{"id":"https://openalex.org/W4294990920","doi":"https://doi.org/10.1371/journal.pcbi.1010452","title":"Architect: A tool for aiding the reconstruction of high-quality metabolic models through improved enzyme annotation","display_name":"Architect: A tool for aiding the reconstruction of high-quality metabolic models through improved enzyme annotation","publication_year":2022,"publication_date":"2022-09-08","ids":{"openalex":"https://openalex.org/W4294990920","doi":"https://doi.org/10.1371/journal.pcbi.1010452","pmid":"https://pubmed.ncbi.nlm.nih.gov/36074804"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1010452","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010452","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1010452","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043745601","display_name":"Nirvana Nursimulu","orcid":"https://orcid.org/0000-0001-5962-5863"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I2801317318","display_name":"Hospital for Sick Children","ror":"https://ror.org/057q4rt57","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I2801317318"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Nirvana Nursimulu","raw_affiliation_strings":["Department of Computer Science, University of Toronto, Toronto, Ontario, Canada","Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada"],"raw_orcid":"https://orcid.org/0000-0001-5962-5863","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Toronto, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I2801317318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086545231","display_name":"Alan M Moses","orcid":"https://orcid.org/0000-0003-3118-3121"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Alan M. Moses","raw_affiliation_strings":["Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada","Department of Computer Science, University of Toronto, Toronto, Ontario, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Department of Computer Science, University of Toronto, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085182984","display_name":"John Parkinson","orcid":"https://orcid.org/0000-0001-9815-1189"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I2801317318","display_name":"Hospital for Sick Children","ror":"https://ror.org/057q4rt57","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I2801317318"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"John Parkinson","raw_affiliation_strings":["Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada","Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada","Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada"],"raw_orcid":"https://orcid.org/0000-0001-9815-1189","affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I2801317318"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5085182984"],"corresponding_institution_ids":["https://openalex.org/I185261750","https://openalex.org/I2801317318"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.3472,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.55779174,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"18","issue":"9","first_page":"e1010452","last_page":"e1010452"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9998999834060669,"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":0.9998999834060669,"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/T10171","display_name":"Biofuel production and bioconversion","score":0.994700014591217,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9896000027656555,"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/computer-science","display_name":"Computer science","score":0.7242711186408997},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5612291097640991},{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.5278016328811646},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5195779800415039},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.4279709756374359},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33363890647888184},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24632173776626587},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1224982738494873},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.11763983964920044},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.09953621029853821}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7242711186408997},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5612291097640991},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.5278016328811646},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5195779800415039},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.4279709756374359},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33363890647888184},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24632173776626587},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1224982738494873},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.11763983964920044},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.09953621029853821},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"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":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","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":"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":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1010452","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010452","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:36074804","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36074804","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:cc75f290167c4c51a45f3eb41448544c","is_oa":true,"landing_page_url":"https://doaj.org/article/cc75f290167c4c51a45f3eb41448544c","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 18, Iss 9, p e1010452 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9488769","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9488769","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1010452","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010452","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4199809130","display_name":null,"funder_award_id":"RGPIN-2019-06852","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320314000","display_name":"Compute Canada","ror":"https://ror.org/03ty8yr27"},{"id":"https://openalex.org/F4320314607","display_name":"Government of Ontario","ror":"https://ror.org/015pzp858"},{"id":"https://openalex.org/F4320319952","display_name":"Canada Foundation for Innovation","ror":"https://ror.org/000az4664"},{"id":"https://openalex.org/F4320322015","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087"},{"id":"https://openalex.org/F4320323654","display_name":"Hospital for Sick Children","ror":"https://ror.org/057q4rt57"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W54887220","https://openalex.org/W1481552892","https://openalex.org/W1574680346","https://openalex.org/W1963012831","https://openalex.org/W1976656799","https://openalex.org/W2005913713","https://openalex.org/W2024038403","https://openalex.org/W2029403511","https://openalex.org/W2045204781","https://openalex.org/W2049381178","https://openalex.org/W2055043387","https://openalex.org/W2060787728","https://openalex.org/W2070787626","https://openalex.org/W2085993965","https://openalex.org/W2100084634","https://openalex.org/W2101417771","https://openalex.org/W2110256992","https://openalex.org/W2111693807","https://openalex.org/W2111973517","https://openalex.org/W2112746567","https://openalex.org/W2117190284","https://openalex.org/W2131366108","https://openalex.org/W2142428670","https://openalex.org/W2148000475","https://openalex.org/W2150746148","https://openalex.org/W2160423401","https://openalex.org/W2170427655","https://openalex.org/W2170505850","https://openalex.org/W2202347610","https://openalex.org/W2517497906","https://openalex.org/W2534303219","https://openalex.org/W2560707317","https://openalex.org/W2605068739","https://openalex.org/W2605504874","https://openalex.org/W2762019694","https://openalex.org/W2764202526","https://openalex.org/W2765384588","https://openalex.org/W2775873384","https://openalex.org/W2800094547","https://openalex.org/W2801106948","https://openalex.org/W2809358912","https://openalex.org/W2900490993","https://openalex.org/W2949418748","https://openalex.org/W2951022399","https://openalex.org/W2951899941","https://openalex.org/W2953321375","https://openalex.org/W2987028578","https://openalex.org/W3010629926","https://openalex.org/W3080133182","https://openalex.org/W3096828292","https://openalex.org/W3102028509","https://openalex.org/W4205247356","https://openalex.org/W4247554111"],"related_works":["https://openalex.org/W2102027645","https://openalex.org/W2107785922","https://openalex.org/W2059359052","https://openalex.org/W2035528219","https://openalex.org/W2402478170","https://openalex.org/W2946410450","https://openalex.org/W2999847357","https://openalex.org/W2993777277","https://openalex.org/W2901823680","https://openalex.org/W2979585142"],"abstract_inverted_index":{"Constraint-based":[0],"modeling":[1,38],"is":[2,67,123,162,177,229],"a":[3,56,62,68,89,100,120,157],"powerful":[4],"framework":[5],"for":[6,33,77,102,125,135,183,227],"studying":[7],"cellular":[8],"metabolism,":[9],"with":[10,206],"applications":[11],"ranging":[12],"from":[13,37,107,132,169],"predicting":[14],"growth":[15],"rates":[16],"and":[17,144,191,209,216,241],"optimizing":[18],"production":[19],"of":[20,50,188,199],"high":[21],"value":[22],"metabolites":[23],"to":[24,92,147,155,219],"identifying":[25],"enzymes":[26],"in":[27,45,179,222],"pathogens":[28],"that":[29],"may":[30],"be":[31,41,237],"targeted":[32],"therapeutic":[34],"interventions.":[35],"Results":[36],"experiments":[39],"can":[40,60,236],"affected":[42],"at":[43,231],"least":[44],"part":[46],"by":[47],"the":[48,51,72,79,170,212],"quality":[49],"metabolic":[52,57,64,83,104,159,175,193],"models":[53],"used.":[54],"Reconstructing":[55],"network":[58,160],"manually":[59],"produce":[61,93],"high-quality":[63,158],"model":[65,105,176],"but":[66],"time-consuming":[69],"task.":[70],"At":[71],"same":[73],"time,":[74],"current":[75],"methods":[76],"automating":[78],"process":[80,90],"typically":[81],"transfer":[82],"function":[84],"based":[85,129,165],"on":[86,130,166,211,248],"sequence":[87],"similarity,":[88],"known":[91],"many":[94],"false":[95],"positives.":[96],"We":[97],"created":[98],"Architect,":[99],"pipeline":[101],"automatic":[103],"reconstruction":[106],"protein":[108],"sequences.":[109],"First,":[110],"it":[111],"performs":[112],"enzyme":[113,189],"annotation":[114],"through":[115],"an":[116,126],"ensemble":[117,171],"approach,":[118],"whereby":[119],"likelihood":[121,167],"score":[122],"computed":[124],"EC":[127],"prediction":[128],"predictions":[131],"existing":[133],"tools;":[134],"this":[136],"step,":[137],"our":[138],"method":[139],"shows":[140],"both":[141],"increased":[142],"precision":[143,208],"recall":[145,210],"compared":[146,218],"individual":[148],"tools.":[149],"Next,":[150],"Architect":[151,200,228,235],"uses":[152],"these":[153],"annotations":[154,190,221],"construct":[156],"which":[161],"then":[163],"gap-filled":[164],"scores":[168],"approach.":[172],"The":[173],"resulting":[174],"output":[178],"SBML":[180],"format,":[181],"suitable":[182],"constraints-based":[184],"analyses.":[185],"Through":[186],"comparisons":[187],"curated":[192],"models,":[194],"we":[195],"demonstrate":[196],"improved":[197],"performance":[198],"over":[201],"other":[202],"state-of-the-art":[203],"tools,":[204],"notably":[205],"higher":[207],"eukaryote":[213],"C.":[214],"elegans":[215],"when":[217],"UniProt":[220],"two":[223],"bacterial":[224],"species.":[225],"Code":[226],"available":[230],"https://github.com/ParkinsonLab/Architect.":[232],"For":[233],"ease-of-use,":[234],"readily":[238],"set":[239],"up":[240],"utilized":[242],"using":[243],"its":[244],"Docker":[245,249],"image,":[246],"maintained":[247],"Hub.":[250]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
