{"id":"https://openalex.org/W2170025661","doi":"https://doi.org/10.1093/bib/bbl036","title":"Resources for integrative systems biology: from data through databases to networks and dynamic system models","display_name":"Resources for integrative systems biology: from data through databases to networks and dynamic system models","publication_year":2006,"publication_date":"2006-10-13","ids":{"openalex":"https://openalex.org/W2170025661","doi":"https://doi.org/10.1093/bib/bbl036","mag":"2170025661","pmid":"https://pubmed.ncbi.nlm.nih.gov/17040977"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbl036","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbl036","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038799823","display_name":"Aylwin Ng","orcid":null},"institutions":[{"id":"https://openalex.org/I196064397","display_name":"Ludwig Cancer Research","ror":"https://ror.org/05923xh51","country_code":"BE","type":"nonprofit","lineage":["https://openalex.org/I196064397","https://openalex.org/I4210150094"]},{"id":"https://openalex.org/I4210106789","display_name":"Ludwig Cancer Research","ror":"https://ror.org/01e473h50","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I4210106789","https://openalex.org/I4210150094"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["BE","GB"],"is_corresponding":true,"raw_author_name":"Aylwin Ng","raw_affiliation_strings":["Bioinformatics and Systems Biology Group, Ludwig Institute for Cancer Research, University College London Branch, 91 Riding House Street, London W1W 7BS, UK"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology Group, Ludwig Institute for Cancer Research, University College London Branch, 91 Riding House Street, London W1W 7BS, UK","institution_ids":["https://openalex.org/I45129253","https://openalex.org/I196064397","https://openalex.org/I4210106789"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026008686","display_name":"Borisas Bursteinas","orcid":"https://orcid.org/0000-0002-0701-5518"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Borisas Bursteinas","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001140222","display_name":"Qiong Gao","orcid":"https://orcid.org/0000-0002-0406-1594"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Qiong Gao","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031687403","display_name":"Ewan Mollison","orcid":"https://orcid.org/0000-0001-7426-5931"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ewan Mollison","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5022425237","display_name":"Marketa Zvelebil","orcid":"https://orcid.org/0000-0001-8018-5591"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Marketa Zvelebil","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5038799823"],"corresponding_institution_ids":["https://openalex.org/I196064397","https://openalex.org/I4210106789","https://openalex.org/I45129253"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":4.2081,"has_fulltext":false,"cited_by_count":82,"citation_normalized_percentile":{"value":0.94776279,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"7","issue":"4","first_page":"318","last_page":"330"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9994999766349792,"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":0.9994999766349792,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994000196456909,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9986000061035156,"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/phenome","display_name":"Phenome","score":0.88828045129776},{"id":"https://openalex.org/keywords/interactome","display_name":"Interactome","score":0.8228292465209961},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.7506823539733887},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6285374164581299},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5979962944984436},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.5722076296806335},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.5299906134605408},{"id":"https://openalex.org/keywords/modelling-biological-systems","display_name":"Modelling biological systems","score":0.4481215476989746},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.35936635732650757},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.34035971760749817},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2575584053993225}],"concepts":[{"id":"https://openalex.org/C7952369","wikidata":"https://www.wikidata.org/wiki/Q844116","display_name":"Phenome","level":4,"score":0.88828045129776},{"id":"https://openalex.org/C9760119","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interactome","level":3,"score":0.8228292465209961},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.7506823539733887},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6285374164581299},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5979962944984436},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.5722076296806335},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.5299906134605408},{"id":"https://openalex.org/C137866125","wikidata":"https://www.wikidata.org/wiki/Q4299308","display_name":"Modelling biological systems","level":3,"score":0.4481215476989746},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.35936635732650757},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34035971760749817},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2575584053993225},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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":"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":"D003625","descriptor_name":"Data Collection","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003625","descriptor_name":"Data Collection","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003625","descriptor_name":"Data Collection","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003625","descriptor_name":"Data Collection","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D003625","descriptor_name":"Data Collection","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D003625","descriptor_name":"Data Collection","qualifier_ui":"Q000592","qualifier_name":"standards","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":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","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":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbl036","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbl036","pdf_url":null,"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:17040977","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17040977","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":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.41999998688697815}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":97,"referenced_works":["https://openalex.org/W74971858","https://openalex.org/W1486283310","https://openalex.org/W1495660511","https://openalex.org/W1499561015","https://openalex.org/W1520694472","https://openalex.org/W1526663103","https://openalex.org/W1544923801","https://openalex.org/W1644749979","https://openalex.org/W1683721845","https://openalex.org/W1884509322","https://openalex.org/W1964443249","https://openalex.org/W1967115261","https://openalex.org/W1967654665","https://openalex.org/W1969040600","https://openalex.org/W1969889522","https://openalex.org/W1971421925","https://openalex.org/W1971425971","https://openalex.org/W1973316812","https://openalex.org/W1977918192","https://openalex.org/W1979853788","https://openalex.org/W1982428412","https://openalex.org/W1988476709","https://openalex.org/W2006933206","https://openalex.org/W2018053002","https://openalex.org/W2018840791","https://openalex.org/W2020561965","https://openalex.org/W2021239799","https://openalex.org/W2021275596","https://openalex.org/W2037036397","https://openalex.org/W2042880070","https://openalex.org/W2044514479","https://openalex.org/W2046872827","https://openalex.org/W2052188398","https://openalex.org/W2055718828","https://openalex.org/W2062744504","https://openalex.org/W2063007776","https://openalex.org/W2063987069","https://openalex.org/W2065219357","https://openalex.org/W2070658593","https://openalex.org/W2070815798","https://openalex.org/W2082621456","https://openalex.org/W2083737836","https://openalex.org/W2084375915","https://openalex.org/W2084619201","https://openalex.org/W2088468751","https://openalex.org/W2094500750","https://openalex.org/W2098851705","https://openalex.org/W2100471807","https://openalex.org/W2107062718","https://openalex.org/W2108896820","https://openalex.org/W2111420033","https://openalex.org/W2112811019","https://openalex.org/W2113019448","https://openalex.org/W2117364474","https://openalex.org/W2119412782","https://openalex.org/W2120679339","https://openalex.org/W2123037718","https://openalex.org/W2123375975","https://openalex.org/W2123500593","https://openalex.org/W2126025430","https://openalex.org/W2130687290","https://openalex.org/W2130706354","https://openalex.org/W2132844342","https://openalex.org/W2134038772","https://openalex.org/W2137082708","https://openalex.org/W2137128504","https://openalex.org/W2137970956","https://openalex.org/W2141144953","https://openalex.org/W2142237411","https://openalex.org/W2143784594","https://openalex.org/W2143894094","https://openalex.org/W2145221987","https://openalex.org/W2145889895","https://openalex.org/W2147714160","https://openalex.org/W2149991291","https://openalex.org/W2150233912","https://openalex.org/W2150317682","https://openalex.org/W2151346683","https://openalex.org/W2152495216","https://openalex.org/W2152653671","https://openalex.org/W2153624566","https://openalex.org/W2155723007","https://openalex.org/W2156070536","https://openalex.org/W2158327292","https://openalex.org/W2158784643","https://openalex.org/W2160751597","https://openalex.org/W2161811833","https://openalex.org/W2166043581","https://openalex.org/W2166633151","https://openalex.org/W2168223461","https://openalex.org/W2169367285","https://openalex.org/W2171458571","https://openalex.org/W4233751197","https://openalex.org/W4245271255","https://openalex.org/W6637523683","https://openalex.org/W6666178826","https://openalex.org/W6685016951"],"related_works":["https://openalex.org/W4372359636","https://openalex.org/W2335922341","https://openalex.org/W2065615506","https://openalex.org/W2074027785","https://openalex.org/W4246474347","https://openalex.org/W4213038194","https://openalex.org/W2063905494","https://openalex.org/W4386563820","https://openalex.org/W2170025661","https://openalex.org/W631732704"],"abstract_inverted_index":{"In":[0,53],"systems":[1,69],"biology,":[2],"biologically":[3],"relevant":[4,67],"quantitative":[5],"modelling":[6],"of":[7,13,27,45,59,75],"physiological":[8],"processes":[9],"requires":[10],"the":[11,25,28,43,60,82],"integration":[12,80],"experimental":[14,46],"data":[15,47,79],"from":[16],"diverse":[17],"sources.":[18],"Recent":[19],"developments":[20],"in":[21,49],"high-throughput":[22],"methodologies":[23],"enable":[24],"analysis":[26],"transcriptome,":[29],"proteome,":[30],"interactome,":[31],"metabolome":[32],"and":[33,62,71,81],"phenome":[34],"on":[35],"a":[36,73],"previously":[37],"unprecedented":[38],"scale,":[39],"thus":[40],"contributing":[41],"to":[42,68,86],"deluge":[44],"held":[48],"numerous":[50],"public":[51],"databases.":[52],"this":[54],"review,":[55],"we":[56],"describe":[57],"some":[58],"databases":[61],"simulation":[63],"tools":[64],"that":[65],"are":[66],"biology":[70],"discuss":[72],"number":[74],"key":[76],"issues":[77],"affecting":[78],"challenges":[83],"these":[84],"pose":[85],"systems-level":[87],"research.":[88]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":11}],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2025-10-10T00:00:00"}
