{"id":"https://openalex.org/W3166024157","doi":"https://doi.org/10.1093/bioinformatics/btab622","title":"DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations","display_name":"DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations","publication_year":2021,"publication_date":"2021-09-02","ids":{"openalex":"https://openalex.org/W3166024157","doi":"https://doi.org/10.1093/bioinformatics/btab622","mag":"3166024157"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab622","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab622","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/21/3974/41091585/btab622.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"preprint","indexed_in":["arxiv","crossref","datacite","doaj"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/21/3974/41091585/btab622.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074416067","display_name":"Almut Heinken","orcid":"https://orcid.org/0000-0001-6938-8072"},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Almut Heinken","raw_affiliation_strings":["Ryan Institute, National University of Galway , H91 TK33 Galway, Ireland","School of Medicine, National University of Galway , H91 TK33 Galway, Ireland","School of Medicine, National University of Galway, H91 TK33 Galway, Ireland"],"affiliations":[{"raw_affiliation_string":"Ryan Institute, National University of Galway , H91 TK33 Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]},{"raw_affiliation_string":"School of Medicine, National University of Galway , H91 TK33 Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]},{"raw_affiliation_string":"School of Medicine, National University of Galway, H91 TK33 Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052638885","display_name":"Stefan\u00eda Magn\u00fasd\u00f3ttir","orcid":"https://orcid.org/0000-0001-6506-8696"},"institutions":[{"id":"https://openalex.org/I3018483916","display_name":"University Medical Center Utrecht","ror":"https://ror.org/0575yy874","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I3018483916"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Stefan\u00eda Magn\u00fasd\u00f3ttir","raw_affiliation_strings":["Center for Molecular Medicine, University Medical Center Utrecht , 3584 CX Utrecht, The Netherlands","\u2021Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands"],"affiliations":[{"raw_affiliation_string":"Center for Molecular Medicine, University Medical Center Utrecht , 3584 CX Utrecht, The Netherlands","institution_ids":["https://openalex.org/I3018483916"]},{"raw_affiliation_string":"\u2021Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands","institution_ids":["https://openalex.org/I3018483916"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069362994","display_name":"Ronan M. T. Fleming","orcid":"https://orcid.org/0000-0001-5346-9812"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]},{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]},{"id":"https://openalex.org/I4210133171","display_name":"Centre for Human Drug Research","ror":"https://ror.org/044hshx49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I4210133171"]}],"countries":["IE","NL"],"is_corresponding":false,"raw_author_name":"Ronan M T Fleming","raw_affiliation_strings":["Leiden Academic Centre for Drug Research, Leiden University , 2333 CC Leiden, The Netherlands","School of Medicine, National University of Galway , H91 TK33 Galway, Ireland","Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands","School of Medicine, National University of Galway, H91 TK33 Galway, Ireland"],"affiliations":[{"raw_affiliation_string":"Leiden Academic Centre for Drug Research, Leiden University , 2333 CC Leiden, The Netherlands","institution_ids":["https://openalex.org/I4210133171","https://openalex.org/I121797337"]},{"raw_affiliation_string":"School of Medicine, National University of Galway , H91 TK33 Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]},{"raw_affiliation_string":"Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands","institution_ids":["https://openalex.org/I4210133171","https://openalex.org/I121797337"]},{"raw_affiliation_string":"School of Medicine, National University of Galway, H91 TK33 Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074725115","display_name":"Ines Thiele","orcid":"https://orcid.org/0000-0002-8071-7110"},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]},{"id":"https://openalex.org/I27577105","display_name":"University College Cork","ror":"https://ror.org/03265fv13","country_code":"IE","type":"education","lineage":["https://openalex.org/I27577105"]},{"id":"https://openalex.org/I4210141138","display_name":"APC Microbiome Institute","ror":"https://ror.org/03f2ct267","country_code":"IE","type":"facility","lineage":["https://openalex.org/I4210141138"]}],"countries":["IE"],"is_corresponding":true,"raw_author_name":"Ines Thiele","raw_affiliation_strings":["APC Microbiome Ireland, University College Cork , T12 K8AF Cork, Ireland","Division of Microbiology, National University of Galway , H91 TK33 Galway, Ireland","Ryan Institute, National University of Galway , H91 TK33 Galway, Ireland","School of Medicine, National University of Galway , H91 TK33 Galway, Ireland","National University of Ireland, Galway#TAB#"],"affiliations":[{"raw_affiliation_string":"APC Microbiome Ireland, University College Cork , T12 K8AF Cork, Ireland","institution_ids":["https://openalex.org/I4210141138","https://openalex.org/I27577105"]},{"raw_affiliation_string":"Division of Microbiology, National University of Galway , H91 TK33 Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]},{"raw_affiliation_string":"Ryan Institute, National University of Galway , H91 TK33 Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]},{"raw_affiliation_string":"School of Medicine, National University of Galway , H91 TK33 Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]},{"raw_affiliation_string":"National University of Ireland, Galway#TAB#","institution_ids":["https://openalex.org/I188760350"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5074725115"],"corresponding_institution_ids":["https://openalex.org/I188760350","https://openalex.org/I27577105","https://openalex.org/I4210141138"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.244,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.52476237,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"37","issue":"21","first_page":"3974","last_page":"3975"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","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/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9886000156402588,"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/toolbox","display_name":"Toolbox","score":0.8910436630249023},{"id":"https://openalex.org/keywords/data-curation","display_name":"Data curation","score":0.6842836141586304},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6530694365501404},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6454923152923584},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.5261625647544861},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.5183649659156799},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37217092514038086},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2919254004955292},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2073320746421814},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19397595524787903},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.16634488105773926},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09618940949440002},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.07324844598770142},{"id":"https://openalex.org/keywords/cartography","display_name":"Cartography","score":0.057869166135787964}],"concepts":[{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.8910436630249023},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.6842836141586304},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6530694365501404},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6454923152923584},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.5261625647544861},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.5183649659156799},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37217092514038086},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2919254004955292},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2073320746421814},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19397595524787903},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.16634488105773926},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09618940949440002},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.07324844598770142},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.057869166135787964},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/btab622","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab622","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/21/3974/41091585/btab622.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:arXiv.org:2106.06638","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2106.06638","pdf_url":"https://arxiv.org/pdf/2106.06638","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:europepmc.org:7463234","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8570805","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8570805","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8570805","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":"Bioinformatics","raw_type":"Text"},{"id":"doi:10.48550/arxiv.2106.06638","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2106.06638","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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"},{"id":"mag:3166024157","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab622","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab622","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/21/3974/41091585/btab622.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1087416387","display_name":null,"funder_award_id":"1U19AG063744-01","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G160496021","display_name":null,"funder_award_id":"RF1AG058942","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G160596578","display_name":"Predicting the effects of gut microbiota and diet on an individual\u2019s drug response and safety","funder_award_id":"757922","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G238180650","display_name":null,"funder_award_id":"1RF1AG058942","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G3719789328","display_name":null,"funder_award_id":"1RF1AG058942-01","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G4956428346","display_name":null,"funder_award_id":"Horizon 2020 research and innovatio","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5036817778","display_name":null,"funder_award_id":"European Union's Horizon 2020 research and innov","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5679185021","display_name":null,"funder_award_id":"1U19AG063744","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G7223442655","display_name":null,"funder_award_id":"U19AG063744","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G7842005466","display_name":null,"funder_award_id":"Horizon 2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8633428685","display_name":null,"funder_award_id":"European Union's Horizon 2020 research and innovat","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320337337","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11"},{"id":"https://openalex.org/F4320338335","display_name":"H2020 European Research Council","ror":"https://ror.org/0472cxd90"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3166024157.pdf","grobid_xml":"https://content.openalex.org/works/W3166024157.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W2085993965","https://openalex.org/W2093666160","https://openalex.org/W2100084634","https://openalex.org/W2559597060","https://openalex.org/W2762019694","https://openalex.org/W2859249641","https://openalex.org/W2950173838","https://openalex.org/W3090689814","https://openalex.org/W3100696020"],"related_works":["https://openalex.org/W3198506764","https://openalex.org/W2146486983","https://openalex.org/W2069114060","https://openalex.org/W2983485154","https://openalex.org/W2516918425","https://openalex.org/W1855042121","https://openalex.org/W2100895919","https://openalex.org/W2613654439","https://openalex.org/W2790540516","https://openalex.org/W1947111251","https://openalex.org/W2409416636","https://openalex.org/W2187259484","https://openalex.org/W1905004247","https://openalex.org/W2969926962","https://openalex.org/W2789127487","https://openalex.org/W2133818367","https://openalex.org/W1967190771","https://openalex.org/W2941035732","https://openalex.org/W3207153379","https://openalex.org/W2164209763"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"Manual":[2],"curation":[3,12],"of":[4,48,50,71],"genome-scale":[5,52],"reconstructions":[6],"is":[7],"laborious,":[8],"yet":[9],"existing":[10],"automated":[11],"tools":[13],"do":[14],"not":[15],"typically":[16],"take":[17],"species-specific":[18],"experimental":[19,67],"and":[20,37,69,80,83],"curated":[21],"genomic":[22],"data":[23,68,93],"into":[24],"account.":[25],"Results":[26],"We":[27],"developed":[28],"Data-drivEn":[29],"METabolic":[30],"nEtwork":[31],"Refinement":[32],"(DEMETER),":[33],"a":[34],"Constraint-Based":[35],"Reconstruction":[36],"Analysis":[38],"(COBRA)":[39],"Toolbox":[40],"extension,":[41],"which":[42],"enables":[43],"the":[44,58,62],"efficient,":[45],"simultaneous":[46],"refinement":[47,70],"thousands":[49],"draft":[51],"reconstructions,":[53],"while":[54],"ensuring":[55],"adherence":[56],"to":[57],"quality":[59],"standards":[60],"in":[61],"field,":[63],"agreement":[64],"with":[65],"available":[66,87,95],"pathways":[72],"based":[73],"on":[74],"manually":[75],"refined":[76],"genome":[77],"annotations.":[78],"Availability":[79],"implementation":[81],"DEMETER":[82],"tutorials":[84],"are":[85,94],"freely":[86],"at":[88,96],"https://github.com/opencobra.":[89],"Supplementary":[90,92],"information":[91],"Bioinformatics":[97],"online.":[98]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
