{"id":"https://openalex.org/W3198506764","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":"2021-11-05","ids":{"openalex":"https://openalex.org/W3198506764","doi":"https://doi.org/10.1093/bioinformatics/btab622","mag":"3198506764","pmid":"https://pubmed.ncbi.nlm.nih.gov/34473240"},"language":"en","primary_location":{"id":"pmid:34473240","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34473240","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":"Bioinformatics (Oxford, England)","raw_type":null},"type":"article","indexed_in":["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/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":["School of Medicine, 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","Ryan Institute, National University of Galway , H91 TK33 Galway, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Medicine, 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":"Ryan Institute, 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","Center for Molecular Medicine, University Medical Center Utrecht , 3584 CX Utrecht, The Netherlands"],"raw_orcid":null,"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":"Center for Molecular Medicine, University Medical Center Utrecht , 3584 CX 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":["School of Medicine, National University of Galway, H91 TK33 Galway, Ireland","Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands","Leiden Academic Centre for Drug Research, Leiden University , 2333 CC Leiden, The Netherlands","School of Medicine, National University of Galway , H91 TK33 Galway, Ireland"],"raw_orcid":null,"affiliations":[{"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":"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":["School of Medicine, National University of Galway, H91 TK33 Galway, Ireland","Ryan Institute, National University of Galway, H91 TK33 Galway, Ireland","Division of Microbiology, National University of Galway, H91 TK33 Galway, Ireland","APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland","Ryan Institute, National University of Galway , H91 TK33 Galway, Ireland","APC Microbiome Ireland, University College Cork , T12 K8AF Cork, Ireland","School of Medicine, National University of Galway , H91 TK33 Galway, Ireland","Division of Microbiology, National University of Galway , H91 TK33 Galway, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Medicine, 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":"Division of Microbiology, National University of Galway, H91 TK33 Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]},{"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":"Ryan Institute, National University of Galway , H91 TK33 Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]},{"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":"School of Medicine, National University of Galway , H91 TK33 Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]},{"raw_affiliation_string":"Division of Microbiology, National University of Galway , H91 TK33 Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5074725115"],"corresponding_institution_ids":["https://openalex.org/I188760350","https://openalex.org/I27577105","https://openalex.org/I4210141138"],"apc_list":null,"apc_paid":null,"fwci":1.8239,"has_fulltext":true,"cited_by_count":33,"citation_normalized_percentile":{"value":0.85977495,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":99},"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9890999794006348,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.8597129583358765},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7314671277999878},{"id":"https://openalex.org/keywords/data-curation","display_name":"Data curation","score":0.6436865329742432},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.574089765548706},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.4878254234790802},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.47744232416152954},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40745246410369873},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3745886981487274},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16226187348365784},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1533014178276062},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1510954201221466},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.06606030464172363}],"concepts":[{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.8597129583358765},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7314671277999878},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.6436865329742432},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.574089765548706},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4878254234790802},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.47744232416152954},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40745246410369873},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3745886981487274},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16226187348365784},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1533014178276062},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1510954201221466},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.06606030464172363},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":1,"locations":[{"id":"pmid:34473240","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34473240","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"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/G1249643857","display_name":null,"funder_award_id":"U19 AG063744","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/G885797569","display_name":null,"funder_award_id":"RF1 AG058942","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"}],"funders":[{"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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":8,"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/W3100696020"],"related_works":["https://openalex.org/W4205140848","https://openalex.org/W2068663075","https://openalex.org/W2978678743","https://openalex.org/W2797837731","https://openalex.org/W2150344375","https://openalex.org/W829257147","https://openalex.org/W3081389670","https://openalex.org/W4390832911","https://openalex.org/W4385302116","https://openalex.org/W1925744677"],"abstract_inverted_index":{"MOTIVATION:":[0],"Manual":[1],"curation":[2,11],"of":[3,47,49,70],"genome-scale":[4,51],"reconstructions":[5],"is":[6],"laborious,":[7],"yet":[8],"existing":[9],"automated":[10],"tools":[12],"do":[13],"not":[14],"typically":[15],"take":[16],"species-specific":[17],"experimental":[18,66],"and":[19,36,68,82],"curated":[20],"genomic":[21],"data":[22,67,92],"into":[23],"account.":[24],"RESULTS:":[25],"We":[26],"developed":[27],"Data-drivEn":[28],"METabolic":[29],"nEtwork":[30],"Refinement":[31],"(DEMETER),":[32],"a":[33],"Constraint-Based":[34],"Reconstruction":[35],"Analysis":[37],"(COBRA)":[38],"Toolbox":[39],"extension,":[40],"which":[41],"enables":[42],"the":[43,57,61],"efficient,":[44],"simultaneous":[45],"refinement":[46,69],"thousands":[48],"draft":[50],"reconstructions,":[52],"while":[53],"ensuring":[54],"adherence":[55],"to":[56],"quality":[58],"standards":[59],"in":[60],"field,":[62],"agreement":[63],"with":[64],"available":[65,86,94],"pathways":[71],"based":[72],"on":[73],"manually":[74],"refined":[75],"genome":[76],"annotations.":[77],"AVAILABILITY":[78],"AND":[79],"IMPLEMENTATION:":[80],"DEMETER":[81],"tutorials":[83],"are":[84,93],"freely":[85],"at":[87,95],"https://github.com/opencobra.":[88],"SUPPLEMENTARY":[89],"INFORMATION:":[90],"Supplementary":[91],"Bioinformatics":[96],"online.":[97]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2}],"updated_date":"2026-07-13T07:31:44.756512","created_date":"2021-09-13T00:00:00"}
