{"id":"https://openalex.org/W2111852359","doi":"https://doi.org/10.1093/database/bav001","title":"EcoliNet: a database of cofunctional gene network for Escherichia coli","display_name":"EcoliNet: a database of cofunctional gene network for Escherichia coli","publication_year":2015,"publication_date":"2015-01-01","ids":{"openalex":"https://openalex.org/W2111852359","doi":"https://doi.org/10.1093/database/bav001","mag":"2111852359","pmid":"https://pubmed.ncbi.nlm.nih.gov/25650278"},"language":"en","primary_location":{"id":"doi:10.1093/database/bav001","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bav001","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bav001/7298509/bav001.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bav001/7298509/bav001.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050657463","display_name":"Hanhae Kim","orcid":null},"institutions":[{"id":"https://openalex.org/I193775966","display_name":"Yonsei University","ror":"https://ror.org/01wjejq96","country_code":"KR","type":"education","lineage":["https://openalex.org/I193775966"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Hanhae Kim","raw_affiliation_strings":["Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea"],"affiliations":[{"raw_affiliation_string":"Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea","institution_ids":["https://openalex.org/I193775966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075624025","display_name":"Jung Eun Shim","orcid":"https://orcid.org/0000-0001-6341-9923"},"institutions":[{"id":"https://openalex.org/I193775966","display_name":"Yonsei University","ror":"https://ror.org/01wjejq96","country_code":"KR","type":"education","lineage":["https://openalex.org/I193775966"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Jung Eun Shim","raw_affiliation_strings":["Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea"],"affiliations":[{"raw_affiliation_string":"Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea","institution_ids":["https://openalex.org/I193775966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049171920","display_name":"Junha Shin","orcid":"https://orcid.org/0000-0003-3175-3446"},"institutions":[{"id":"https://openalex.org/I193775966","display_name":"Yonsei University","ror":"https://ror.org/01wjejq96","country_code":"KR","type":"education","lineage":["https://openalex.org/I193775966"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Junha Shin","raw_affiliation_strings":["Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea"],"affiliations":[{"raw_affiliation_string":"Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea","institution_ids":["https://openalex.org/I193775966"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035867403","display_name":"Insuk Lee","orcid":"https://orcid.org/0000-0003-3146-6180"},"institutions":[{"id":"https://openalex.org/I193775966","display_name":"Yonsei University","ror":"https://ror.org/01wjejq96","country_code":"KR","type":"education","lineage":["https://openalex.org/I193775966"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Insuk Lee","raw_affiliation_strings":["Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea"],"affiliations":[{"raw_affiliation_string":"Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea","institution_ids":["https://openalex.org/I193775966"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5050657463"],"corresponding_institution_ids":["https://openalex.org/I193775966"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":1.8109,"has_fulltext":true,"cited_by_count":42,"citation_normalized_percentile":{"value":0.85097783,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"2015","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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":0.9980000257492065,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9918000102043152,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6395760178565979},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6163040995597839},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6022592186927795},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5884379148483276},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.5737971067428589},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5594639778137207},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5135276913642883},{"id":"https://openalex.org/keywords/model-organism","display_name":"Model organism","score":0.4962504506111145},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.45515507459640503},{"id":"https://openalex.org/keywords/gene-prediction","display_name":"Gene prediction","score":0.45004802942276},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4356972873210907},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.42868179082870483},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.37816572189331055},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.20926666259765625}],"concepts":[{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6395760178565979},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6163040995597839},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6022592186927795},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5884379148483276},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.5737971067428589},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5594639778137207},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5135276913642883},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.4962504506111145},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.45515507459640503},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.45004802942276},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4356972873210907},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.42868179082870483},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.37816572189331055},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.20926666259765625},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/database/bav001","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bav001","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bav001/7298509/bav001.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},{"id":"pmid:25650278","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25650278","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:europepmc.org:3302229","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4314589","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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/bav001","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bav001","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bav001/7298509/bav001.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4699999988079071,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G5017536821","display_name":null,"funder_award_id":"2012M3A9C7050151","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G5423939921","display_name":null,"funder_award_id":"2012M3A9C","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G6320152228","display_name":null,"funder_award_id":"2010-0017649","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G7459535004","display_name":null,"funder_award_id":"2012M3A9B4028641","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2111852359.pdf","grobid_xml":"https://content.openalex.org/works/W2111852359.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1566952502","https://openalex.org/W1980578041","https://openalex.org/W1981933378","https://openalex.org/W1995117714","https://openalex.org/W2003516452","https://openalex.org/W2007174731","https://openalex.org/W2010577059","https://openalex.org/W2018756605","https://openalex.org/W2031418322","https://openalex.org/W2037442572","https://openalex.org/W2043377651","https://openalex.org/W2046618236","https://openalex.org/W2048593866","https://openalex.org/W2057885377","https://openalex.org/W2074755764","https://openalex.org/W2076469310","https://openalex.org/W2095867585","https://openalex.org/W2105924489","https://openalex.org/W2107249189","https://openalex.org/W2107424557","https://openalex.org/W2107644675","https://openalex.org/W2107717979","https://openalex.org/W2108102049","https://openalex.org/W2109138480","https://openalex.org/W2118258530","https://openalex.org/W2126991359","https://openalex.org/W2127596034","https://openalex.org/W2128601422","https://openalex.org/W2130687290","https://openalex.org/W2137012036","https://openalex.org/W2145000359","https://openalex.org/W2165253681","https://openalex.org/W2170806980","https://openalex.org/W4230770774","https://openalex.org/W4240852056","https://openalex.org/W4252706339","https://openalex.org/W6645995274"],"related_works":["https://openalex.org/W4223896405","https://openalex.org/W2059629050","https://openalex.org/W2258998699","https://openalex.org/W3013644380","https://openalex.org/W2074740504","https://openalex.org/W1996935079","https://openalex.org/W3210243923","https://openalex.org/W2145833061","https://openalex.org/W4290380913","https://openalex.org/W1998405066"],"abstract_inverted_index":{"During":[0],"the":[1,67,89,102,108,113,131],"past":[2],"several":[3],"decades,":[4],"Escherichia":[5],"coli":[6,43,69,115],"has":[7,71,96],"been":[8,24],"a":[9,58,84,120,161,170,188,194],"treasure":[10],"chest":[11],"for":[12,107,142,160,193,209],"molecular":[13,16,61],"biology.":[14,52],"The":[15],"mechanisms":[17],"of":[18,60,66,92,104,112,122,130,164,206],"many":[19],"fundamental":[20],"cellular":[21],"processes":[22],"have":[23,118,168],"discovered":[25],"through":[26],"research":[27,34],"on":[28,37],"this":[29],"bacterium.":[30],"Although":[31],"much":[32],"basic":[33],"now":[35],"focuses":[36],"more":[38,63],"complex":[39],"model":[40],"organisms,":[41],"E.":[42,68,114],"still":[44],"remains":[45],"important":[46],"in":[47,98,155,187],"metabolic":[48],"engineering":[49],"and":[50],"synthetic":[51],"Despite":[53],"its":[54],"long":[55],"history":[56],"as":[57,213],"subject":[59],"investigation,":[62],"than":[64],"one-third":[65],"genome":[70,128],"no":[72],"pathway":[73,105,189],"annotation":[74,106],"supported":[75],"by":[76],"either":[77],"experimental":[78],"evidence":[79],"or":[80,190],"manual":[81],"curation.":[82],"Recently,":[83],"network-assisted":[85],"genetics":[86],"approach":[87],"to":[88,182],"efficient":[90],"identification":[91],"novel":[93,157,184,191],"gene":[94,124,207],"functions":[95,192],"increased":[97],"popularity.":[99],"To":[100],"accelerate":[101],"speed":[103],"remaining":[109],"uncharacterized":[110],"part":[111],"genome,":[116],"we":[117],"constructed":[119],"database":[121],"cofunctional":[123,198],"network":[125,178],"with":[126],"near-complete":[127],"coverage":[129],"organism,":[132],"dubbed":[133],"EcoliNet.":[134],"We":[135,167],"find":[136],"that":[137,150],"EcoliNet":[138,181],"is":[139],"highly":[140],"predictive":[141],"diverse":[143],"bacterial":[144,165,211],"phenotypes,":[145],"including":[146],"antibiotic":[147],"response,":[148],"indicating":[149],"it":[151],"will":[152],"be":[153,201],"useful":[154],"prioritizing":[156],"candidate":[158],"genes":[159,185],"wide":[162],"spectrum":[163],"phenotypes.":[166],"implemented":[169],"web":[171],"server":[172],"where":[173],"biologists":[174],"can":[175,200],"easily":[176],"run":[177],"algorithms":[179],"over":[180],"predict":[183],"involved":[186],"gene.":[195],"All":[196],"integrated":[197],"associations":[199],"downloaded,":[202],"enabling":[203],"orthology-based":[204],"reconstruction":[205],"networks":[208],"other":[210],"species":[212],"well.":[214],"Database":[215],"URL:":[216],"http://www.inetbio.org/ecolinet.":[217]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":7},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
