{"id":"https://openalex.org/W4293081019","doi":"https://doi.org/10.1093/bib/bbac328","title":"Principal microbial groups: compositional alternative to phylogenetic grouping of microbiome data","display_name":"Principal microbial groups: compositional alternative to phylogenetic grouping of microbiome data","publication_year":2022,"publication_date":"2022-08-25","ids":{"openalex":"https://openalex.org/W4293081019","doi":"https://doi.org/10.1093/bib/bbac328","pmid":"https://pubmed.ncbi.nlm.nih.gov/36007229"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac328","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac328","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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031794793","display_name":"Asl\u0131 Boyraz","orcid":"https://orcid.org/0000-0001-9431-2221"},"institutions":[{"id":"https://openalex.org/I161597582","display_name":"Recep Tayyip Erdo\u011fan University","ror":"https://ror.org/0468j1635","country_code":"TR","type":"education","lineage":["https://openalex.org/I161597582"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Asl\u0131 Boyraz","raw_affiliation_strings":["Department of Computer Programming , Recep Tayyip Erdo\u011fan University, Arde\u015fen Vocational School, Rize, 53400 , Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Programming , Recep Tayyip Erdo\u011fan University, Arde\u015fen Vocational School, Rize, 53400 , Turkey","institution_ids":["https://openalex.org/I161597582"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067275109","display_name":"Vera Pawlowsky\u2010Glahn","orcid":"https://orcid.org/0000-0001-9775-6434"},"institutions":[{"id":"https://openalex.org/I251424209","display_name":"Universitat de Girona","ror":"https://ror.org/01xdxns91","country_code":"ES","type":"education","lineage":["https://openalex.org/I251424209"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Vera Pawlowsky-Glahn","raw_affiliation_strings":["Department of Computer Sciences , Applied Mathematics and Statistics, University of Girona, Campus Montilivi, 17003 Girona , Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Sciences , Applied Mathematics and Statistics, University of Girona, Campus Montilivi, 17003 Girona , Spain","institution_ids":["https://openalex.org/I251424209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031078665","display_name":"Juan Jos\u00e9 Egozcue","orcid":"https://orcid.org/0000-0002-5144-4483"},"institutions":[{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Juan Jos\u00e9 Egozcue","raw_affiliation_strings":["Department of Civil and Environmental Engineering , Universitat Polit\u00e9cnica de Catalunya, Barcelona, 08034 , Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Civil and Environmental Engineering , Universitat Polit\u00e9cnica de Catalunya, Barcelona, 08034 , Spain","institution_ids":["https://openalex.org/I9617848"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037079774","display_name":"Aybar C. Acar","orcid":"https://orcid.org/0000-0001-5694-8675"},"institutions":[{"id":"https://openalex.org/I201799495","display_name":"Middle East Technical University","ror":"https://ror.org/014weej12","country_code":"TR","type":"education","lineage":["https://openalex.org/I201799495"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Aybar Can Acar","raw_affiliation_strings":["Department of Medical Informatics , Middle East Technical University, Ankara Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Informatics , Middle East Technical University, Ankara Turkey","institution_ids":["https://openalex.org/I201799495"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5031794793"],"corresponding_institution_ids":["https://openalex.org/I161597582"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.2775,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.6280913,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"23","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12157","display_name":"Geochemistry and Geologic Mapping","score":0.9979000091552734,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T12157","display_name":"Geochemistry and Geologic Mapping","score":0.9979000091552734,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10257","display_name":"Oral microbiology and periodontitis research","score":0.9872000217437744,"subfield":{"id":"https://openalex.org/subfields/3506","display_name":"Periodontics"},"field":{"id":"https://openalex.org/fields/35","display_name":"Dentistry"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9682999849319458,"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/microbiome","display_name":"Microbiome","score":0.6443304419517517},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6264060735702515},{"id":"https://openalex.org/keywords/principal","display_name":"Principal (computer security)","score":0.5700744390487671},{"id":"https://openalex.org/keywords/compositional-data","display_name":"Compositional data","score":0.5290507078170776},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5017518997192383},{"id":"https://openalex.org/keywords/taxon","display_name":"Taxon","score":0.4823986291885376},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.46818506717681885},{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.45347291231155396},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3597838282585144},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.321010023355484},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3013454079627991},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.28069591522216797},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2607099115848541},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.24362874031066895},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.19417747855186462},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12923797965049744}],"concepts":[{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.6443304419517517},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6264060735702515},{"id":"https://openalex.org/C144559511","wikidata":"https://www.wikidata.org/wiki/Q2986279","display_name":"Principal (computer security)","level":2,"score":0.5700744390487671},{"id":"https://openalex.org/C2781147490","wikidata":"https://www.wikidata.org/wiki/Q5156808","display_name":"Compositional data","level":2,"score":0.5290507078170776},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5017518997192383},{"id":"https://openalex.org/C71640776","wikidata":"https://www.wikidata.org/wiki/Q16521","display_name":"Taxon","level":2,"score":0.4823986291885376},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.46818506717681885},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.45347291231155396},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3597838282585144},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.321010023355484},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3013454079627991},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.28069591522216797},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2607099115848541},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.24362874031066895},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.19417747855186462},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12923797965049744},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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}],"mesh":[{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","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":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbac328","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac328","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:36007229","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36007229","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:dugi-doc.udg.edu:10256/28121","is_oa":false,"landing_page_url":"http://hdl.handle.net/10256/28121","pdf_url":null,"source":{"id":"https://openalex.org/S4306401633","display_name":"Universitat de Girona Digital Repository (Universitat de Girona)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I251424209","host_organization_name":"Universitat de Girona","host_organization_lineage":["https://openalex.org/I251424209"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Articles publicats (D-IMA)","raw_type":"peer-reviewed"},{"id":"pmh:oai:https://open.metu.edu.tr:11511/100168","is_oa":false,"landing_page_url":"https://hdl.handle.net/11511/100168","pdf_url":null,"source":{"id":"https://openalex.org/S4306402495","display_name":"OpenMETU (Middle East Technical University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I201799495","host_organization_name":"Middle East Technical University","host_organization_lineage":["https://openalex.org/I201799495"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3866360941","display_name":null,"funder_award_id":"1059B141601395","funder_id":"https://openalex.org/F4320322626","funder_display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu"}],"funders":[{"id":"https://openalex.org/F4320322626","display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu","ror":"https://ror.org/04w9kkr77"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":67,"referenced_works":["https://openalex.org/W289857456","https://openalex.org/W374884248","https://openalex.org/W1523266228","https://openalex.org/W1864161604","https://openalex.org/W1891411045","https://openalex.org/W1964027278","https://openalex.org/W2009009124","https://openalex.org/W2022080111","https://openalex.org/W2028582941","https://openalex.org/W2033829415","https://openalex.org/W2034875436","https://openalex.org/W2051567523","https://openalex.org/W2067676386","https://openalex.org/W2070876428","https://openalex.org/W2078112764","https://openalex.org/W2090187219","https://openalex.org/W2112408821","https://openalex.org/W2153796345","https://openalex.org/W2163903604","https://openalex.org/W2170325206","https://openalex.org/W2326641739","https://openalex.org/W2340700016","https://openalex.org/W2398836226","https://openalex.org/W2463312000","https://openalex.org/W2473355215","https://openalex.org/W2506906012","https://openalex.org/W2510675082","https://openalex.org/W2573450200","https://openalex.org/W2575771770","https://openalex.org/W2592172277","https://openalex.org/W2595926651","https://openalex.org/W2769486068","https://openalex.org/W2769542288","https://openalex.org/W2785349689","https://openalex.org/W2794407684","https://openalex.org/W2884386248","https://openalex.org/W2909668868","https://openalex.org/W2914348147","https://openalex.org/W2943091811","https://openalex.org/W2949960840","https://openalex.org/W2950746887","https://openalex.org/W2962019792","https://openalex.org/W2963447910","https://openalex.org/W2975619549","https://openalex.org/W2995895849","https://openalex.org/W2998646257","https://openalex.org/W3014325341","https://openalex.org/W3025053000","https://openalex.org/W3033330873","https://openalex.org/W3037559613","https://openalex.org/W3090361282","https://openalex.org/W3092327810","https://openalex.org/W3111898295","https://openalex.org/W3119962804","https://openalex.org/W3125745788","https://openalex.org/W3127298225","https://openalex.org/W3129102895","https://openalex.org/W3131747315","https://openalex.org/W3132461044","https://openalex.org/W3145834862","https://openalex.org/W3197666941","https://openalex.org/W6610338564","https://openalex.org/W6631263138","https://openalex.org/W6631383449","https://openalex.org/W6734286551","https://openalex.org/W6790585510","https://openalex.org/W7020984933"],"related_works":["https://openalex.org/W4213334743","https://openalex.org/W4376607463","https://openalex.org/W2604155846","https://openalex.org/W3121185202","https://openalex.org/W2790850565","https://openalex.org/W4388834263","https://openalex.org/W1983943311","https://openalex.org/W4206185765","https://openalex.org/W3176621072","https://openalex.org/W3088497233"],"abstract_inverted_index":{"Statistical":[0],"and":[1,16,25,121,205],"machine":[2],"learning":[3],"techniques":[4],"based":[5,79],"on":[6,81],"relative":[7,82],"abundances":[8,83],"have":[9],"been":[10],"used":[11,143,175],"to":[12,17,87,166],"predict":[13],"health":[14],"conditions":[15],"identify":[18],"microbial":[19,172],"biomarkers.":[20],"However,":[21],"high":[22],"dimensionality,":[23],"sparsity":[24],"the":[26,36,39,94,114,123,181,195],"compositional":[27,95,155],"nature":[28],"of":[29,99,119,125,130,171,197],"microbiome":[30,44],"data":[31,96,192,207],"represent":[32],"statistical":[33],"challenges.":[34],"On":[35],"other":[37],"hand,":[38],"taxon":[40,88,167],"grouping":[41,168],"allows":[42],"summarizing":[43],"abundance":[45],"with":[46,62,127,183],"a":[47,51,63,70,137,150,184,190],"coarser":[48],"resolution":[49],"in":[50,136,199],"lower":[52],"dimension,":[53],"but":[54],"it":[55],"presents":[56],"new":[57],"challenges":[58],"when":[59],"correlating":[60],"taxa":[61],"disease.":[64],"In":[65],"this":[66],"work,":[67],"we":[68],"present":[69,135],"novel":[71],"approach":[72],"that":[73,162],"groups":[74,104],"Operational":[75],"Taxonomical":[76],"Units":[77],"(OTUs)":[78],"only":[80],"as":[84,149,158],"an":[85,159,164],"alternative":[86,165],"grouping.":[89],"The":[90,102,111,202],"proposed":[91],"procedure":[92,112,161,182],"acknowledges":[93],"making":[97],"use":[98],"principal":[100],"balances.":[101],"identified":[103],"are":[105,133,210],"called":[106],"Principal":[107],"Microbial":[108],"Groups":[109],"(PMGs).":[110],"reduces":[113],"need":[115],"for":[116,144,154,169,176,194,208],"user-defined":[117],"aggregation":[118,160],"$\\textrm{OTU}$s":[120],"offers":[122],"possibility":[124],"working":[126],"coarse":[128],"group":[129],"$\\textrm{OTU}$s,":[131],"which":[132],"not":[134],"phylogenetic":[138],"tree.":[139],"PMGs":[140,188,209],"can":[141],"be":[142],"two":[145],"different":[146],"goals:":[147],"(1)":[148],"dimensionality":[151],"reduction":[152],"method":[153],"data,":[156],"(2)":[157],"provides":[163],"construction":[170],"balances":[173],"afterward":[174],"disease":[177],"prediction.":[178],"We":[179],"illustrate":[180],"cirrhosis":[185],"study":[186],"data.":[187],"provide":[189],"coherent":[191],"analysis":[193],"search":[196],"biomarkers":[198],"human":[200],"microbiota.":[201],"source":[203],"code":[204],"demo":[206],"available":[211],"at:":[212],"https://github.com/asliboyraz/PMGs.":[213]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-06-06T09:05:17.133730","created_date":"2025-10-10T00:00:00"}
