{"id":"https://openalex.org/W3196948502","doi":"https://doi.org/10.1371/journal.pcbi.1009105","title":"Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis","display_name":"Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis","publication_year":2021,"publication_date":"2021-09-07","ids":{"openalex":"https://openalex.org/W3196948502","doi":"https://doi.org/10.1371/journal.pcbi.1009105","mag":"3196948502","pmid":"https://pubmed.ncbi.nlm.nih.gov/34492007"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1009105","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009105","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1009105","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029500459","display_name":"Cecilia Wieder","orcid":"https://orcid.org/0000-0003-1548-4346"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Cecilia Wieder","raw_affiliation_strings":["Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0003-1548-4346","affiliations":[{"raw_affiliation_string":"Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081946997","display_name":"Cl\u00e9ment Frainay","orcid":"https://orcid.org/0000-0003-4313-2786"},"institutions":[{"id":"https://openalex.org/I134560555","display_name":"Universit\u00e9 Toulouse III - Paul Sabatier","ror":"https://ror.org/02v6kpv12","country_code":"FR","type":"education","lineage":["https://openalex.org/I134560555"]},{"id":"https://openalex.org/I176063091","display_name":"\u00c9cole Nationale V\u00e9t\u00e9rinaire de Toulouse","ror":"https://ror.org/03m3gzv89","country_code":"FR","type":"education","lineage":["https://openalex.org/I176063091","https://openalex.org/I4210117091"]},{"id":"https://openalex.org/I17866349","display_name":"Universit\u00e9 F\u00e9d\u00e9rale de Toulouse Midi-Pyr\u00e9n\u00e9es","ror":"https://ror.org/004raaa70","country_code":"FR","type":"education","lineage":["https://openalex.org/I17866349"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210100066","display_name":"Toxicologie Alimentaire","ror":"https://ror.org/0111a5077","country_code":"FR","type":"facility","lineage":["https://openalex.org/I176063091","https://openalex.org/I4210088668","https://openalex.org/I4210089154","https://openalex.org/I4210100066","https://openalex.org/I4210117091","https://openalex.org/I4405258862","https://openalex.org/I4405258862"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Cl\u00e9ment Frainay","raw_affiliation_strings":["Toxalim (Research Centre in Food Toxicology), Universit\u00e9 de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France"],"raw_orcid":"https://orcid.org/0000-0003-4313-2786","affiliations":[{"raw_affiliation_string":"Toxalim (Research Centre in Food Toxicology), Universit\u00e9 de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France","institution_ids":["https://openalex.org/I4210100066","https://openalex.org/I17866349","https://openalex.org/I134560555","https://openalex.org/I176063091","https://openalex.org/I4210088668"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051880093","display_name":"Nathalie Poupin","orcid":"https://orcid.org/0000-0002-3393-1405"},"institutions":[{"id":"https://openalex.org/I134560555","display_name":"Universit\u00e9 Toulouse III - Paul Sabatier","ror":"https://ror.org/02v6kpv12","country_code":"FR","type":"education","lineage":["https://openalex.org/I134560555"]},{"id":"https://openalex.org/I176063091","display_name":"\u00c9cole Nationale V\u00e9t\u00e9rinaire de Toulouse","ror":"https://ror.org/03m3gzv89","country_code":"FR","type":"education","lineage":["https://openalex.org/I176063091","https://openalex.org/I4210117091"]},{"id":"https://openalex.org/I17866349","display_name":"Universit\u00e9 F\u00e9d\u00e9rale de Toulouse Midi-Pyr\u00e9n\u00e9es","ror":"https://ror.org/004raaa70","country_code":"FR","type":"education","lineage":["https://openalex.org/I17866349"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210100066","display_name":"Toxicologie Alimentaire","ror":"https://ror.org/0111a5077","country_code":"FR","type":"facility","lineage":["https://openalex.org/I176063091","https://openalex.org/I4210088668","https://openalex.org/I4210089154","https://openalex.org/I4210100066","https://openalex.org/I4210117091","https://openalex.org/I4405258862","https://openalex.org/I4405258862"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Nathalie Poupin","raw_affiliation_strings":["Toxalim (Research Centre in Food Toxicology), Universit\u00e9 de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France"],"raw_orcid":"https://orcid.org/0000-0002-3393-1405","affiliations":[{"raw_affiliation_string":"Toxalim (Research Centre in Food Toxicology), Universit\u00e9 de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France","institution_ids":["https://openalex.org/I4210100066","https://openalex.org/I17866349","https://openalex.org/I134560555","https://openalex.org/I176063091","https://openalex.org/I4210088668"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006843566","display_name":"Pablo Rodr\u00edguez-Mier","orcid":"https://orcid.org/0000-0002-4938-4418"},"institutions":[{"id":"https://openalex.org/I134560555","display_name":"Universit\u00e9 Toulouse III - Paul Sabatier","ror":"https://ror.org/02v6kpv12","country_code":"FR","type":"education","lineage":["https://openalex.org/I134560555"]},{"id":"https://openalex.org/I176063091","display_name":"\u00c9cole Nationale V\u00e9t\u00e9rinaire de Toulouse","ror":"https://ror.org/03m3gzv89","country_code":"FR","type":"education","lineage":["https://openalex.org/I176063091","https://openalex.org/I4210117091"]},{"id":"https://openalex.org/I17866349","display_name":"Universit\u00e9 F\u00e9d\u00e9rale de Toulouse Midi-Pyr\u00e9n\u00e9es","ror":"https://ror.org/004raaa70","country_code":"FR","type":"education","lineage":["https://openalex.org/I17866349"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210100066","display_name":"Toxicologie Alimentaire","ror":"https://ror.org/0111a5077","country_code":"FR","type":"facility","lineage":["https://openalex.org/I176063091","https://openalex.org/I4210088668","https://openalex.org/I4210089154","https://openalex.org/I4210100066","https://openalex.org/I4210117091","https://openalex.org/I4405258862","https://openalex.org/I4405258862"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Pablo Rodr\u00edguez-Mier","raw_affiliation_strings":["Toxalim (Research Centre in Food Toxicology), Universit\u00e9 de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France"],"raw_orcid":"https://orcid.org/0000-0002-4938-4418","affiliations":[{"raw_affiliation_string":"Toxalim (Research Centre in Food Toxicology), Universit\u00e9 de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France","institution_ids":["https://openalex.org/I4210100066","https://openalex.org/I17866349","https://openalex.org/I134560555","https://openalex.org/I176063091","https://openalex.org/I4210088668"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031143055","display_name":"Florence Vinson","orcid":"https://orcid.org/0000-0001-8143-8183"},"institutions":[{"id":"https://openalex.org/I134560555","display_name":"Universit\u00e9 Toulouse III - Paul Sabatier","ror":"https://ror.org/02v6kpv12","country_code":"FR","type":"education","lineage":["https://openalex.org/I134560555"]},{"id":"https://openalex.org/I176063091","display_name":"\u00c9cole Nationale V\u00e9t\u00e9rinaire de Toulouse","ror":"https://ror.org/03m3gzv89","country_code":"FR","type":"education","lineage":["https://openalex.org/I176063091","https://openalex.org/I4210117091"]},{"id":"https://openalex.org/I17866349","display_name":"Universit\u00e9 F\u00e9d\u00e9rale de Toulouse Midi-Pyr\u00e9n\u00e9es","ror":"https://ror.org/004raaa70","country_code":"FR","type":"education","lineage":["https://openalex.org/I17866349"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210100066","display_name":"Toxicologie Alimentaire","ror":"https://ror.org/0111a5077","country_code":"FR","type":"facility","lineage":["https://openalex.org/I176063091","https://openalex.org/I4210088668","https://openalex.org/I4210089154","https://openalex.org/I4210100066","https://openalex.org/I4210117091","https://openalex.org/I4405258862","https://openalex.org/I4405258862"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Florence Vinson","raw_affiliation_strings":["Toxalim (Research Centre in Food Toxicology), Universit\u00e9 de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France"],"raw_orcid":"https://orcid.org/0000-0001-8143-8183","affiliations":[{"raw_affiliation_string":"Toxalim (Research Centre in Food Toxicology), Universit\u00e9 de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France","institution_ids":["https://openalex.org/I4210100066","https://openalex.org/I17866349","https://openalex.org/I134560555","https://openalex.org/I176063091","https://openalex.org/I4210088668"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049665024","display_name":"Juliette Cooke","orcid":"https://orcid.org/0000-0003-2085-0339"},"institutions":[{"id":"https://openalex.org/I134560555","display_name":"Universit\u00e9 Toulouse III - Paul Sabatier","ror":"https://ror.org/02v6kpv12","country_code":"FR","type":"education","lineage":["https://openalex.org/I134560555"]},{"id":"https://openalex.org/I176063091","display_name":"\u00c9cole Nationale V\u00e9t\u00e9rinaire de Toulouse","ror":"https://ror.org/03m3gzv89","country_code":"FR","type":"education","lineage":["https://openalex.org/I176063091","https://openalex.org/I4210117091"]},{"id":"https://openalex.org/I17866349","display_name":"Universit\u00e9 F\u00e9d\u00e9rale de Toulouse Midi-Pyr\u00e9n\u00e9es","ror":"https://ror.org/004raaa70","country_code":"FR","type":"education","lineage":["https://openalex.org/I17866349"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210100066","display_name":"Toxicologie Alimentaire","ror":"https://ror.org/0111a5077","country_code":"FR","type":"facility","lineage":["https://openalex.org/I176063091","https://openalex.org/I4210088668","https://openalex.org/I4210089154","https://openalex.org/I4210100066","https://openalex.org/I4210117091","https://openalex.org/I4405258862","https://openalex.org/I4405258862"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Juliette Cooke","raw_affiliation_strings":["Toxalim (Research Centre in Food Toxicology), Universit\u00e9 de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France"],"raw_orcid":"https://orcid.org/0000-0003-2085-0339","affiliations":[{"raw_affiliation_string":"Toxalim (Research Centre in Food Toxicology), Universit\u00e9 de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France","institution_ids":["https://openalex.org/I4210100066","https://openalex.org/I17866349","https://openalex.org/I134560555","https://openalex.org/I176063091","https://openalex.org/I4210088668"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003933808","display_name":"Rachel Lai","orcid":"https://orcid.org/0000-0003-3418-850X"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Rachel PJ Lai","raw_affiliation_strings":["Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0003-3418-850X","affiliations":[{"raw_affiliation_string":"Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064846441","display_name":"Jacob G. Bundy","orcid":"https://orcid.org/0000-0002-1164-8465"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jacob G. Bundy","raw_affiliation_strings":["Section of Biomolecular Medicine, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-1164-8465","affiliations":[{"raw_affiliation_string":"Section of Biomolecular Medicine, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008100854","display_name":"Fabien Jourdan","orcid":"https://orcid.org/0000-0001-9401-2894"},"institutions":[{"id":"https://openalex.org/I134560555","display_name":"Universit\u00e9 Toulouse III - Paul Sabatier","ror":"https://ror.org/02v6kpv12","country_code":"FR","type":"education","lineage":["https://openalex.org/I134560555"]},{"id":"https://openalex.org/I176063091","display_name":"\u00c9cole Nationale V\u00e9t\u00e9rinaire de Toulouse","ror":"https://ror.org/03m3gzv89","country_code":"FR","type":"education","lineage":["https://openalex.org/I176063091","https://openalex.org/I4210117091"]},{"id":"https://openalex.org/I17866349","display_name":"Universit\u00e9 F\u00e9d\u00e9rale de Toulouse Midi-Pyr\u00e9n\u00e9es","ror":"https://ror.org/004raaa70","country_code":"FR","type":"education","lineage":["https://openalex.org/I17866349"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210100066","display_name":"Toxicologie Alimentaire","ror":"https://ror.org/0111a5077","country_code":"FR","type":"facility","lineage":["https://openalex.org/I176063091","https://openalex.org/I4210088668","https://openalex.org/I4210089154","https://openalex.org/I4210100066","https://openalex.org/I4210117091","https://openalex.org/I4405258862","https://openalex.org/I4405258862"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Fabien Jourdan","raw_affiliation_strings":["MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France","Toxalim (Research Centre in Food Toxicology), Universit\u00e9 de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France"],"raw_orcid":"https://orcid.org/0000-0001-9401-2894","affiliations":[{"raw_affiliation_string":"MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France","institution_ids":[]},{"raw_affiliation_string":"Toxalim (Research Centre in Food Toxicology), Universit\u00e9 de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France","institution_ids":["https://openalex.org/I4210100066","https://openalex.org/I17866349","https://openalex.org/I134560555","https://openalex.org/I176063091","https://openalex.org/I4210088668"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056339769","display_name":"Timothy M. D. Ebbels","orcid":"https://orcid.org/0000-0002-3372-8423"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Timothy Ebbels","raw_affiliation_strings":["Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5056339769"],"corresponding_institution_ids":["https://openalex.org/I47508984"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":10.261,"has_fulltext":true,"cited_by_count":177,"citation_normalized_percentile":{"value":0.99040282,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"17","issue":"9","first_page":"e1009105","last_page":"e1009105"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","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":0.9915000200271606,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9778000116348267,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/metabolomics","display_name":"Metabolomics","score":0.8668584227561951},{"id":"https://openalex.org/keywords/kegg","display_name":"KEGG","score":0.665486752986908},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.567339301109314},{"id":"https://openalex.org/keywords/pathway-analysis","display_name":"Pathway analysis","score":0.5237565040588379},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.48399829864501953},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.45979616045951843},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45667099952697754},{"id":"https://openalex.org/keywords/metabolic-pathway","display_name":"Metabolic pathway","score":0.42975887656211853},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36219513416290283},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3381268382072449},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27841734886169434},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09255897998809814},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.07772302627563477},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.06550732254981995}],"concepts":[{"id":"https://openalex.org/C21565614","wikidata":"https://www.wikidata.org/wiki/Q12149006","display_name":"Metabolomics","level":2,"score":0.8668584227561951},{"id":"https://openalex.org/C152724338","wikidata":"https://www.wikidata.org/wiki/Q909442","display_name":"KEGG","level":5,"score":0.665486752986908},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.567339301109314},{"id":"https://openalex.org/C2779230013","wikidata":"https://www.wikidata.org/wiki/Q25303877","display_name":"Pathway analysis","level":4,"score":0.5237565040588379},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48399829864501953},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.45979616045951843},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45667099952697754},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.42975887656211853},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36219513416290283},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3381268382072449},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27841734886169434},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09255897998809814},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.07772302627563477},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.06550732254981995},{"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","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":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","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":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","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":true},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","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":true},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1009105","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009105","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:34492007","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34492007","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:HAL:hal-03344682v1","is_oa":true,"landing_page_url":"https://hal.inrae.fr/hal-03344682","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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":"PLoS Computational Biology, 2021, 17 (9), &#x27E8;10.1371/journal.pcbi.1009105&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:doaj.org/article:38f5454156524f19b62777d46227717a","is_oa":true,"landing_page_url":"https://doaj.org/article/38f5454156524f19b62777d46227717a","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 17, Iss 9, p e1009105 (2021)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:7340447","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8448349","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:8448349","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8448349","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1009105","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009105","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1050179613","display_name":"STEROID PROTECTION FROM TUBERCULOSIS-ASSOCIATED IMMUNE RECONSTITUTION INFLAMMATORY SYNDROME","funder_award_id":"MR/R008922/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G1090516614","display_name":null,"funder_award_id":"R01 HL133932-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1502031688","display_name":null,"funder_award_id":"MR/S019669/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G1701253693","display_name":null,"funder_award_id":"222837/Z/21/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G1790795098","display_name":null,"funder_award_id":"BB/T007974/2","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G2014166693","display_name":"Standardised metabolite annotation workflows for enhanced biological interpretation in metabolomic data repositories","funder_award_id":"BB/T007974/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G2459364264","display_name":null,"funder_award_id":"BB/T007974/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G2747416232","display_name":"MetClassNet: Kombination von Multinetzwerken zur \u00dcberbr\u00fcck der L\u00fccke zwsichen Genomskalischen metabolischen Modellen und der nicht zielgerichteten Metabolomik","funder_award_id":"431572533","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G2760557121","display_name":null,"funder_award_id":"DFG: 431572533","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G3214677586","display_name":null,"funder_award_id":"MR/R008922/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G4511766892","display_name":null,"funder_award_id":"R01 HL133932","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G4697447500","display_name":"New approaches to bridge the gap between genome-scale metabolic networks and untargeted metabolomics","funder_award_id":"ANR-19-CE45-0021","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G5792672869","display_name":null,"funder_award_id":"HL133932","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6393878258","display_name":"Standardised metabolite annotation workflows for enhanced biological interpretation in metabolomic data repositories","funder_award_id":"BB/T007974/2","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G7598247955","display_name":null,"funder_award_id":"DFG: 431572533","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8003643215","display_name":null,"funder_award_id":"ANR-INBS-0010","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G8318455765","display_name":null,"funder_award_id":"ANR-19","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G8431882926","display_name":null,"funder_award_id":"222837/Z/21/Z","funder_id":"https://openalex.org/F4320307874","funder_display_name":"Wellcome"},{"id":"https://openalex.org/G8907031238","display_name":"D\u00e9veloppement d'une infrastructure fran\u00e7aise distribu\u00e9e pour la m\u00e9tabolomique d\u00e9di\u00e9e \u00e0 l'innovation","funder_award_id":"ANR-11-INBS-0010","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320307874","display_name":"Wellcome","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320313290","display_name":"Ontario Institute for Cancer Research","ror":"https://ror.org/043q8yx54"},{"id":"https://openalex.org/F4320313933","display_name":"Minist\u00e8re de l'Enseignement sup\u00e9rieur, de la Recherche et de l'Innovation","ror":null},{"id":"https://openalex.org/F4320319990","display_name":"National Institute for Health and Care Research","ror":"https://ror.org/0187kwz08"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"},{"id":"https://openalex.org/F4320336039","display_name":"NIHR Imperial Biomedical Research Centre","ror":"https://ror.org/01kmhx639"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":64,"referenced_works":["https://openalex.org/W117085007","https://openalex.org/W1535641839","https://openalex.org/W1560020441","https://openalex.org/W1611854178","https://openalex.org/W1954643541","https://openalex.org/W1989277387","https://openalex.org/W2093999858","https://openalex.org/W2100980426","https://openalex.org/W2102899487","https://openalex.org/W2110065044","https://openalex.org/W2118588291","https://openalex.org/W2135000328","https://openalex.org/W2151014102","https://openalex.org/W2157253968","https://openalex.org/W2159482845","https://openalex.org/W2162143298","https://openalex.org/W2224812643","https://openalex.org/W2287154159","https://openalex.org/W2517051411","https://openalex.org/W2556428520","https://openalex.org/W2577168473","https://openalex.org/W2618870156","https://openalex.org/W2749464300","https://openalex.org/W2754965172","https://openalex.org/W2765161617","https://openalex.org/W2781939187","https://openalex.org/W2782327081","https://openalex.org/W2794105678","https://openalex.org/W2800340189","https://openalex.org/W2802585007","https://openalex.org/W2803664483","https://openalex.org/W2805362922","https://openalex.org/W2806179048","https://openalex.org/W2857924514","https://openalex.org/W2891967723","https://openalex.org/W2907209357","https://openalex.org/W2907919699","https://openalex.org/W2912621306","https://openalex.org/W2918355935","https://openalex.org/W2949004447","https://openalex.org/W2950115754","https://openalex.org/W2951846550","https://openalex.org/W2974971672","https://openalex.org/W2979832776","https://openalex.org/W2985897872","https://openalex.org/W2989619704","https://openalex.org/W2993372100","https://openalex.org/W2996060386","https://openalex.org/W3000137095","https://openalex.org/W3013440247","https://openalex.org/W3023697611","https://openalex.org/W3105982350","https://openalex.org/W3118592187","https://openalex.org/W3122914802","https://openalex.org/W3128461805","https://openalex.org/W3134754773","https://openalex.org/W3136308181","https://openalex.org/W3153543576","https://openalex.org/W3195098488","https://openalex.org/W4231254854","https://openalex.org/W4237335579","https://openalex.org/W4240861547","https://openalex.org/W4301818537","https://openalex.org/W6813094581"],"related_works":["https://openalex.org/W4401441519","https://openalex.org/W4402761624","https://openalex.org/W4288069755","https://openalex.org/W1726300337","https://openalex.org/W1854805732","https://openalex.org/W3201283333","https://openalex.org/W3180007124","https://openalex.org/W4206444712","https://openalex.org/W4229007988","https://openalex.org/W2378339845"],"abstract_inverted_index":{"Over-representation":[0],"analysis":[1,9,199,230],"(ORA)":[2],"is":[3],"one":[4],"of":[5,16,23,87,98,107,129,144,151,171,176,205,210,217,228],"the":[6,13,20,27,42,67,108,125,142,148,208,226],"commonest":[7],"pathway":[8,75,112,198,229],"approaches":[10],"used":[11,77],"for":[12,92,189,207],"functional":[14],"interpretation":[15],"metabolomics":[17,138],"datasets.":[18,182],"Despite":[19],"widespread":[21],"use":[22,86,209],"ORA":[24,83,157,190,211],"in":[25,63,80,95,123,168,212,231],"metabolomics,":[26,213],"community":[28],"lacks":[29],"guidelines":[30],"detailing":[31],"its":[32],"best-practice":[33],"use.":[34],"Many":[35],"factors":[36],"have":[37,49,185],"a":[38,88,203,215,222],"pronounced":[39],"impact":[40],"on":[41],"results,":[43],"but":[44],"to":[45,119,137],"date":[46],"their":[47],"effects":[48],"received":[50],"little":[51],"systematic":[52],"attention.":[53],"Using":[54],"five":[55],"publicly":[56],"available":[57],"datasets,":[58],"we":[59],"demonstrated":[60],"that":[61,134],"changes":[62],"parameters":[64],"such":[65,140],"as":[66,141,163,165,192,194,221],"background":[68,90],"set,":[69,91],"differential":[70],"metabolite":[71,160],"selection":[72],"methods,":[73],"and":[74,116,127,147,174],"database":[76,102],"can":[78],"result":[79],"profoundly":[81],"different":[82,121,152],"results.":[84,158],"The":[85],"non-assay-specific":[89],"example,":[93],"resulted":[94,167],"large":[96],"numbers":[97],"false-positive":[99,172],"pathways.":[100,132],"Pathway":[101],"choice,":[103],"evaluated":[104],"using":[105,196],"three":[106],"most":[109],"popular":[110],"metabolic":[111],"databases":[113],"(KEGG,":[114],"Reactome,":[115],"BioCyc),":[117],"led":[118],"vastly":[120],"results":[122,184],"both":[124,169],"number":[126],"function":[128],"significantly":[130],"enriched":[131],"Factors":[133],"are":[135],"specific":[136],"data,":[139],"reliability":[143],"compound":[145],"identification":[146],"chemical":[149],"bias":[150],"analytical":[153],"platforms":[154],"also":[155],"impacted":[156],"Simulated":[159],"misidentification":[161],"rates":[162],"low":[164],"4%":[166],"gain":[170],"pathways":[173,179],"loss":[175],"truly":[177],"significant":[178],"across":[180],"all":[181],"Our":[183],"several":[186],"practical":[187],"implications":[188],"users,":[191],"well":[193],"those":[195],"alternative":[197],"methods.":[200],"We":[201],"offer":[202],"set":[204,216],"recommendations":[206],"alongside":[214],"minimal":[218],"reporting":[219],"guidelines,":[220],"first":[223],"step":[224],"towards":[225],"standardisation":[227],"metabolomics.":[232]},"counts_by_year":[{"year":2026,"cited_by_count":25},{"year":2025,"cited_by_count":42},{"year":2024,"cited_by_count":57},{"year":2023,"cited_by_count":33},{"year":2022,"cited_by_count":20}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
