{"id":"https://openalex.org/W2152456759","doi":"https://doi.org/10.1093/database/bat059","title":"Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance","display_name":"Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance","publication_year":2013,"publication_date":"2013-01-01","ids":{"openalex":"https://openalex.org/W2152456759","doi":"https://doi.org/10.1093/database/bat059","mag":"2152456759","pmid":"https://pubmed.ncbi.nlm.nih.gov/23935056"},"language":"en","primary_location":{"id":"doi:10.1093/database/bat059","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bat059","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bat059/16733959/bat059.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/bat059/16733959/bat059.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022865164","display_name":"Ben Heavner","orcid":"https://orcid.org/0000-0003-2898-9044"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]},{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]}],"countries":["GB","US"],"is_corresponding":false,"raw_author_name":"Benjamin D. Heavner","raw_affiliation_strings":["Institute for Systems Biology, 401 Terry Ave N., Seattle, WA 98109, USA, 2Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, M1 7DN, UK and 3Biomass Conversion Laboratory, Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology, 401 Terry Ave N., Seattle, WA 98109, USA, 2Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, M1 7DN, UK and 3Biomass Conversion Laboratory, Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I28407311","https://openalex.org/I3148997608"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084775701","display_name":"Kieran Smallbone","orcid":"https://orcid.org/0000-0003-2815-7045"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]},{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]}],"countries":["GB","US"],"is_corresponding":false,"raw_author_name":"Kieran Smallbone","raw_affiliation_strings":["Institute for Systems Biology, 401 Terry Ave N., Seattle, WA 98109, USA, 2Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, M1 7DN, UK and 3Biomass Conversion Laboratory, Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology, 401 Terry Ave N., Seattle, WA 98109, USA, 2Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, M1 7DN, UK and 3Biomass Conversion Laboratory, Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I28407311","https://openalex.org/I3148997608"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034589050","display_name":"Nathan D. Price","orcid":"https://orcid.org/0000-0002-4157-0267"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]},{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]}],"countries":["GB","US"],"is_corresponding":false,"raw_author_name":"Nathan D. Price","raw_affiliation_strings":["Institute for Systems Biology, 401 Terry Ave N., Seattle, WA 98109, USA, 2Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, M1 7DN, UK and 3Biomass Conversion Laboratory, Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology, 401 Terry Ave N., Seattle, WA 98109, USA, 2Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, M1 7DN, UK and 3Biomass Conversion Laboratory, Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I28407311","https://openalex.org/I3148997608"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103410799","display_name":"Larry P. Walker","orcid":null},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]},{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]}],"countries":["GB","US"],"is_corresponding":true,"raw_author_name":"Larry P. Walker","raw_affiliation_strings":["Institute for Systems Biology, 401 Terry Ave N., Seattle, WA 98109, USA, 2Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, M1 7DN, UK and 3Biomass Conversion Laboratory, Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology, 401 Terry Ave N., Seattle, WA 98109, USA, 2Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, M1 7DN, UK and 3Biomass Conversion Laboratory, Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I28407311","https://openalex.org/I3148997608"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5103410799"],"corresponding_institution_ids":["https://openalex.org/I205783295","https://openalex.org/I28407311","https://openalex.org/I3148997608"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":5.6343,"has_fulltext":true,"cited_by_count":110,"citation_normalized_percentile":{"value":0.97005344,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":100},"biblio":{"volume":"2013","issue":null,"first_page":"bat059","last_page":"bat059"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":1.0,"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":1.0,"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":0.9973000288009644,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9950000047683716,"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/sbml","display_name":"SBML","score":0.9578303098678589},{"id":"https://openalex.org/keywords/flux-balance-analysis","display_name":"Flux balance analysis","score":0.8424932360649109},{"id":"https://openalex.org/keywords/yeast","display_name":"Yeast","score":0.6050959825515747},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.6035412549972534},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6032497882843018},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5896986126899719},{"id":"https://openalex.org/keywords/saccharomyces-cerevisiae","display_name":"Saccharomyces cerevisiae","score":0.557651698589325},{"id":"https://openalex.org/keywords/auxotrophy","display_name":"Auxotrophy","score":0.5522343516349792},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.5423588752746582},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5049501061439514},{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.4883987307548523},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.44068339467048645},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3869014382362366},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2668118476867676},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23173052072525024},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22970205545425415},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.09090319275856018}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9578303098678589},{"id":"https://openalex.org/C167091322","wikidata":"https://www.wikidata.org/wiki/Q5463029","display_name":"Flux balance analysis","level":2,"score":0.8424932360649109},{"id":"https://openalex.org/C2779222958","wikidata":"https://www.wikidata.org/wiki/Q45422","display_name":"Yeast","level":2,"score":0.6050959825515747},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.6035412549972534},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6032497882843018},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5896986126899719},{"id":"https://openalex.org/C2777576037","wikidata":"https://www.wikidata.org/wiki/Q719725","display_name":"Saccharomyces cerevisiae","level":3,"score":0.557651698589325},{"id":"https://openalex.org/C20950039","wikidata":"https://www.wikidata.org/wiki/Q578111","display_name":"Auxotrophy","level":4,"score":0.5522343516349792},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.5423588752746582},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5049501061439514},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.4883987307548523},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.44068339467048645},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3869014382362366},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2668118476867676},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23173052072525024},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22970205545425415},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.09090319275856018},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.0},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000332","descriptor_name":"Aerobiosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000332","descriptor_name":"Aerobiosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000332","descriptor_name":"Aerobiosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000332","descriptor_name":"Aerobiosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000693","descriptor_name":"Anaerobiosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000693","descriptor_name":"Anaerobiosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000693","descriptor_name":"Anaerobiosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000693","descriptor_name":"Anaerobiosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005800","descriptor_name":"Genes, Fungal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005800","descriptor_name":"Genes, Fungal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005800","descriptor_name":"Genes, Fungal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005800","descriptor_name":"Genes, Fungal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","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":"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},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/database/bat059","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bat059","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bat059/16733959/bat059.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":"pmh:oai:europepmc.org:2732892","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3739857","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmid:23935056","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23935056","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:eprints.maths.manchester.ac.uk.MIMS.EPrints:2335","is_oa":false,"landing_page_url":"http://eprints.maths.manchester.ac.uk/2335/1/bat059.full.pdf","pdf_url":"http://eprints.maths.manchester.ac.uk/2335/1/bat059.full.pdf","source":{"id":"https://openalex.org/S4306400452","display_name":"MIMS EPrints (University of Southampton)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I43439940","host_organization_name":"University of Southampton","host_organization_lineage":["https://openalex.org/I43439940"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/database/bat059","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bat059","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bat059/16733959/bat059.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":[],"awards":[{"id":"https://openalex.org/G1487637710","display_name":null,"funder_award_id":"2P50GM076547","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3490036508","display_name":null,"funder_award_id":"289434","funder_id":"https://openalex.org/F4320338366","funder_display_name":"FP7 Food, Agriculture and Fisheries, Biotechnology"},{"id":"https://openalex.org/G3617780538","display_name":null,"funder_award_id":"DTOS59-07-G-00052","funder_id":"https://openalex.org/F4320306108","funder_display_name":"U.S. Department of Transportation"}],"funders":[{"id":"https://openalex.org/F4320306108","display_name":"U.S. Department of Transportation","ror":"https://ror.org/02xfw2e90"},{"id":"https://openalex.org/F4320306114","display_name":"U.S. Department of Agriculture","ror":"https://ror.org/01na82s61"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320338366","display_name":"FP7 Food, Agriculture and Fisheries, Biotechnology","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2152456759.pdf","grobid_xml":"https://content.openalex.org/works/W2152456759.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W1588282782","https://openalex.org/W1996529795","https://openalex.org/W1998633945","https://openalex.org/W2020561965","https://openalex.org/W2030776070","https://openalex.org/W2043283814","https://openalex.org/W2047632644","https://openalex.org/W2054719673","https://openalex.org/W2060985838","https://openalex.org/W2069890151","https://openalex.org/W2080864219","https://openalex.org/W2092838569","https://openalex.org/W2102221598","https://openalex.org/W2107007801","https://openalex.org/W2107432340","https://openalex.org/W2115559271","https://openalex.org/W2140611297","https://openalex.org/W2140948740","https://openalex.org/W2147472054","https://openalex.org/W2150908245","https://openalex.org/W2151450092","https://openalex.org/W2152549251","https://openalex.org/W2605068739","https://openalex.org/W4212920271","https://openalex.org/W6649394197","https://openalex.org/W6658027128","https://openalex.org/W6662615058","https://openalex.org/W6665905149","https://openalex.org/W6667778704","https://openalex.org/W6670564778","https://openalex.org/W6673931457","https://openalex.org/W6675361192","https://openalex.org/W6676018264","https://openalex.org/W6676191954","https://openalex.org/W6677257300","https://openalex.org/W6680903756","https://openalex.org/W6681711848","https://openalex.org/W6682252439","https://openalex.org/W6682382136","https://openalex.org/W6682497444","https://openalex.org/W7075673388"],"related_works":["https://openalex.org/W1971436540","https://openalex.org/W4241916770","https://openalex.org/W2289008616","https://openalex.org/W1863756066","https://openalex.org/W1999460937","https://openalex.org/W2020641517","https://openalex.org/W2374260038","https://openalex.org/W2216418212","https://openalex.org/W2075919068","https://openalex.org/W2157084984"],"abstract_inverted_index":{"Updates":[0],"to":[1,14,24,32,37,39,44,67,71,182],"maintain":[2],"a":[3,143,154,215,226,238],"state-of-the":[4],"art":[5],"reconstruction":[6,150,239],"of":[7,18,48,56,78,138,169],"the":[8,46,49,57,68,74,99,136,140,167,178,218,230,250],"yeast":[9,19,59,96],"metabolic":[10,60,76],"network":[11,61,77,149,179],"are":[12,92,180,193],"essential":[13],"reflect":[15],"our":[16],"understanding":[17],"metabolism":[20],"and":[21,36,112,114,175,191,237],"functional":[22],"organization,":[23],"eliminate":[25],"any":[26],"inaccuracies":[27],"identified":[28],"in":[29,88,122,166,177],"earlier":[30],"iterations,":[31],"improve":[33],"predictive":[34,116],"accuracy":[35,137],"continue":[38],"expand":[40],"into":[41],"novel":[42],"subsystems":[43],"extend":[45],"comprehensiveness":[47],"model.":[50],"Here,":[51],"we":[52],"present":[53],"version":[54],"6":[55,83,107,134,204],"consensus":[58],"(Yeast":[62],"6)":[63],"as":[64,153,186,210],"an":[65],"update":[66],"community":[69],"effort":[70],"computationally":[72],"reconstruct":[73],"genome-scale":[75],"Saccharomyces":[79],"cerevisiae":[80],"S288c.":[81],"Yeast":[82,104,106,133,203],"comprises":[84],"1458":[85],"metabolites":[86],"participating":[87],"1888":[89],"reactions,":[90],"which":[91,244],"annotated":[93,195],"with":[94,103,128,162,196,229],"900":[95],"genes":[97],"encoding":[98],"catalyzing":[100],"enzymes.":[101],"Compared":[102],"5,":[105],"demonstrates":[108],"improved":[109],"sensitivity,":[110],"specificity":[111],"positive":[113],"negative":[115],"values":[117],"for":[118,234,243,254],"predicting":[119,139],"gene":[120],"essentiality":[121],"glucose-limited":[123],"aerobic":[124],"conditions":[125],"when":[126],"analyzed":[127],"flux":[129],"balance":[130],"analysis.":[131],"Additionally,":[132],"improves":[135],"likelihood":[141],"that":[142,199],"mutation":[144],"will":[145],"cause":[146],"auxotrophy.":[147],"The":[148],"is":[151,205,246],"available":[152,207],"Systems":[155],"Biology":[156],"Markup":[157],"Language":[158],"(SBML)":[159],"file":[160],"enriched":[161],"Minimium":[163],"Information":[164],"Requested":[165],"Annotation":[168],"Biochemical":[170],"Models":[171],"(MIRIAM)-compliant":[172],"annotations.":[173],"Small-":[174],"macromolecules":[176],"referenced":[181],"authoritative":[183],"databases":[184],"such":[185],"Uniprot":[187],"or":[188],"ChEBI.":[189],"Molecules":[190],"reactions":[192,242,252],"also":[194],"appropriate":[197],"publications":[198],"contain":[200],"supporting":[201],"evidence.":[202],"freely":[206],"at":[208],"http://yeast.sf.net/":[209,259],"three":[211],"separate":[212],"SBML":[213,219],"files:":[214],"model":[216,227],"using":[217],"level":[220],"3":[221],"Flux":[222],"Balance":[223],"Constraint":[224],"package,":[225],"compatible":[228],"MATLAB\u00ae":[231],"COBRA":[232],"Toolbox":[233],"backward":[235],"compatibility":[236],"containing":[240],"only":[241],"there":[245],"experimental":[247],"evidence":[248],"(without":[249],"non-biological":[251],"necessary":[253],"simulating":[255],"growth).":[256],"Database":[257],"URL:":[258]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":11},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":12},{"year":2016,"cited_by_count":14},{"year":2015,"cited_by_count":13},{"year":2014,"cited_by_count":12},{"year":2013,"cited_by_count":2}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}