{"id":"https://openalex.org/W2809336338","doi":"https://doi.org/10.1186/s12918-018-0593-7","title":"How accurate is automated gap filling of metabolic models?","display_name":"How accurate is automated gap filling of metabolic models?","publication_year":2018,"publication_date":"2018-06-19","ids":{"openalex":"https://openalex.org/W2809336338","doi":"https://doi.org/10.1186/s12918-018-0593-7","mag":"2809336338","pmid":"https://pubmed.ncbi.nlm.nih.gov/29914471"},"language":"en","primary_location":{"id":"doi:10.1186/s12918-018-0593-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-018-0593-7","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-018-0593-7","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-018-0593-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082071104","display_name":"Peter D. Karp","orcid":"https://orcid.org/0000-0002-5876-6418"},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Peter D. Karp","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, 94025, USA. pkarp@ai.sri.com","Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, 94025, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, 94025, USA. pkarp@ai.sri.com","institution_ids":["https://openalex.org/I1298353152"]},{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091668355","display_name":"Daniel Weaver","orcid":"https://orcid.org/0000-0002-2906-3019"},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel Weaver","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, 94025, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053894822","display_name":"Mario Latendresse","orcid":"https://orcid.org/0000-0002-6292-0158"},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mario Latendresse","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, 94025, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5082071104"],"corresponding_institution_ids":["https://openalex.org/I1298353152"],"apc_list":null,"apc_paid":null,"fwci":2.234,"has_fulltext":true,"cited_by_count":56,"citation_normalized_percentile":{"value":0.8875872,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"12","issue":"1","first_page":"73","last_page":"73"},"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/T10171","display_name":"Biofuel production and bioconversion","score":0.9950000047683716,"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/T10404","display_name":"Enzyme Catalysis and Immobilization","score":0.982200026512146,"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":0.6338054537773132},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.5621046423912048},{"id":"https://openalex.org/keywords/bifidobacterium-longum","display_name":"Bifidobacterium longum","score":0.554816484451294},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5445270538330078},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5090786814689636},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.43637269735336304},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.35634472966194153},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3497394323348999},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32250329852104187},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.25446265935897827},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2124963402748108},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.11718055605888367}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6338054537773132},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.5621046423912048},{"id":"https://openalex.org/C2776996202","wikidata":"https://www.wikidata.org/wiki/Q4904768","display_name":"Bifidobacterium longum","level":5,"score":0.554816484451294},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5445270538330078},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5090786814689636},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.43637269735336304},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.35634472966194153},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3497394323348999},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32250329852104187},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.25446265935897827},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2124963402748108},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.11718055605888367},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C100544194","wikidata":"https://www.wikidata.org/wiki/Q41760","display_name":"Fermentation","level":2,"score":0.0},{"id":"https://openalex.org/C2780206646","wikidata":"https://www.wikidata.org/wiki/Q1061596","display_name":"Lactobacillus","level":3,"score":0.0},{"id":"https://openalex.org/C2780305828","wikidata":"https://www.wikidata.org/wiki/Q132656","display_name":"Bifidobacterium","level":4,"score":0.0}],"mesh":[{"descriptor_ui":"D000069978","descriptor_name":"Bifidobacterium longum","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000069978","descriptor_name":"Bifidobacterium longum","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000069978","descriptor_name":"Bifidobacterium longum","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008660","descriptor_name":"Metabolism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008660","descriptor_name":"Metabolism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008660","descriptor_name":"Metabolism","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":"D018533","descriptor_name":"Biomass","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018533","descriptor_name":"Biomass","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018533","descriptor_name":"Biomass","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12918-018-0593-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-018-0593-7","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-018-0593-7","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:29914471","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29914471","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":"BMC systems biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:a81e31b0b495437b96a4fbdd9e87df3c","is_oa":true,"landing_page_url":"https://doaj.org/article/a81e31b0b495437b96a4fbdd9e87df3c","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Systems Biology, Vol 12, Iss 1, Pp 1-11 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4967842","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6006690","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:6006690","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6006690","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12918-018-0593-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-018-0593-7","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-018-0593-7","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2856777376","display_name":null,"funder_award_id":"GM075742","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G69280378","display_name":null,"funder_award_id":"GM075742","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2809336338.pdf","grobid_xml":"https://content.openalex.org/works/W2809336338.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1976325156","https://openalex.org/W1991194699","https://openalex.org/W1996047071","https://openalex.org/W1997037290","https://openalex.org/W1998727374","https://openalex.org/W2064997088","https://openalex.org/W2072101365","https://openalex.org/W2073837631","https://openalex.org/W2083189525","https://openalex.org/W2085993965","https://openalex.org/W2092529097","https://openalex.org/W2093768709","https://openalex.org/W2098676247","https://openalex.org/W2100084634","https://openalex.org/W2118053673","https://openalex.org/W2119211408","https://openalex.org/W2128601422","https://openalex.org/W2132092950","https://openalex.org/W2133452284","https://openalex.org/W2157084984","https://openalex.org/W2168465568","https://openalex.org/W2559597060","https://openalex.org/W2775873384","https://openalex.org/W2794727335","https://openalex.org/W2951705055","https://openalex.org/W4236875018"],"related_works":["https://openalex.org/W3188661910","https://openalex.org/W3188222114","https://openalex.org/W2392672625","https://openalex.org/W2564867311","https://openalex.org/W2782428046","https://openalex.org/W2161968779","https://openalex.org/W3208076072","https://openalex.org/W2120758982","https://openalex.org/W2387965106","https://openalex.org/W2521771323"],"abstract_inverted_index":{"Our":[0],"conclusion":[1],"is":[2,9],"that":[3],"manual":[4,21],"curation":[5],"of":[6,16,35,49],"gap-filler":[7],"results":[8],"needed":[10],"to":[11,31,45],"obtain":[12],"high-accuracy":[13],"models.":[14],"Many":[15],"the":[17,20,33,38,46],"differences":[18],"between":[19],"and":[22],"automatic":[23],"solutions":[24],"resulted":[25],"from":[26],"using":[27],"expert":[28],"biological":[29],"knowledge":[30],"direct":[32],"choice":[34],"reactions":[36,43],"within":[37],"curated":[39],"solution,":[40],"such":[41],"as":[42],"specific":[44],"anaerobic":[47],"lifestyle":[48],"B.":[50],"longum.":[51]},"counts_by_year":[{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
