{"id":"https://openalex.org/W4323031768","doi":"https://doi.org/10.3389/fbinf.2023.1157956","title":"Exploring microbial functional biodiversity at the protein family level\u2014From metagenomic sequence reads to annotated protein clusters","display_name":"Exploring microbial functional biodiversity at the protein family level\u2014From metagenomic sequence reads to annotated protein clusters","publication_year":2023,"publication_date":"2023-03-03","ids":{"openalex":"https://openalex.org/W4323031768","doi":"https://doi.org/10.3389/fbinf.2023.1157956","pmid":"https://pubmed.ncbi.nlm.nih.gov/36959975"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2023.1157956","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1157956","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1157956/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1157956/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038035082","display_name":"Fotis A. Baltoumas","orcid":"https://orcid.org/0000-0002-2870-2931"},"institutions":[{"id":"https://openalex.org/I6820528","display_name":"Alexander Fleming Biomedical Sciences Research Center","ror":"https://ror.org/013x0ky90","country_code":"GR","type":"facility","lineage":["https://openalex.org/I6820528"]}],"countries":["GR"],"is_corresponding":true,"raw_author_name":"Fotis A. Baltoumas","raw_affiliation_strings":["Institute for Fundamental Biomedical Research, BSRC \"Alexander Fleming\", Vari, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Fundamental Biomedical Research, BSRC \"Alexander Fleming\", Vari, Greece","institution_ids":["https://openalex.org/I6820528"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039988707","display_name":"Evangelos Karatzas","orcid":"https://orcid.org/0000-0001-9132-8981"},"institutions":[{"id":"https://openalex.org/I6820528","display_name":"Alexander Fleming Biomedical Sciences Research Center","ror":"https://ror.org/013x0ky90","country_code":"GR","type":"facility","lineage":["https://openalex.org/I6820528"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Evangelos Karatzas","raw_affiliation_strings":["Institute for Fundamental Biomedical Research, BSRC \"Alexander Fleming\", Vari, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Fundamental Biomedical Research, BSRC \"Alexander Fleming\", Vari, Greece","institution_ids":["https://openalex.org/I6820528"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081848590","display_name":"David P\u00e1ez-Espino","orcid":"https://orcid.org/0000-0002-2939-5398"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I196679689","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I196679689","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David Paez-Espino","raw_affiliation_strings":["Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States","institution_ids":["https://openalex.org/I196679689","https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002775558","display_name":"Nefeli K. Venetsianou","orcid":null},"institutions":[{"id":"https://openalex.org/I6820528","display_name":"Alexander Fleming Biomedical Sciences Research Center","ror":"https://ror.org/013x0ky90","country_code":"GR","type":"facility","lineage":["https://openalex.org/I6820528"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Nefeli K. Venetsianou","raw_affiliation_strings":["Institute for Fundamental Biomedical Research, BSRC \"Alexander Fleming\", Vari, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Fundamental Biomedical Research, BSRC \"Alexander Fleming\", Vari, Greece","institution_ids":["https://openalex.org/I6820528"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033236033","display_name":"Eleni Aplakidou","orcid":"https://orcid.org/0009-0002-0737-4817"},"institutions":[{"id":"https://openalex.org/I6820528","display_name":"Alexander Fleming Biomedical Sciences Research Center","ror":"https://ror.org/013x0ky90","country_code":"GR","type":"facility","lineage":["https://openalex.org/I6820528"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Eleni Aplakidou","raw_affiliation_strings":["Institute for Fundamental Biomedical Research, BSRC \"Alexander Fleming\", Vari, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Fundamental Biomedical Research, BSRC \"Alexander Fleming\", Vari, Greece","institution_ids":["https://openalex.org/I6820528"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077143574","display_name":"Anastasis Oulas","orcid":"https://orcid.org/0000-0002-9350-7577"},"institutions":[{"id":"https://openalex.org/I55905543","display_name":"Cyprus Institute of Neurology and Genetics","ror":"https://ror.org/01ggsp920","country_code":"CY","type":"nonprofit","lineage":["https://openalex.org/I55905543"]}],"countries":["CY"],"is_corresponding":false,"raw_author_name":"Anastasis Oulas","raw_affiliation_strings":["The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus","institution_ids":["https://openalex.org/I55905543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104045098","display_name":"ROBERT FINN","orcid":"https://orcid.org/0000-0001-8626-2148"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Robert D. Finn","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084204507","display_name":"Sergey Ovchinnikov","orcid":"https://orcid.org/0000-0003-2774-2744"},"institutions":[{"id":"https://openalex.org/I2801851002","display_name":"Harvard University Press","ror":"https://ror.org/006v7bf86","country_code":"US","type":"other","lineage":["https://openalex.org/I136199984","https://openalex.org/I2801851002"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sergey Ovchinnikov","raw_affiliation_strings":["John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA, United States","institution_ids":["https://openalex.org/I2801851002"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025850900","display_name":"Evangelos Pafilis","orcid":"https://orcid.org/0000-0001-5079-0125"},"institutions":[{"id":"https://openalex.org/I4210131924","display_name":"Hellenic Centre for Marine Research","ror":"https://ror.org/038kffh84","country_code":"GR","type":"facility","lineage":["https://openalex.org/I4210131924"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Evangelos Pafilis","raw_affiliation_strings":["Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece","institution_ids":["https://openalex.org/I4210131924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023696415","display_name":"Nikos C. Kyrpides","orcid":"https://orcid.org/0000-0002-6131-0462"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I196679689","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I196679689","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nikos C. Kyrpides","raw_affiliation_strings":["Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States","institution_ids":["https://openalex.org/I196679689","https://openalex.org/I148283060"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088991393","display_name":"Georgios A. Pavlopoulos","orcid":"https://orcid.org/0000-0002-4577-8276"},"institutions":[{"id":"https://openalex.org/I200777214","display_name":"National and Kapodistrian University of Athens","ror":"https://ror.org/04gnjpq42","country_code":"GR","type":"education","lineage":["https://openalex.org/I200777214"]},{"id":"https://openalex.org/I24897511","display_name":"Hellenic Military Academy","ror":"https://ror.org/01esc8r67","country_code":"GR","type":"education","lineage":["https://openalex.org/I24897511"]},{"id":"https://openalex.org/I6820528","display_name":"Alexander Fleming Biomedical Sciences Research Center","ror":"https://ror.org/013x0ky90","country_code":"GR","type":"facility","lineage":["https://openalex.org/I6820528"]}],"countries":["GR"],"is_corresponding":true,"raw_author_name":"Georgios A. Pavlopoulos","raw_affiliation_strings":["Center of New Biotechnologies and Precision Medicine, Department of Medicine, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece","Hellenic Army Academy, Vari, Greece","Institute for Fundamental Biomedical Research, BSRC \"Alexander Fleming\", Vari, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of New Biotechnologies and Precision Medicine, Department of Medicine, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece","institution_ids":["https://openalex.org/I200777214"]},{"raw_affiliation_string":"Hellenic Army Academy, Vari, Greece","institution_ids":["https://openalex.org/I24897511"]},{"raw_affiliation_string":"Institute for Fundamental Biomedical Research, BSRC \"Alexander Fleming\", Vari, Greece","institution_ids":["https://openalex.org/I6820528"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5023696415","https://openalex.org/A5038035082","https://openalex.org/A5088991393"],"corresponding_institution_ids":["https://openalex.org/I148283060","https://openalex.org/I196679689","https://openalex.org/I200777214","https://openalex.org/I24897511","https://openalex.org/I6820528"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":2.5826,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.89570842,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"3","issue":null,"first_page":"1157956","last_page":"1157956"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic 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/T10015","display_name":"Genomics and Phylogenetic 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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9908000230789185,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9868999719619751,"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/metagenomics","display_name":"Metagenomics","score":0.896889865398407},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.606850266456604},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5810586214065552},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5061091780662537},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.4728291928768158},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.4715069830417633},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4582045078277588},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4340224862098694},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3926742970943451},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.38974884152412415},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.323908269405365},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2726801633834839},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.17837244272232056},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17620781064033508},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13993549346923828},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.12194252014160156},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.0802743136882782}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.896889865398407},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.606850266456604},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5810586214065552},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5061091780662537},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.4728291928768158},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.4715069830417633},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4582045078277588},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4340224862098694},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3926742970943451},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.38974884152412415},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.323908269405365},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2726801633834839},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.17837244272232056},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17620781064033508},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13993549346923828},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.12194252014160156},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0802743136882782}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.3389/fbinf.2023.1157956","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1157956","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1157956/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36959975","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36959975","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt6rw4218s","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/6rw4218s","pdf_url":"https://escholarship.org/content/qt6rw4218s/qt6rw4218s.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"Frontiers in Bioinformatics, vol 3","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10029925","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10029925","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10029925/pdf/fbinf-03-1157956.pdf","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":"Front Bioinform","raw_type":"Text"},{"id":"pmh:ark:/13030/qt6rw4218s","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:doaj.org/article:f02d335b56704ff4a762c935e45990f2","is_oa":true,"landing_page_url":"https://doaj.org/article/f02d335b56704ff4a762c935e45990f2","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":"Frontiers in Bioinformatics, Vol 3 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2023.1157956","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1157956","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1157956/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.7400000095367432,"id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G1286236842","display_name":null,"funder_award_id":"-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G3083819904","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G4501827968","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4565140552","display_name":null,"funder_award_id":"-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G498139845","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G5602503670","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320316170","funder_display_name":"Joint Genome Institute"},{"id":"https://openalex.org/G6348972864","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6558272803","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7205239661","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320316170","funder_display_name":"Joint Genome Institute"},{"id":"https://openalex.org/G7368046788","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G8707089225","display_name":null,"funder_award_id":"1855-BOLOGNA","funder_id":"https://openalex.org/F4320327859","funder_display_name":"Hellenic Foundation for Research and Innovation"},{"id":"https://openalex.org/G969889393","display_name":null,"funder_award_id":"DE-AC02-","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320316170","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337"},{"id":"https://openalex.org/F4320327859","display_name":"Hellenic Foundation for Research and Innovation","ror":null},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4323031768.pdf"},"referenced_works_count":392,"referenced_works":["https://openalex.org/W95014119","https://openalex.org/W128985141","https://openalex.org/W1496710979","https://openalex.org/W1496933752","https://openalex.org/W1547034848","https://openalex.org/W1590240800","https://openalex.org/W1600613454","https://openalex.org/W1703384511","https://openalex.org/W1783384641","https://openalex.org/W1803102843","https://openalex.org/W1822648038","https://openalex.org/W1878521557","https://openalex.org/W1965540415","https://openalex.org/W1965582988","https://openalex.org/W1971015996","https://openalex.org/W1973862547","https://openalex.org/W1976666280","https://openalex.org/W1981264193","https://openalex.org/W1987134040","https://openalex.org/W1988387203","https://openalex.org/W1989348205","https://openalex.org/W1997673861","https://openalex.org/W2000860171","https://openalex.org/W2001699795","https://openalex.org/W2008545402","https://openalex.org/W2010002522","https://openalex.org/W2011301426","https://openalex.org/W2018446288","https://openalex.org/W2031207772","https://openalex.org/W2035890032","https://openalex.org/W2040704692","https://openalex.org/W2041117131","https://openalex.org/W2042119041","https://openalex.org/W2045204781","https://openalex.org/W2046986600","https://openalex.org/W2048673910","https://openalex.org/W2051545676","https://openalex.org/W2054720302","https://openalex.org/W2055043387","https://openalex.org/W2061042699","https://openalex.org/W2064384066","https://openalex.org/W2067558362","https://openalex.org/W2069689025","https://openalex.org/W2072966557","https://openalex.org/W2074231493","https://openalex.org/W2075563069","https://openalex.org/W2085926377","https://openalex.org/W2091648599","https://openalex.org/W2091922579","https://openalex.org/W2095036253","https://openalex.org/W2096093282","https://openalex.org/W2097706568","https://openalex.org/W2098290178","https://openalex.org/W2099468911","https://openalex.org/W2100585269","https://openalex.org/W2100670078","https://openalex.org/W2101220662","https://openalex.org/W2101291993","https://openalex.org/W2102245393","https://openalex.org/W2103441770","https://openalex.org/W2103901746","https://openalex.org/W2106090237","https://openalex.org/W2106208020","https://openalex.org/W2106263380","https://openalex.org/W2106474670","https://openalex.org/W2107158607","https://openalex.org/W2107717979","https://openalex.org/W2107867854","https://openalex.org/W2108588173","https://openalex.org/W2109848222","https://openalex.org/W2110300022","https://openalex.org/W2111373249","https://openalex.org/W2111858824","https://openalex.org/W2112113834","https://openalex.org/W2113679889","https://openalex.org/W2114463320","https://openalex.org/W2114520383","https://openalex.org/W2114850508","https://openalex.org/W2115888213","https://openalex.org/W2116034137","https://openalex.org/W2117077088","https://openalex.org/W2117484859","https://openalex.org/W2117683095","https://openalex.org/W2118001436","https://openalex.org/W2120608174","https://openalex.org/W2121826197","https://openalex.org/W2124088653","https://openalex.org/W2124309259","https://openalex.org/W2124351063","https://openalex.org/W2127175247","https://openalex.org/W2127322768","https://openalex.org/W2127391962","https://openalex.org/W2127556561","https://openalex.org/W2127596034","https://openalex.org/W2128124531","https://openalex.org/W2128386749","https://openalex.org/W2128484254","https://openalex.org/W2129010073","https://openalex.org/W2129296076","https://openalex.org/W2130124027","https://openalex.org/W2130137303","https://openalex.org/W2130410032","https://openalex.org/W2130479394","https://openalex.org/W2131026689","https://openalex.org/W2131271579","https://openalex.org/W2131681506","https://openalex.org/W2132926880","https://openalex.org/W2133212095","https://openalex.org/W2134751812","https://openalex.org/W2135621733","https://openalex.org/W2136145671","https://openalex.org/W2136850043","https://openalex.org/W2138122982","https://openalex.org/W2140437680","https://openalex.org/W2141152740","https://openalex.org/W2141202455","https://openalex.org/W2141394464","https://openalex.org/W2141920662","https://openalex.org/W2143235667","https://openalex.org/W2143485490","https://openalex.org/W2148698435","https://openalex.org/W2149525061","https://openalex.org/W2150208009","https://openalex.org/W2152770371","https://openalex.org/W2153233077","https://openalex.org/W2153490111","https://openalex.org/W2153990926","https://openalex.org/W2156125289","https://openalex.org/W2156247618","https://openalex.org/W2156701707","https://openalex.org/W2156995746","https://openalex.org/W2158266834","https://openalex.org/W2158406706","https://openalex.org/W2159092541","https://openalex.org/W2159903739","https://openalex.org/W2159957100","https://openalex.org/W2160313295","https://openalex.org/W2160378127","https://openalex.org/W2160697532","https://openalex.org/W2160734881","https://openalex.org/W2161151688","https://openalex.org/W2161493476","https://openalex.org/W2162039942","https://openalex.org/W2162602080","https://openalex.org/W2162704968","https://openalex.org/W2163166295","https://openalex.org/W2164412449","https://openalex.org/W2165232124","https://openalex.org/W2165446840","https://openalex.org/W2165532730","https://openalex.org/W2168330474","https://openalex.org/W2170471837","https://openalex.org/W2170551349","https://openalex.org/W2171559274","https://openalex.org/W2194399613","https://openalex.org/W2223774172","https://openalex.org/W2228104733","https://openalex.org/W2229420368","https://openalex.org/W2260297624","https://openalex.org/W2270324082","https://openalex.org/W2275721306","https://openalex.org/W2292314415","https://openalex.org/W2302501749","https://openalex.org/W2337508844","https://openalex.org/W2337747100","https://openalex.org/W2341364667","https://openalex.org/W2345791363","https://openalex.org/W2407244250","https://openalex.org/W2420659973","https://openalex.org/W2461532279","https://openalex.org/W2470052926","https://openalex.org/W2486729015","https://openalex.org/W2513506562","https://openalex.org/W2514474978","https://openalex.org/W2514983714","https://openalex.org/W2521644033","https://openalex.org/W2526038422","https://openalex.org/W2543855063","https://openalex.org/W2555870966","https://openalex.org/W2558411436","https://openalex.org/W2559088283","https://openalex.org/W2559581118","https://openalex.org/W2574496196","https://openalex.org/W2599417231","https://openalex.org/W2610952444","https://openalex.org/W2615147949","https://openalex.org/W2623492145","https://openalex.org/W2732139758","https://openalex.org/W2736887218","https://openalex.org/W2740966378","https://openalex.org/W2748559568","https://openalex.org/W2754579667","https://openalex.org/W2755111416","https://openalex.org/W2756958651","https://openalex.org/W2758004011","https://openalex.org/W2759143570","https://openalex.org/W2760000637","https://openalex.org/W2765281411","https://openalex.org/W2766239397","https://openalex.org/W2766330607","https://openalex.org/W2766358903","https://openalex.org/W2766822634","https://openalex.org/W2780263532","https://openalex.org/W2781869913","https://openalex.org/W2781953684","https://openalex.org/W2792729061","https://openalex.org/W2794879929","https://openalex.org/W2796491734","https://openalex.org/W2797956284","https://openalex.org/W2804476733","https://openalex.org/W2804523481","https://openalex.org/W2807423349","https://openalex.org/W2810271683","https://openalex.org/W2810538097","https://openalex.org/W2886112809","https://openalex.org/W2889220616","https://openalex.org/W2895532240","https://openalex.org/W2897233545","https://openalex.org/W2900030356","https://openalex.org/W2900984733","https://openalex.org/W2901620691","https://openalex.org/W2904155504","https://openalex.org/W2904625720","https://openalex.org/W2938828179","https://openalex.org/W2938868597","https://openalex.org/W2941112903","https://openalex.org/W2944245644","https://openalex.org/W2944870141","https://openalex.org/W2946173685","https://openalex.org/W2949223833","https://openalex.org/W2949342052","https://openalex.org/W2949629831","https://openalex.org/W2950310673","https://openalex.org/W2950354111","https://openalex.org/W2950489962","https://openalex.org/W2950884444","https://openalex.org/W2950954328","https://openalex.org/W2951160681","https://openalex.org/W2953008890","https://openalex.org/W2955099493","https://openalex.org/W2963276645","https://openalex.org/W2969443468","https://openalex.org/W2972348732","https://openalex.org/W2972411752","https://openalex.org/W2976704092","https://openalex.org/W2978740330","https://openalex.org/W2981123106","https://openalex.org/W2981413553","https://openalex.org/W2983165568","https://openalex.org/W2984761660","https://openalex.org/W2984894304","https://openalex.org/W2986906238","https://openalex.org/W2986996910","https://openalex.org/W2988411281","https://openalex.org/W2989052455","https://openalex.org/W2990618091","https://openalex.org/W2991157178","https://openalex.org/W2991171606","https://openalex.org/W2992976869","https://openalex.org/W2995081665","https://openalex.org/W2996065690","https://openalex.org/W3003110834","https://openalex.org/W3003366856","https://openalex.org/W3003422837","https://openalex.org/W3009533854","https://openalex.org/W3014607123","https://openalex.org/W3024376490","https://openalex.org/W3025857586","https://openalex.org/W3027089056","https://openalex.org/W3032758350","https://openalex.org/W3033129278","https://openalex.org/W3035762603","https://openalex.org/W3035764705","https://openalex.org/W3039380610","https://openalex.org/W3044917564","https://openalex.org/W3045315617","https://openalex.org/W3046109898","https://openalex.org/W3046751266","https://openalex.org/W3048090444","https://openalex.org/W3048716002","https://openalex.org/W3083798988","https://openalex.org/W3091506611","https://openalex.org/W3091956242","https://openalex.org/W3092054218","https://openalex.org/W3093954610","https://openalex.org/W3094967361","https://openalex.org/W3095583226","https://openalex.org/W3097008984","https://openalex.org/W3099768174","https://openalex.org/W3100348855","https://openalex.org/W3100584158","https://openalex.org/W3104596207","https://openalex.org/W3106745904","https://openalex.org/W3107541694","https://openalex.org/W3109640704","https://openalex.org/W3109735703","https://openalex.org/W3112376646","https://openalex.org/W3112600195","https://openalex.org/W3120530641","https://openalex.org/W3127656915","https://openalex.org/W3128701120","https://openalex.org/W3131993635","https://openalex.org/W3132754944","https://openalex.org/W3133550758","https://openalex.org/W3135822094","https://openalex.org/W3135997498","https://openalex.org/W3137047737","https://openalex.org/W3138897353","https://openalex.org/W3149078497","https://openalex.org/W3154755494","https://openalex.org/W3161251590","https://openalex.org/W3161596995","https://openalex.org/W3163043262","https://openalex.org/W3167160660","https://openalex.org/W3177828909","https://openalex.org/W3178564164","https://openalex.org/W3183475563","https://openalex.org/W3185212334","https://openalex.org/W3186179742","https://openalex.org/W3193650118","https://openalex.org/W3194795934","https://openalex.org/W3195010157","https://openalex.org/W3198923619","https://openalex.org/W3202547677","https://openalex.org/W3203343200","https://openalex.org/W3203529427","https://openalex.org/W3206307177","https://openalex.org/W3211795092","https://openalex.org/W3211795435","https://openalex.org/W3212152134","https://openalex.org/W3213153027","https://openalex.org/W3213436318","https://openalex.org/W3215751839","https://openalex.org/W3215918380","https://openalex.org/W3217463608","https://openalex.org/W4200340819","https://openalex.org/W4200525857","https://openalex.org/W4200553915","https://openalex.org/W4205192056","https://openalex.org/W4206950245","https://openalex.org/W4210366024","https://openalex.org/W4210840673","https://openalex.org/W4213164504","https://openalex.org/W4220807255","https://openalex.org/W4220828441","https://openalex.org/W4220869955","https://openalex.org/W4221081166","https://openalex.org/W4221138532","https://openalex.org/W4225393550","https://openalex.org/W4226000774","https://openalex.org/W4233120011","https://openalex.org/W4233453958","https://openalex.org/W4235848672","https://openalex.org/W4238157267","https://openalex.org/W4240852056","https://openalex.org/W4244569433","https://openalex.org/W4250119831","https://openalex.org/W4250359879","https://openalex.org/W4253751566","https://openalex.org/W4256051031","https://openalex.org/W4256333965","https://openalex.org/W4280501739","https://openalex.org/W4281790889","https://openalex.org/W4282922306","https://openalex.org/W4282939468","https://openalex.org/W4285303391","https://openalex.org/W4286500588","https://openalex.org/W4286669150","https://openalex.org/W4289593660","https://openalex.org/W4291017647","https://openalex.org/W4292636454","https://openalex.org/W4295138387","https://openalex.org/W4296164039","https://openalex.org/W4296776269","https://openalex.org/W4297398491","https://openalex.org/W4302013328","https://openalex.org/W4307386237","https://openalex.org/W4307846647","https://openalex.org/W4308026396","https://openalex.org/W4309157457","https://openalex.org/W4309305993","https://openalex.org/W4309326290","https://openalex.org/W4310157184","https://openalex.org/W4321611856","https://openalex.org/W4321636615","https://openalex.org/W4327550249","https://openalex.org/W4375858802","https://openalex.org/W4378713584","https://openalex.org/W6683565055","https://openalex.org/W6772738354","https://openalex.org/W6784427192","https://openalex.org/W6849964755"],"related_works":["https://openalex.org/W638577851","https://openalex.org/W2968354375","https://openalex.org/W2359440920","https://openalex.org/W2889550857","https://openalex.org/W3013372948","https://openalex.org/W3135997498","https://openalex.org/W4242417330","https://openalex.org/W2392768766","https://openalex.org/W3198631238","https://openalex.org/W2058118494"],"abstract_inverted_index":{"Metagenomics":[0],"has":[1,14],"enabled":[2],"accessing":[3],"the":[4,16,40,69,82,108],"genetic":[5],"repertoire":[6],"of":[7,18],"natural":[8],"microbial":[9],"communities.":[10],"Metagenome":[11],"shotgun":[12],"sequencing":[13],"become":[15],"method":[17],"choice":[19],"for":[20,89,116],"studying":[21],"and":[22,38,67,92,103,112,126],"classifying":[23],"microorganisms":[24],"from":[25,43],"various":[26,114],"environments.":[27],"To":[28],"this":[29,56],"end,":[30],"several":[31],"methods":[32],"have":[33],"been":[34],"developed":[35],"to":[36,46,63,78,121],"process":[37],"analyze":[39],"sequence":[41],"data":[42,110],"raw":[44],"reads":[45],"end-products":[47],"such":[48,65],"as":[49,98,100],"predicted":[50],"protein":[51,83,117],"sequences":[52],"or":[53],"families.":[54],"In":[55],"article,":[57],"we":[58,93,106],"provide":[59,87],"a":[60],"thorough":[61],"review":[62],"simplify":[64],"processes":[66],"discuss":[68],"alternative":[70],"methodologies":[71],"that":[72],"can":[73],"be":[74],"followed":[75],"in":[76],"order":[77],"explore":[79],"biodiversity":[80],"at":[81],"family":[84,118],"level.":[85],"We":[86],"details":[88],"analysis":[90],"tools":[91],"comment":[94],"on":[95],"their":[96,101],"scalability":[97],"well":[99],"advantages":[102],"disadvantages.":[104],"Finally,":[105],"report":[107],"available":[109],"repositories":[111],"recommend":[113],"approaches":[115],"annotation":[119],"related":[120],"phylogenetic":[122],"distribution,":[123],"structure":[124],"prediction":[125],"metadata":[127],"enrichment.":[128]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1}],"updated_date":"2026-06-05T09:01:59.212387","created_date":"2025-10-10T00:00:00"}
