{"id":"https://openalex.org/W4294012193","doi":"https://doi.org/10.1093/bioinformatics/btac596","title":"MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions","display_name":"MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions","publication_year":2022,"publication_date":"2022-09-01","ids":{"openalex":"https://openalex.org/W4294012193","doi":"https://doi.org/10.1093/bioinformatics/btac596","pmid":"https://pubmed.ncbi.nlm.nih.gov/36047841"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac596","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac596","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btac596/45884328/btac596.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btac596/45884328/btac596.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074725115","display_name":"Ines Thiele","orcid":"https://orcid.org/0000-0002-8071-7110"},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]},{"id":"https://openalex.org/I27577105","display_name":"University College Cork","ror":"https://ror.org/03265fv13","country_code":"IE","type":"education","lineage":["https://openalex.org/I27577105"]},{"id":"https://openalex.org/I4210141138","display_name":"APC Microbiome Institute","ror":"https://ror.org/03f2ct267","country_code":"IE","type":"facility","lineage":["https://openalex.org/I4210141138"]}],"countries":["IE"],"is_corresponding":true,"raw_author_name":"Ines Thiele","raw_affiliation_strings":["APC Microbiome Ireland, University College Cork , Cork T12K8AF, Ireland","Division of Microbiology, University of Galway , Galway H91TK33, Ireland","Ryan Institute, University of Galway , Galway H91TK33, Ireland","School of Medicine, University of Galway , Galway H91TK33, Ireland"],"affiliations":[{"raw_affiliation_string":"APC Microbiome Ireland, University College Cork , Cork T12K8AF, Ireland","institution_ids":["https://openalex.org/I4210141138","https://openalex.org/I27577105"]},{"raw_affiliation_string":"Division of Microbiology, University of Galway , Galway H91TK33, Ireland","institution_ids":["https://openalex.org/I188760350"]},{"raw_affiliation_string":"Ryan Institute, University of Galway , Galway H91TK33, Ireland","institution_ids":["https://openalex.org/I188760350"]},{"raw_affiliation_string":"School of Medicine, University of Galway , Galway H91TK33, Ireland","institution_ids":["https://openalex.org/I188760350"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010812707","display_name":"German Preciat","orcid":"https://orcid.org/0000-0003-4903-9515"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]},{"id":"https://openalex.org/I4210133171","display_name":"Centre for Human Drug Research","ror":"https://ror.org/044hshx49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I4210133171"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"German Preciat","raw_affiliation_strings":["Analytical BioSciences Division, Leiden Academic Centre for Drug Research, Leiden University , 2311 EZ, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Analytical BioSciences Division, Leiden Academic Centre for Drug Research, Leiden University , 2311 EZ, The Netherlands","institution_ids":["https://openalex.org/I4210133171","https://openalex.org/I121797337"]}]},{"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/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]},{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]},{"id":"https://openalex.org/I4210133171","display_name":"Centre for Human Drug Research","ror":"https://ror.org/044hshx49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I4210133171"]}],"countries":["IE","NL"],"is_corresponding":false,"raw_author_name":"Ronan M T Fleming","raw_affiliation_strings":["Analytical BioSciences Division, Leiden Academic Centre for Drug Research, Leiden University , 2311 EZ, The Netherlands","School of Medicine, University of Galway , Galway H91TK33, Ireland"],"affiliations":[{"raw_affiliation_string":"Analytical BioSciences Division, Leiden Academic Centre for Drug Research, Leiden University , 2311 EZ, The Netherlands","institution_ids":["https://openalex.org/I4210133171","https://openalex.org/I121797337"]},{"raw_affiliation_string":"School of Medicine, University of Galway , Galway H91TK33, Ireland","institution_ids":["https://openalex.org/I188760350"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5074725115"],"corresponding_institution_ids":["https://openalex.org/I188760350","https://openalex.org/I27577105","https://openalex.org/I4210141138"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.6076,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.64533363,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"38","issue":"20","first_page":"4831","last_page":"4832"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9997000098228455,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9997000098228455,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9995999932289124,"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":0.9944000244140625,"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/toolbox","display_name":"Toolbox","score":0.8154869079589844},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.7562345266342163},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7280613780021667},{"id":"https://openalex.org/keywords/metabolite","display_name":"Metabolite","score":0.7206667065620422},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.5628275275230408},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5152695178985596},{"id":"https://openalex.org/keywords/metabolomics","display_name":"Metabolomics","score":0.5101897716522217},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4247642755508423},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.41259026527404785},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2801351547241211},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1945328712463379},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.10424897074699402},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10104244947433472},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.06621906161308289}],"concepts":[{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.8154869079589844},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7562345266342163},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7280613780021667},{"id":"https://openalex.org/C2777477808","wikidata":"https://www.wikidata.org/wiki/Q407595","display_name":"Metabolite","level":2,"score":0.7206667065620422},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.5628275275230408},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5152695178985596},{"id":"https://openalex.org/C21565614","wikidata":"https://www.wikidata.org/wiki/Q12149006","display_name":"Metabolomics","level":2,"score":0.5101897716522217},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4247642755508423},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.41259026527404785},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2801351547241211},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1945328712463379},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.10424897074699402},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10104244947433472},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.06621906161308289}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","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":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":false},{"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":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btac596","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac596","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btac596/45884328/btac596.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36047841","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36047841","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9563688","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9563688","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:scholarlypublications.universiteitleiden.nl:item_3512400","is_oa":true,"landing_page_url":"https://hdl.handle.net/1887/3512400","pdf_url":null,"source":{"id":"https://openalex.org/S4306400850","display_name":"Leiden Repository (Leiden University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I121797337","host_organization_name":"Leiden University","host_organization_lineage":["https://openalex.org/I121797337"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Article / Letter to editor"},{"id":"pmh:ul:oai:scholarlypublications.universiteitleiden.nl:item_3512400","is_oa":true,"landing_page_url":"http://hdl.handle.net/1887/3512400","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 38(20), 4831 - 4832","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac596","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac596","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btac596/45884328/btac596.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G160496021","display_name":null,"funder_award_id":"RF1AG058942","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G160596578","display_name":"Predicting the effects of gut microbiota and diet on an individual\u2019s drug response and safety","funder_award_id":"757922","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4956428346","display_name":null,"funder_award_id":"Horizon 2020 research and innovatio","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5036817778","display_name":null,"funder_award_id":"European Union's Horizon 2020 research and innov","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7223442655","display_name":null,"funder_award_id":"U19AG063744","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G8318064016","display_name":null,"funder_award_id":"Horizon","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8633428685","display_name":null,"funder_award_id":"European Union's Horizon 2020 research and innovat","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320337337","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4294012193.pdf","grobid_xml":"https://content.openalex.org/works/W4294012193.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W2085993965","https://openalex.org/W2120680184","https://openalex.org/W2140611297","https://openalex.org/W2161568599","https://openalex.org/W2169678694","https://openalex.org/W2559588208","https://openalex.org/W2762019694","https://openalex.org/W2767683865","https://openalex.org/W2789128799","https://openalex.org/W2899070097","https://openalex.org/W2950173838","https://openalex.org/W3010629926","https://openalex.org/W3029912146","https://openalex.org/W3198506764"],"related_works":["https://openalex.org/W2007897985","https://openalex.org/W2951891306","https://openalex.org/W2337831726","https://openalex.org/W2890957471","https://openalex.org/W2483024785","https://openalex.org/W2508694782","https://openalex.org/W3111798230","https://openalex.org/W2482268455","https://openalex.org/W3003414789","https://openalex.org/W4281681561"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3}],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2025-10-10T00:00:00"}
