{"id":"https://openalex.org/W4312197939","doi":"https://doi.org/10.1093/bib/bbac553","title":"Comprehensive investigation of pathway enrichment methods for functional interpretation of LC\u2013MS global metabolomics data","display_name":"Comprehensive investigation of pathway enrichment methods for functional interpretation of LC\u2013MS global metabolomics data","publication_year":2022,"publication_date":"2022-12-26","ids":{"openalex":"https://openalex.org/W4312197939","doi":"https://doi.org/10.1093/bib/bbac553","pmid":"https://pubmed.ncbi.nlm.nih.gov/36572652"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac553","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac553","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9851290","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085873420","display_name":"Yao L\u00fc","orcid":"https://orcid.org/0000-0002-0787-6449"},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Yao Lu","raw_affiliation_strings":["Department of Microbiology and Immunology, McGill University , Quebec, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Immunology, McGill University , Quebec, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073424887","display_name":"Zhiqiang Pang","orcid":"https://orcid.org/0000-0003-1654-7556"},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Zhiqiang Pang","raw_affiliation_strings":["Institute of Parasitology, McGill University , Quebec, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Parasitology, McGill University , Quebec, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073663029","display_name":"Jianguo Xia","orcid":"https://orcid.org/0000-0003-2040-2624"},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Jianguo Xia","raw_affiliation_strings":["Department of Microbiology and Immunology, McGill University , Quebec, Canada","Institute of Parasitology, McGill University , Quebec, Canada"],"raw_orcid":"https://orcid.org/0000-0003-2040-2624","affiliations":[{"raw_affiliation_string":"Department of Microbiology and Immunology, McGill University , Quebec, Canada","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"Institute of Parasitology, McGill University , Quebec, Canada","institution_ids":["https://openalex.org/I5023651"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5073663029"],"corresponding_institution_ids":["https://openalex.org/I5023651"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":11.9599,"has_fulltext":false,"cited_by_count":156,"citation_normalized_percentile":{"value":0.99297733,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"24","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9983999729156494,"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":0.9983999729156494,"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/T10066","display_name":"Gut microbiota and health","score":0.00019999999494757503,"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":9.999999747378752e-05,"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/metabolomics","display_name":"Metabolomics","score":0.9111341834068298},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6068461537361145},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5693457722663879},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.530910849571228},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.4724460244178772},{"id":"https://openalex.org/keywords/metabolite","display_name":"Metabolite","score":0.42583325505256653},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.41888701915740967},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3487101197242737},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28496992588043213},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2626722455024719},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22660276293754578},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.0723562240600586}],"concepts":[{"id":"https://openalex.org/C21565614","wikidata":"https://www.wikidata.org/wiki/Q12149006","display_name":"Metabolomics","level":2,"score":0.9111341834068298},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6068461537361145},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5693457722663879},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.530910849571228},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4724460244178772},{"id":"https://openalex.org/C2777477808","wikidata":"https://www.wikidata.org/wiki/Q407595","display_name":"Metabolite","level":2,"score":0.42583325505256653},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.41888701915740967},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3487101197242737},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28496992588043213},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2626722455024719},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22660276293754578},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0723562240600586},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbac553","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac553","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36572652","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36572652","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9851290","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9851290","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:9851290","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9851290","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7378091322","display_name":null,"funder_award_id":"U01 CA235493","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":74,"referenced_works":["https://openalex.org/W1611854178","https://openalex.org/W1848567445","https://openalex.org/W1998767819","https://openalex.org/W2003524197","https://openalex.org/W2019402080","https://openalex.org/W2025944550","https://openalex.org/W2053098824","https://openalex.org/W2070977314","https://openalex.org/W2084533385","https://openalex.org/W2100980426","https://openalex.org/W2123060905","https://openalex.org/W2124180807","https://openalex.org/W2127938920","https://openalex.org/W2129099812","https://openalex.org/W2130410032","https://openalex.org/W2134736660","https://openalex.org/W2145265944","https://openalex.org/W2145885671","https://openalex.org/W2151763757","https://openalex.org/W2166574880","https://openalex.org/W2167540852","https://openalex.org/W2183346825","https://openalex.org/W2301389244","https://openalex.org/W2311374380","https://openalex.org/W2472544934","https://openalex.org/W2482440470","https://openalex.org/W2516826190","https://openalex.org/W2572747554","https://openalex.org/W2593436144","https://openalex.org/W2756727801","https://openalex.org/W2765207987","https://openalex.org/W2769063482","https://openalex.org/W2772875656","https://openalex.org/W2781939187","https://openalex.org/W2793555725","https://openalex.org/W2803664483","https://openalex.org/W2807134042","https://openalex.org/W2888303476","https://openalex.org/W2902454325","https://openalex.org/W2903406988","https://openalex.org/W2916376502","https://openalex.org/W2922805334","https://openalex.org/W2951891306","https://openalex.org/W2972554015","https://openalex.org/W2977870980","https://openalex.org/W2981736362","https://openalex.org/W2984996233","https://openalex.org/W2996714860","https://openalex.org/W3004747635","https://openalex.org/W3023343624","https://openalex.org/W3028711203","https://openalex.org/W3080789666","https://openalex.org/W3096168027","https://openalex.org/W3119787852","https://openalex.org/W3128461805","https://openalex.org/W3136308181","https://openalex.org/W3159995035","https://openalex.org/W3164655444","https://openalex.org/W3172048409","https://openalex.org/W3182447987","https://openalex.org/W3193733845","https://openalex.org/W3196948502","https://openalex.org/W3210957482","https://openalex.org/W4200345909","https://openalex.org/W4214724358","https://openalex.org/W4226298065","https://openalex.org/W4280646423","https://openalex.org/W4281786643","https://openalex.org/W4282939468","https://openalex.org/W4283017342","https://openalex.org/W4288685292","https://openalex.org/W4296691261","https://openalex.org/W6720512875","https://openalex.org/W6809380964"],"related_works":["https://openalex.org/W2521903434","https://openalex.org/W1753739957","https://openalex.org/W2361861616","https://openalex.org/W2085913165","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2011282322","https://openalex.org/W2218034408","https://openalex.org/W3084209502","https://openalex.org/W1988419672"],"abstract_inverted_index":{"BACKGROUND:":[0],"Global":[1],"or":[2,24],"untargeted":[3],"metabolomics":[4,34,69,121,234],"is":[5,90,178],"widely":[6],"used":[7],"to":[8,22,73,94,98,180,209],"comprehensively":[9],"investigate":[10],"metabolic":[11],"profiles":[12],"under":[13,138],"various":[14],"pathophysiological":[15],"conditions":[16],"such":[17],"as":[18],"inflammations,":[19],"infections,":[20],"responses":[21],"exposures":[23],"interactions":[25],"with":[26,58],"microbial":[27],"communities.":[28],"However,":[29,71],"biological":[30],"interpretation":[31,65],"of":[32,46,54,66,110,150,213],"global":[33,68,233],"data":[35,191],"remains":[36],"a":[37,107,148,174,214],"daunting":[38],"task.":[39],"Recent":[40],"years":[41],"have":[42,105,146,171],"seen":[43],"growing":[44],"applications":[45],"pathway":[47,116,215],"enrichment":[48,117,132,201],"analysis":[49],"based":[50,185],"on":[51,142,186,196],"putative":[52],"annotations":[53],"liquid":[55],"chromatography":[56],"coupled":[57],"mass":[59],"spectrometry":[60],"(LC-MS)":[61],"peaks":[62],"for":[63,166],"functional":[64,193],"LC-MS-based":[67],"data.":[70],"due":[72],"intricate":[74],"peak-metabolite":[75],"and":[76,115,130,136,157,188,200,227],"metabolite-pathway":[77],"relationships,":[78],"considerable":[79],"variations":[80],"are":[81],"observed":[82,172],"among":[83],"results":[84],"obtained":[85,165],"using":[86,189,224],"different":[87,139],"approaches.":[88],"There":[89],"an":[91,206],"urgent":[92],"need":[93],"benchmark":[95,108],"these":[96],"approaches":[97,114],"inform":[99],"the":[100,143,167,197,211],"best":[101],"practices.":[102],"RESULTS:":[103],"We":[104,170],"conducted":[106],"study":[109],"common":[111],"peak":[112,127,153],"annotation":[113,128,176],"methods":[118,129,223],"in":[119],"current":[120,198],"studies.":[122],"Representative":[123],"approaches,":[124],"including":[125],"three":[126],"four":[131],"methods,":[133,202],"were":[134],"selected":[135],"benchmarked":[137],"scenarios.":[140],"Based":[141,195],"results,":[144],"we":[145,203,220],"provided":[147],"set":[149],"recommendations":[151],"regarding":[152],"annotation,":[154],"ranking":[155],"metrics":[156],"feature":[158],"selection.":[159],"The":[160],"overall":[161],"better":[162],"performance":[163],"was":[164],"mummichog":[168],"approach.":[169],"that":[173],"~30%":[175],"rate":[177],"sufficient":[179],"achieve":[181],"high":[182],"recall":[183],"(~90%":[184],"mummichog),":[187],"semi-annotated":[190],"improves":[192],"interpretation.":[194],"platforms":[199],"further":[204],"propose":[205],"identifiability":[207],"index":[208],"indicate":[210],"possibility":[212],"being":[216],"reliably":[217],"identified.":[218],"Finally,":[219],"evaluated":[221],"all":[222],"11":[225],"COVID-19":[226],"8":[228],"inflammatory":[229],"bowel":[230],"diseases":[231],"(IBD)":[232],"datasets.":[235]},"counts_by_year":[{"year":2026,"cited_by_count":20},{"year":2025,"cited_by_count":53},{"year":2024,"cited_by_count":61},{"year":2023,"cited_by_count":22}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
