org/W2963680560","https://openalex.org/W2751696165","https://openalex.org/W2006595428","https://openalex.org/W2146744007","https://openalex.org/W2127219350","https://openalex.org/W2128797622","https://openalex.org/W2103017472","https://openalex.org/W2020561965","https://openalex.org/W2125615370","https://openalex.org/W2795410052","https://openalex.org/W1576463881","https://openalex.org/W186706612","https://openalex.org/W2129659530","https://openalex.org/W1534442584","https://openalex.org/W2248224412","https://openalex.org/W2088247044","https://openalex.org/W2405036568","https://openalex.org/W2732790226","https://openalex.org/W2054616552","https://openalex.org/W2415442706"],"abstract_inverted_index":{"The":[0,65,166],"creation":[1],"of":[2,32,72,107,137,168,183],"quantitative,":[3],"simulatable,":[4],"Systems":[5,52],"Biology":[6,53],"Markup":[7],"Language":[8,91],"(SBML)":[9],"models":[10,174],"that":[11,23,95,102,151],"accurately":[12],"simulate":[13],"the":[14,28,46,51,57,69,108],"system":[15],"under":[16],"study":[17],"is":[18,79,157],"a":[19,88,104,142,176,180],"time-intensive":[20],"manual":[21],"process":[22],"requires":[24],"careful":[25],"checking.":[26,149,187],"Currently,":[27],"rules":[29],"and":[30,36,56,59,76,101,121,124,129,160,186],"constraints":[31,73],"model":[33,148,184],"creation,":[34],"curation,":[35],"annotation":[37],"are":[38,133],"distributed":[39],"over":[40,128],"at":[41],"least":[42],"three":[43,98],"separate":[44],"documents:":[45],"SBML":[47,131,173],"schema":[48],"document":[49,67],"(XSD),":[50],"Ontology":[54,90],"(SBO),":[55],"\u201cStructures":[58],"Facilities":[60],"for":[61,147,163,172],"Model":[62,114],"Definition\u201d":[63],"document.":[64],"latter":[66],"contains":[68,103],"richest":[70],"set":[71],"on":[74],"models,":[75],"yet":[77],"it":[78],"not":[80],"amenable":[81,145],"to":[82,155],"computational":[83,164],"processing.":[84],"We":[85],"have":[86],"developed":[87],"Web":[89],"(OWL)":[92],"knowledge":[93,171],"base":[94],"integrates":[96],"these":[97],"structure":[99],"documents,":[100],"representative":[105],"sample":[106],"information":[109],"contained":[110],"within":[111],"them.":[112],"This":[113],"Format":[115],"OWL":[116,138],"(MFO)":[117],"performs":[118],"both":[119],"structural":[120,170],"constraint":[122],"integration":[123,167],"can":[125],"be":[126],"reasoned":[127],"validated.":[130],"Models":[132],"represented":[134],"as":[135],"individuals":[136],"classes,":[139],"resulting":[140],"in":[141],"single":[143,177],"computationally":[144],"resource":[146,178],"Knowledge":[150],"was":[152],"only":[153],"accessible":[154],"humans":[156],"now":[158],"explicitly":[159],"directly":[161],"available":[162],"approaches.":[165],"all":[169],"into":[175],"creates":[179],"new":[181],"style":[182],"development":[185]},"counts_by_year":[{"year":2014,"cited_by_count":1}],"updated_date":"2025-11-06T06:51:31.235846","created_date":"2025-10-10T00:00:00"}
