{"id":"https://openalex.org/W2035360701","doi":"https://doi.org/10.1093/bib/bbv003","title":"Critical assessment of genome-scale metabolic networks: the need for a unified standard","display_name":"Critical assessment of genome-scale metabolic networks: the need for a unified standard","publication_year":2015,"publication_date":"2015-02-28","ids":{"openalex":"https://openalex.org/W2035360701","doi":"https://doi.org/10.1093/bib/bbv003","mag":"2035360701","pmid":"https://pubmed.ncbi.nlm.nih.gov/25725218"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbv003","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbv003","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5045741050","display_name":"Aarthi Ravikrishnan","orcid":"https://orcid.org/0000-0003-2391-0202"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"A. Ravikrishnan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5011489319","display_name":"Karthik Raman","orcid":"https://orcid.org/0000-0002-9311-7093"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"K. Raman","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":5.2715,"has_fulltext":false,"cited_by_count":97,"citation_normalized_percentile":{"value":0.96273901,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":100},"biblio":{"volume":"16","issue":"6","first_page":"1057","last_page":"1068"},"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":0.9965000152587891,"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":0.9937999844551086,"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":0.740014910697937},{"id":"https://openalex.org/keywords/constraint","display_name":"Constraint (computer-aided design)","score":0.703392505645752},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.6979928016662598},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.6294618844985962},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.5133708715438843},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.5072981715202332},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.4520750045776367},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4517185688018799},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.43283605575561523},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.41273611783981323},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.41022664308547974},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3933124244213104},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19494232535362244},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18450748920440674},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.17697519063949585},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10483604669570923},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.0837511420249939}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.740014910697937},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.703392505645752},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.6979928016662598},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.6294618844985962},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.5133708715438843},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.5072981715202332},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4520750045776367},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4517185688018799},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.43283605575561523},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.41273611783981323},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.41022664308547974},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3933124244213104},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19494232535362244},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18450748920440674},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.17697519063949585},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10483604669570923},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0837511420249939},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"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/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"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":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","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":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbv003","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbv003","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25725218","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25725218","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322211","display_name":"Indian Institute of Technology Madras","ror":"https://ror.org/03v0r5n49"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":98,"referenced_works":["https://openalex.org/W1966497610","https://openalex.org/W1969709265","https://openalex.org/W1972744800","https://openalex.org/W1972990890","https://openalex.org/W1976812345","https://openalex.org/W1983566611","https://openalex.org/W1984345785","https://openalex.org/W1996529795","https://openalex.org/W1996912752","https://openalex.org/W1998633945","https://openalex.org/W1999938932","https://openalex.org/W2004340874","https://openalex.org/W2006672203","https://openalex.org/W2010250442","https://openalex.org/W2010930876","https://openalex.org/W2011494429","https://openalex.org/W2018591360","https://openalex.org/W2019974881","https://openalex.org/W2020561965","https://openalex.org/W2022012525","https://openalex.org/W2029403511","https://openalex.org/W2030776070","https://openalex.org/W2046653743","https://openalex.org/W2048465561","https://openalex.org/W2054719673","https://openalex.org/W2056305771","https://openalex.org/W2069909946","https://openalex.org/W2075919068","https://openalex.org/W2078355959","https://openalex.org/W2078775934","https://openalex.org/W2080461503","https://openalex.org/W2081492047","https://openalex.org/W2082382448","https://openalex.org/W2085966233","https://openalex.org/W2087928503","https://openalex.org/W2089943097","https://openalex.org/W2090120515","https://openalex.org/W2096097217","https://openalex.org/W2098337987","https://openalex.org/W2098450614","https://openalex.org/W2100084634","https://openalex.org/W2101417771","https://openalex.org/W2101501829","https://openalex.org/W2102164505","https://openalex.org/W2106135293","https://openalex.org/W2108078368","https://openalex.org/W2111421616","https://openalex.org/W2112165937","https://openalex.org/W2112463359","https://openalex.org/W2112662291","https://openalex.org/W2115559271","https://openalex.org/W2117474489","https://openalex.org/W2119315087","https://openalex.org/W2120796786","https://openalex.org/W2123698848","https://openalex.org/W2124419982","https://openalex.org/W2126175129","https://openalex.org/W2126546123","https://openalex.org/W2127553917","https://openalex.org/W2128572161","https://openalex.org/W2128601422","https://openalex.org/W2129877320","https://openalex.org/W2133510724","https://openalex.org/W2136177512","https://openalex.org/W2137450588","https://openalex.org/W2138121585","https://openalex.org/W2138127621","https://openalex.org/W2140611297","https://openalex.org/W2141144953","https://openalex.org/W2141360045","https://openalex.org/W2142428670","https://openalex.org/W2144000913","https://openalex.org/W2146737319","https://openalex.org/W2147472054","https://openalex.org/W2148853951","https://openalex.org/W2150908245","https://openalex.org/W2153251212","https://openalex.org/W2155102754","https://openalex.org/W2156409537","https://openalex.org/W2159482845","https://openalex.org/W2160648343","https://openalex.org/W2161568599","https://openalex.org/W2161732286","https://openalex.org/W2162237022","https://openalex.org/W2164111097","https://openalex.org/W2165254936","https://openalex.org/W2165373392","https://openalex.org/W2166456241","https://openalex.org/W2167539386","https://openalex.org/W2168465568","https://openalex.org/W2170319684","https://openalex.org/W2170427655","https://openalex.org/W2171769617","https://openalex.org/W2171911221","https://openalex.org/W4237293127","https://openalex.org/W4245145908","https://openalex.org/W4248664566","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W2082621456","https://openalex.org/W2981332207","https://openalex.org/W2159912904","https://openalex.org/W2150908245","https://openalex.org/W2211443823","https://openalex.org/W2043776573","https://openalex.org/W2216418212","https://openalex.org/W2020641517","https://openalex.org/W2075919068","https://openalex.org/W2047632644"],"abstract_inverted_index":{"Genome-scale":[0],"metabolic":[1,10,46,59,104,201],"networks":[2,11,30,60,105],"have":[3,154],"been":[4],"reconstructed":[5,200],"for":[6,45,165,175,180],"several":[7,137],"organisms.":[8,55],"These":[9,29],"provide":[12],"detailed":[13],"information":[14,156],"about":[15],"the":[16,19,23,84,122,126,173,191,197],"metabolism":[17],"inside":[18],"cells,":[20],"coupled":[21],"with":[22,73,115],"genomic,":[24],"proteomic":[25],"and":[26,38,67,82,88,106,111,144,162,195],"thermodynamic":[27],"information.":[28],"are":[31,61],"widely":[32,177],"simulated":[33],"using":[34,69,130],"'constraint-based'":[35],"modelling":[36],"techniques":[37],"find":[39,148],"applications":[40],"ranging":[41],"from":[42],"strain":[43],"improvement":[44],"engineering":[47],"to":[48,80,117],"prediction":[49],"of":[50,57,76,121,128,193,199],"drug":[51],"targets":[52],"in":[53,63,86,189],"pathogenic":[54],"Components":[56],"these":[58],"represented":[62],"multiple":[64,92],"file":[65],"formats":[66],"also":[68,147],"different":[70],"markup":[71],"languages,":[72],"varying":[74],"levels":[75],"annotations;":[77],"this":[78,95],"leads":[79],"inconsistencies":[81],"increases":[83],"complexities":[85],"comparing":[87],"analysing":[89],"reconstructions":[90],"on":[91,159],"platforms.":[93],"In":[94],"work,":[96],"we":[97],"critically":[98],"examine":[99],"nearly":[100],"100":[101],"published":[102],"genome-scale":[103],"their":[107],"corresponding":[108],"constraint-based":[109,182],"models":[110,151],"discuss":[112],"various":[113],"issues":[114],"respect":[116],"model":[118],"quality.":[119],"One":[120],"major":[123],"concerns":[124],"is":[125],"lack":[127],"annotations":[129],"standard":[131,179,186],"identifiers":[132],"that":[133,149],"can":[134,187],"uniquely":[135],"describe":[136],"components":[138],"such":[139],"as":[140],"metabolites,":[141],"genes,":[142],"proteins":[143],"reactions.":[145],"We":[146],"many":[150],"do":[152],"not":[153],"complete":[155],"regarding":[157],"constraints":[158],"reactions":[160],"fluxes":[161],"objective":[163],"functions":[164],"carrying":[166],"out":[167],"simulations.":[168],"Overall,":[169],"our":[170],"analysis":[171],"highlights":[172],"need":[174],"a":[176],"acceptable":[178],"representing":[181],"models.":[183,202],"A":[184],"rigorous":[185],"help":[188],"streamlining":[190],"process":[192],"reconstruction":[194],"improve":[196],"quality":[198]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":13},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":12},{"year":2017,"cited_by_count":14},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}