{"id":"https://openalex.org/W3095049046","doi":"https://doi.org/10.1093/nar/gkaa992","title":"MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models","display_name":"MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models","publication_year":2020,"publication_date":"2020-10-27","ids":{"openalex":"https://openalex.org/W3095049046","doi":"https://doi.org/10.1093/nar/gkaa992","mag":"3095049046","pmid":"https://pubmed.ncbi.nlm.nih.gov/33156326"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkaa992","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkaa992","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/nar/gkaa992","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039131441","display_name":"S\u00e9bastien Moretti","orcid":"https://orcid.org/0000-0003-3947-488X"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"S\u00e9bastien Moretti","raw_affiliation_strings":["Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland"],"affiliations":[{"raw_affiliation_string":"Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103423371","display_name":"Van Du T. Tran","orcid":"https://orcid.org/0000-0003-2074-5029"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Van\u00a0Du\u00a0T Tran","raw_affiliation_strings":["Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland"],"affiliations":[{"raw_affiliation_string":"Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017135540","display_name":"Florence Mehl","orcid":"https://orcid.org/0000-0002-9619-1707"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Florence Mehl","raw_affiliation_strings":["Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland"],"affiliations":[{"raw_affiliation_string":"Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001478163","display_name":"Mark Ibberson","orcid":"https://orcid.org/0000-0003-3152-5670"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Mark Ibberson","raw_affiliation_strings":["Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland"],"affiliations":[{"raw_affiliation_string":"Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006006798","display_name":"Marco Pagni","orcid":"https://orcid.org/0000-0001-9292-9463"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Marco Pagni","raw_affiliation_strings":["Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland"],"affiliations":[{"raw_affiliation_string":"Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5039131441"],"corresponding_institution_ids":["https://openalex.org/I12708293"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":7.5923,"has_fulltext":false,"cited_by_count":187,"citation_normalized_percentile":{"value":0.98277979,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"49","issue":"D1","first_page":"D570","last_page":"D574"},"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":0.9914000034332275,"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":0.9858999848365784,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/namespace","display_name":"Namespace","score":0.9617440700531006},{"id":"https://openalex.org/keywords/sparql","display_name":"SPARQL","score":0.9028936624526978},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7981792688369751},{"id":"https://openalex.org/keywords/rdf","display_name":"RDF","score":0.7132051587104797},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6085429191589355},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.59844970703125},{"id":"https://openalex.org/keywords/resource","display_name":"Resource (disambiguation)","score":0.4673514664173126},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.42397475242614746},{"id":"https://openalex.org/keywords/flat-file-database","display_name":"Flat file database","score":0.4156806468963623},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40126776695251465},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3108653724193573},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3042394816875458},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.27493178844451904}],"concepts":[{"id":"https://openalex.org/C2778383056","wikidata":"https://www.wikidata.org/wiki/Q873636","display_name":"Namespace","level":2,"score":0.9617440700531006},{"id":"https://openalex.org/C41009113","wikidata":"https://www.wikidata.org/wiki/Q54871","display_name":"SPARQL","level":4,"score":0.9028936624526978},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7981792688369751},{"id":"https://openalex.org/C147497476","wikidata":"https://www.wikidata.org/wiki/Q54872","display_name":"RDF","level":3,"score":0.7132051587104797},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6085429191589355},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.59844970703125},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.4673514664173126},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.42397475242614746},{"id":"https://openalex.org/C201743585","wikidata":"https://www.wikidata.org/wiki/Q1373925","display_name":"Flat file database","level":5,"score":0.4156806468963623},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40126776695251465},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3108653724193573},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3042394816875458},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.27493178844451904},{"id":"https://openalex.org/C13674803","wikidata":"https://www.wikidata.org/wiki/Q7627301","display_name":"Stub file","level":3,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C21729314","wikidata":"https://www.wikidata.org/wiki/Q7896858","display_name":"Unix file types","level":4,"score":0.0},{"id":"https://openalex.org/C95637964","wikidata":"https://www.wikidata.org/wiki/Q82753","display_name":"Computer file","level":2,"score":0.0},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0}],"mesh":[{"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":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","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":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkaa992","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkaa992","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:33156326","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33156326","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7778905","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7778905","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":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkaa992","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkaa992","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5699999928474426,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W1935434993","https://openalex.org/W1952732684","https://openalex.org/W1989277387","https://openalex.org/W1994028898","https://openalex.org/W2068526246","https://openalex.org/W2076262841","https://openalex.org/W2100084634","https://openalex.org/W2107409961","https://openalex.org/W2111796963","https://openalex.org/W2116687544","https://openalex.org/W2117306286","https://openalex.org/W2124653577","https://openalex.org/W2142678478","https://openalex.org/W2165373392","https://openalex.org/W2167539386","https://openalex.org/W2170427655","https://openalex.org/W2174759676","https://openalex.org/W2543238710","https://openalex.org/W2554210752","https://openalex.org/W2559588208","https://openalex.org/W2627067371","https://openalex.org/W2762019694","https://openalex.org/W2766958291","https://openalex.org/W2767088268","https://openalex.org/W2767683865","https://openalex.org/W2781587170","https://openalex.org/W2781637109","https://openalex.org/W2789128799","https://openalex.org/W2790730158","https://openalex.org/W2805168103","https://openalex.org/W2885949449","https://openalex.org/W2892125910","https://openalex.org/W2895341279","https://openalex.org/W2949726389","https://openalex.org/W2952015518","https://openalex.org/W2952894564","https://openalex.org/W2953213185","https://openalex.org/W2953278221","https://openalex.org/W2987028578","https://openalex.org/W3010629926","https://openalex.org/W3026996309","https://openalex.org/W3043026144","https://openalex.org/W3080133182","https://openalex.org/W3081478800","https://openalex.org/W3136918052","https://openalex.org/W3211402536","https://openalex.org/W6770172025","https://openalex.org/W6813094581"],"related_works":["https://openalex.org/W2615202182","https://openalex.org/W4206665951","https://openalex.org/W3085073370","https://openalex.org/W2904139343","https://openalex.org/W2529794967","https://openalex.org/W2604011835","https://openalex.org/W2978246852","https://openalex.org/W2295924417","https://openalex.org/W4241483715","https://openalex.org/W2484233589"],"abstract_inverted_index":{"MetaNetX/MNXref":[0],"is":[1,63],"a":[2,94],"reconciliation":[3],"of":[4,32,44,66],"metabolites":[5],"and":[6,15,57,84],"biochemical":[7],"reactions":[8],"providing":[9],"cross-links":[10],"between":[11],"major":[12,61],"public":[13],"biochemistry":[14],"Genome-Scale":[16],"Metabolic":[17],"Network":[18],"(GSMN)":[19],"databases.":[20],"The":[21,47],"new":[22],"release":[23],"brings":[24],"several":[25],"improvements":[26],"with":[27,35],"respect":[28],"to":[29,39,53,69,81],"the":[30,33,41,54,82,87],"quality":[31],"reconciliation,":[34],"particular":[36],"attention":[37],"dedicated":[38],"preserving":[40],"intrinsic":[42],"properties":[43],"GSMN":[45],"models.":[46],"MetaNetX":[48],"website":[49,83],"(https://www.metanetx.org/)":[50],"provides":[51,73],"access":[52],"full":[55],"database":[56],"online":[58],"services.":[59],"A":[60],"improvement":[62],"for":[64],"mapping":[65],"user-provided":[67],"GSMNs":[68],"MXNref,":[70],"which":[71],"now":[72,90],"diagnostic":[74],"messages":[75],"about":[76],"model":[77],"content.":[78],"In":[79],"addition":[80],"flat":[85],"files,":[86],"resource":[88],"can":[89],"be":[91],"accessed":[92],"through":[93],"SPARQL":[95],"endpoint":[96],"(https://rdf.metanetx.org).":[97]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":45},{"year":2024,"cited_by_count":44},{"year":2023,"cited_by_count":36},{"year":2022,"cited_by_count":32},{"year":2021,"cited_by_count":23}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
