{"id":"https://openalex.org/W2161568599","doi":"https://doi.org/10.1186/1758-2946-6-2","title":"Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2","display_name":"Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2","publication_year":2014,"publication_date":"2014-01-27","ids":{"openalex":"https://openalex.org/W2161568599","doi":"https://doi.org/10.1186/1758-2946-6-2","mag":"2161568599","pmid":"https://pubmed.ncbi.nlm.nih.gov/24468196"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-6-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-6-2","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-6-2","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-6-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047777958","display_name":"Hulda S. Haraldsd\u00f3ttir","orcid":null},"institutions":[{"id":"https://openalex.org/I165368041","display_name":"University of Iceland","ror":"https://ror.org/01db6h964","country_code":"IS","type":"education","lineage":["https://openalex.org/I165368041"]}],"countries":["IS"],"is_corresponding":false,"raw_author_name":"Hulda S Haraldsd\u00f3ttir","raw_affiliation_strings":["Center for Systems Biology, University of Iceland, Sturlugata 8, IS-101, Reykjavik, Iceland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Systems Biology, University of Iceland, Sturlugata 8, IS-101, Reykjavik, Iceland","institution_ids":["https://openalex.org/I165368041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074725115","display_name":"Ines Thiele","orcid":"https://orcid.org/0000-0002-8071-7110"},"institutions":[{"id":"https://openalex.org/I165368041","display_name":"University of Iceland","ror":"https://ror.org/01db6h964","country_code":"IS","type":"education","lineage":["https://openalex.org/I165368041"]},{"id":"https://openalex.org/I186903577","display_name":"University of Luxembourg","ror":"https://ror.org/036x5ad56","country_code":"LU","type":"education","lineage":["https://openalex.org/I186903577"]}],"countries":["IS","LU"],"is_corresponding":false,"raw_author_name":"Ines Thiele","raw_affiliation_strings":["Center for Systems Biology, University of Iceland, Sturlugata 8, IS-101, Reykjavik, Iceland","Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Systems Biology, University of Iceland, Sturlugata 8, IS-101, Reykjavik, Iceland","institution_ids":["https://openalex.org/I165368041"]},{"raw_affiliation_string":"Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg","institution_ids":["https://openalex.org/I186903577"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069362994","display_name":"Ronan M. T. Fleming","orcid":"https://orcid.org/0000-0001-5346-9812"},"institutions":[{"id":"https://openalex.org/I165368041","display_name":"University of Iceland","ror":"https://ror.org/01db6h964","country_code":"IS","type":"education","lineage":["https://openalex.org/I165368041"]}],"countries":["IS"],"is_corresponding":true,"raw_author_name":"Ronan MT Fleming","raw_affiliation_strings":["Center for Systems Biology, University of Iceland, Sturlugata 8, IS-101 Reykjavik, Iceland. ronan.mt.fleming@gmail.com","Center for Systems Biology, University of Iceland, Sturlugata 8, IS-101, Reykjavik, Iceland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Systems Biology, University of Iceland, Sturlugata 8, IS-101 Reykjavik, Iceland. ronan.mt.fleming@gmail.com","institution_ids":["https://openalex.org/I165368041"]},{"raw_affiliation_string":"Center for Systems Biology, University of Iceland, Sturlugata 8, IS-101, Reykjavik, Iceland","institution_ids":["https://openalex.org/I165368041"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5069362994"],"corresponding_institution_ids":["https://openalex.org/I165368041"],"apc_list":{"value":2190,"currency":"USD","value_usd":2190},"apc_paid":{"value":2190,"currency":"USD","value_usd":2190},"fwci":1.3,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.79793141,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"6","issue":"1","first_page":"2","last_page":"2"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.534500002861023,"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":0.534500002861023,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.44339999556541443,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0017999999690800905,"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/identifier","display_name":"Identifier","score":0.9189728498458862},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8179761171340942},{"id":"https://openalex.org/keywords/metabolite","display_name":"Metabolite","score":0.4885028600692749},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.46400585770606995},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.45753318071365356},{"id":"https://openalex.org/keywords/unique-identifier","display_name":"Unique identifier","score":0.4533329904079437},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4099735617637634},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3636559247970581},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22557902336120605},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12454003095626831}],"concepts":[{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.9189728498458862},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8179761171340942},{"id":"https://openalex.org/C2777477808","wikidata":"https://www.wikidata.org/wiki/Q407595","display_name":"Metabolite","level":2,"score":0.4885028600692749},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.46400585770606995},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.45753318071365356},{"id":"https://openalex.org/C119839945","wikidata":"https://www.wikidata.org/wiki/Q6545185","display_name":"Unique identifier","level":3,"score":0.4533329904079437},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4099735617637634},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3636559247970581},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22557902336120605},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12454003095626831},{"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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/1758-2946-6-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-6-2","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-6-2","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:24468196","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24468196","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":"Journal of cheminformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:2913391","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3917611","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:orbilu.uni.lu:10993/16278","is_oa":true,"landing_page_url":"http://www.jcheminf.com/content/6/1/2","pdf_url":null,"source":{"id":"https://openalex.org/S4306401815","display_name":"Open Repository and Bibliography (University of Luxembourg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I186903577","host_organization_name":"University of Luxembourg","host_organization_lineage":["https://openalex.org/I186903577"],"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":"Journal of Cheminformatics, 6, 2 (2014)","raw_type":"http://purl.org/coar/resource_type/c_6501"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-6-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-6-2","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-6-2","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8656748826","display_name":null,"funder_award_id":"FNR/A12/01","funder_id":"https://openalex.org/F4320321038","funder_display_name":"Fonds National de la Recherche Luxembourg"}],"funders":[{"id":"https://openalex.org/F4320321038","display_name":"Fonds National de la Recherche Luxembourg","ror":"https://ror.org/039z13y21"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2161568599.pdf","grobid_xml":"https://content.openalex.org/works/W2161568599.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1529898704","https://openalex.org/W1601495365","https://openalex.org/W1983464445","https://openalex.org/W1997733142","https://openalex.org/W1998767819","https://openalex.org/W1999619962","https://openalex.org/W1999640817","https://openalex.org/W2014323212","https://openalex.org/W2034994407","https://openalex.org/W2041610798","https://openalex.org/W2063028213","https://openalex.org/W2065198029","https://openalex.org/W2085993965","https://openalex.org/W2087563523","https://openalex.org/W2090347317","https://openalex.org/W2096769282","https://openalex.org/W2099787654","https://openalex.org/W2100084634","https://openalex.org/W2103795997","https://openalex.org/W2104108767","https://openalex.org/W2122709242","https://openalex.org/W2129370330","https://openalex.org/W2132218677","https://openalex.org/W2136149318","https://openalex.org/W2140611297","https://openalex.org/W2144322446","https://openalex.org/W2159482845","https://openalex.org/W2162314899","https://openalex.org/W2165612309","https://openalex.org/W2165681080","https://openalex.org/W2171653977","https://openalex.org/W2171769617","https://openalex.org/W4233659707","https://openalex.org/W4256259619","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W2413568490","https://openalex.org/W1913624564","https://openalex.org/W3130054399","https://openalex.org/W4301062032","https://openalex.org/W2343500026","https://openalex.org/W2319837024","https://openalex.org/W2390627310","https://openalex.org/W2033159440","https://openalex.org/W2413664130","https://openalex.org/W2051731675"],"abstract_inverted_index":{"BACKGROUND:":[0],"An":[1],"important":[2],"step":[3],"in":[4,28,147,160,230,266,283],"the":[5,89,102,120,134,140,153,163,218,251,259],"reconstruction":[6,165],"of":[7,13,52,75,126,136,142,166,177,207,214,261],"a":[8,111],"metabolic":[9,29,47,149,268],"network":[10],"is":[11,57],"annotation":[12],"metabolites.":[14,53,210],"Metabolites":[15],"are":[16],"generally":[17,49],"annotated":[18],"with":[19],"various":[20],"database":[21],"or":[22,34],"structure":[23],"based":[24,129,247],"identifiers.":[25,82,190],"Metabolite":[26],"annotations":[27,56,76],"reconstructions":[30,48],"may":[31],"be":[32,40,277],"incorrect":[33],"incomplete":[35],"and":[36,91,106],"thus":[37],"need":[38],"to":[39,43,64,157,187,194,224,258,279,285,288],"updated":[41,239],"prior":[42],"their":[44],"use.":[45],"Genome-scale":[46],"include":[50],"hundreds":[51],"Manually":[54],"updating":[55,74,158,176],"therefore":[58],"highly":[59],"laborious.":[60],"This":[61],"prompted":[62],"us":[63,223],"look":[65],"for":[66,88,115,139,201],"open-source":[67],"software":[68],"applications":[69,86,99,138,172],"that":[70,244,275],"could":[71,276],"facilitate":[72],"automatic":[73,175],"by":[77,199],"mapping":[78,116,143,262],"between":[79,117,144,263],"available":[80],"metabolite":[81,145,178,228,264],"We":[83,151,191,242,270],"identified":[84,271],"three":[85,171],"developed":[87],"metabolomics":[90],"chemical":[92],"informatics":[93],"communities":[94],"as":[95,250],"potential":[96],"solutions.":[97],"The":[98,108],"were":[100,192,216,238],"MetMask,":[101],"Chemical":[103,219,252],"Translation":[104,220,253],"System,":[105],"UniChem.":[107],"first":[109],"implements":[110],"\"metabolite":[112],"masking\"":[113],"strategy":[114],"identifiers":[118,146,159,203,229,237,265],"whereas":[119],"latter":[121],"two":[122],"implement":[123],"different":[124],"versions":[125],"an":[127,245,281],"InChI":[128,246],"strategy.":[130],"Here":[131],"we":[132],"evaluated":[133],"suitability":[135],"these":[137],"task":[141,260],"genome-scale":[148,267],"reconstructions.":[150,269],"applied":[152],"best":[154],"suited":[155,257],"application":[156,248,282],"Recon":[161,231],"2,":[162],"latest":[164],"human":[167],"metabolism.":[168],"RESULTS:":[169],"All":[170,233],"enabled":[173,222],"partially":[174],"identifiers,":[179],"but":[180,234],"significant":[181],"manual":[182,197],"effort":[183,198],"was":[184,255],"still":[185],"required":[186],"fully":[188],"update":[189,225],"able":[193],"reduce":[195],"this":[196,289],"searching":[200],"new":[202],"using":[204],"multiple":[205,212],"types":[206,213],"information":[208,215],"about":[209],"When":[211],"combined,":[217],"System":[221,254],"over":[226],"3,500":[227],"2.":[232],"approximately":[235],"200":[236],"automatically.":[240],"CONCLUSIONS:":[241],"found":[243],"such":[249,280],"better":[256],"several":[272],"features,":[273],"however,":[274],"added":[278],"order":[284],"tailor":[286],"it":[287],"task.":[290]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
