{"id":"https://openalex.org/W2855293443","doi":"https://doi.org/10.1186/s12859-018-2182-6","title":"Deep learning models for bacteria taxonomic classification of metagenomic data","display_name":"Deep learning models for bacteria taxonomic classification of metagenomic data","publication_year":2018,"publication_date":"2018-07-01","ids":{"openalex":"https://openalex.org/W2855293443","doi":"https://doi.org/10.1186/s12859-018-2182-6","mag":"2855293443","pmid":"https://pubmed.ncbi.nlm.nih.gov/30066629"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-018-2182-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2182-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2182-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2182-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027676813","display_name":"Antonino Fiannaca","orcid":"https://orcid.org/0000-0002-0114-4984"},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Antonino Fiannaca","raw_affiliation_strings":["CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, 153, Palermo, Italy. antonino.fiannaca@icar.cnr.it","CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, 153, Palermo, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, 153, Palermo, Italy. antonino.fiannaca@icar.cnr.it","institution_ids":["https://openalex.org/I4210155236"]},{"raw_affiliation_string":"CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, 153, Palermo, Italy","institution_ids":["https://openalex.org/I4210155236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059920636","display_name":"Laura La Paglia","orcid":"https://orcid.org/0000-0002-1077-5657"},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Laura La Paglia","raw_affiliation_strings":["CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, 153, Palermo, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, 153, Palermo, Italy","institution_ids":["https://openalex.org/I4210155236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052997301","display_name":"Massimo La Rosa","orcid":"https://orcid.org/0000-0001-6718-7269"},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Massimo La Rosa","raw_affiliation_strings":["CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, 153, Palermo, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, 153, Palermo, Italy","institution_ids":["https://openalex.org/I4210155236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089392019","display_name":"Giosu\u00e8 Lo Bosco","orcid":"https://orcid.org/0000-0002-1602-0693"},"institutions":[{"id":"https://openalex.org/I900890020","display_name":"University of Palermo","ror":"https://ror.org/044k9ta02","country_code":"IT","type":"education","lineage":["https://openalex.org/I900890020"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giosue\u2019 Lo Bosco","raw_affiliation_strings":["Dipartimento di Matematica e Informatica, Universit\u00e0 degli studi di Palermo, Via Archirafi, 34, Palermo, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Matematica e Informatica, Universit\u00e0 degli studi di Palermo, Via Archirafi, 34, Palermo, Italy","institution_ids":["https://openalex.org/I900890020"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081400947","display_name":"Giovanni Renda","orcid":null},"institutions":[{"id":"https://openalex.org/I900890020","display_name":"University of Palermo","ror":"https://ror.org/044k9ta02","country_code":"IT","type":"education","lineage":["https://openalex.org/I900890020"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giovanni Renda","raw_affiliation_strings":["Dipartimento dell'Innovazione Industriale e Digitale, Universit\u00e0 degli studi di Palermo, Viale Delle Scienze, ed.6, Palermo, Italy","Dipartimento dell\u2019Innovazione Industriale e Digitale, Universit\u00e0 degli studi di Palermo, Viale Delle Scienze, ed.6, Palermo, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento dell'Innovazione Industriale e Digitale, Universit\u00e0 degli studi di Palermo, Viale Delle Scienze, ed.6, Palermo, Italy","institution_ids":["https://openalex.org/I900890020"]},{"raw_affiliation_string":"Dipartimento dell\u2019Innovazione Industriale e Digitale, Universit\u00e0 degli studi di Palermo, Viale Delle Scienze, ed.6, Palermo, Italy","institution_ids":["https://openalex.org/I900890020"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011731694","display_name":"Riccardo Rizzo","orcid":"https://orcid.org/0000-0001-5007-6925"},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Riccardo Rizzo","raw_affiliation_strings":["CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, 153, Palermo, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, 153, Palermo, Italy","institution_ids":["https://openalex.org/I4210155236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046377602","display_name":"Salvatore Gaglio","orcid":"https://orcid.org/0000-0002-5480-2100"},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I900890020","display_name":"University of Palermo","ror":"https://ror.org/044k9ta02","country_code":"IT","type":"education","lineage":["https://openalex.org/I900890020"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Salvatore Gaglio","raw_affiliation_strings":["CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, 153, Palermo, Italy","Dipartimento dell'Innovazione Industriale e Digitale, Universit\u00e0 degli studi di Palermo, Viale Delle Scienze, ed.6, Palermo, Italy","Dipartimento dell\u2019Innovazione Industriale e Digitale, Universit\u00e0 degli studi di Palermo, Viale Delle Scienze, ed.6, Palermo, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, 153, Palermo, Italy","institution_ids":["https://openalex.org/I4210155236"]},{"raw_affiliation_string":"Dipartimento dell'Innovazione Industriale e Digitale, Universit\u00e0 degli studi di Palermo, Viale Delle Scienze, ed.6, Palermo, Italy","institution_ids":["https://openalex.org/I900890020"]},{"raw_affiliation_string":"Dipartimento dell\u2019Innovazione Industriale e Digitale, Universit\u00e0 degli studi di Palermo, Viale Delle Scienze, ed.6, Palermo, Italy","institution_ids":["https://openalex.org/I900890020"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015541058","display_name":"Alfonso Urso","orcid":"https://orcid.org/0000-0003-3018-1458"},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alfonso Urso","raw_affiliation_strings":["CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, 153, Palermo, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, 153, Palermo, Italy","institution_ids":["https://openalex.org/I4210155236"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5027676813"],"corresponding_institution_ids":["https://openalex.org/I4210155236"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":5.6026,"has_fulltext":true,"cited_by_count":148,"citation_normalized_percentile":{"value":0.97144958,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"19","issue":"S7","first_page":"198","last_page":"198"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6313999891281128,"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":0.6313999891281128,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.15399999916553497,"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":0.07249999791383743,"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/metagenomics","display_name":"Metagenomics","score":0.7561101913452148},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.7112834453582764},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.5993887186050415},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.5430265665054321},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5183635354042053},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49362266063690186},{"id":"https://openalex.org/keywords/amplicon","display_name":"Amplicon","score":0.4849739074707031},{"id":"https://openalex.org/keywords/hypervariable-region","display_name":"Hypervariable region","score":0.4770768880844116},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4714920222759247},{"id":"https://openalex.org/keywords/shotgun-sequencing","display_name":"Shotgun sequencing","score":0.4622255563735962},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4381089508533478},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4219006896018982},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.39539384841918945},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.35102641582489014},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17461073398590088},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0921163260936737}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.7561101913452148},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7112834453582764},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.5993887186050415},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.5430265665054321},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5183635354042053},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49362266063690186},{"id":"https://openalex.org/C8185291","wikidata":"https://www.wikidata.org/wiki/Q2844457","display_name":"Amplicon","level":4,"score":0.4849739074707031},{"id":"https://openalex.org/C81566733","wikidata":"https://www.wikidata.org/wiki/Q1047544","display_name":"Hypervariable region","level":3,"score":0.4770768880844116},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4714920222759247},{"id":"https://openalex.org/C101985253","wikidata":"https://www.wikidata.org/wiki/Q1073526","display_name":"Shotgun sequencing","level":4,"score":0.4622255563735962},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4381089508533478},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4219006896018982},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.39539384841918945},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.35102641582489014},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17461073398590088},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0921163260936737},{"id":"https://openalex.org/C49105822","wikidata":"https://www.wikidata.org/wiki/Q176996","display_name":"Polymerase chain reaction","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-018-2182-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2182-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2182-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30066629","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30066629","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:c3e67c7435164eda91db30a62fc485f1","is_oa":false,"landing_page_url":"https://doaj.org/article/c3e67c7435164eda91db30a62fc485f1","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 19, Iss S7, Pp 61-76 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5024610","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6069770","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:iris.unipa.it:10447/292404","is_oa":true,"landing_page_url":"http://hdl.handle.net/10447/292404","pdf_url":null,"source":{"id":"https://openalex.org/S4306401065","display_name":"Nova Science Publishers (Nova Science Publishers, Inc.)","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6069770","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6069770","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-018-2182-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2182-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2182-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.49000000953674316,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2855293443.pdf","grobid_xml":"https://content.openalex.org/works/W2855293443.grobid-xml"},"referenced_works_count":62,"referenced_works":["https://openalex.org/W42763705","https://openalex.org/W46498078","https://openalex.org/W1019830208","https://openalex.org/W1123205372","https://openalex.org/W1835750348","https://openalex.org/W1890802958","https://openalex.org/W1939004772","https://openalex.org/W1965555277","https://openalex.org/W1998601670","https://openalex.org/W1999113425","https://openalex.org/W2008528231","https://openalex.org/W2023574331","https://openalex.org/W2023615726","https://openalex.org/W2031324152","https://openalex.org/W2041561663","https://openalex.org/W2047669659","https://openalex.org/W2047775854","https://openalex.org/W2060758175","https://openalex.org/W2064632793","https://openalex.org/W2071841602","https://openalex.org/W2087189381","https://openalex.org/W2088711515","https://openalex.org/W2097160089","https://openalex.org/W2100495367","https://openalex.org/W2112796928","https://openalex.org/W2116064496","https://openalex.org/W2116895571","https://openalex.org/W2121918723","https://openalex.org/W2123009189","https://openalex.org/W2124715997","https://openalex.org/W2128769815","https://openalex.org/W2136922672","https://openalex.org/W2138636857","https://openalex.org/W2149573313","https://openalex.org/W2152336584","https://openalex.org/W2152885278","https://openalex.org/W2153137490","https://openalex.org/W2163940893","https://openalex.org/W2163977673","https://openalex.org/W2166123725","https://openalex.org/W2167062509","https://openalex.org/W2171309014","https://openalex.org/W2189564721","https://openalex.org/W2229420368","https://openalex.org/W2239696860","https://openalex.org/W2257287664","https://openalex.org/W2306610272","https://openalex.org/W2311607323","https://openalex.org/W2320723632","https://openalex.org/W2433743436","https://openalex.org/W2507089332","https://openalex.org/W2587659621","https://openalex.org/W2600202123","https://openalex.org/W2607864135","https://openalex.org/W2611006723","https://openalex.org/W2919115771","https://openalex.org/W2963546206","https://openalex.org/W4211258437","https://openalex.org/W4233303333","https://openalex.org/W4249301765","https://openalex.org/W4289306860","https://openalex.org/W4292935612"],"related_works":["https://openalex.org/W3043668926","https://openalex.org/W3036436206","https://openalex.org/W4238948313","https://openalex.org/W4389452281","https://openalex.org/W3111832393","https://openalex.org/W3000916974","https://openalex.org/W3183189600","https://openalex.org/W3134948850","https://openalex.org/W2573498001","https://openalex.org/W2987572536"],"abstract_inverted_index":{"BACKGROUND:":[0],"An":[1],"open":[2],"challenge":[3],"in":[4,117,288],"translational":[5],"bioinformatics":[6],"is":[7,43,79],"the":[8,22,36,47,77,91,143,205,215,232,245,265,303,323],"analysis":[9],"of":[10,50,129,138,254],"sequenced":[11],"metagenomes":[12],"from":[13,53,153],"various":[14],"environmental":[15],"samples.":[16],"Of":[17],"course,":[18],"several":[19],"studies":[20],"demonstrated":[21],"16S":[23,57,87,99,155,275],"ribosomal":[24],"RNA":[25],"could":[26,319],"be":[27,134,320,336],"considered":[28],"as":[29,167,227,306],"a":[30,86,122,161,170,192,220,274,297,307],"barcode":[31],"for":[32,114,126,136,195,223,310,314,327,339],"bacteria":[33,224,312],"classification":[34,128,216,278,298],"at":[35,235,244],"genus":[37,246],"level,":[38,247],"but":[39],"till":[40],"now":[41],"it":[42,334],"hard":[44],"to":[45,81,85,164,203,294,331],"identify":[46],"correct":[48],"composition":[49],"metagenomic":[51,130,328],"data":[52,59],"RNA-seq":[54],"short-read":[55,58,276],"data.":[56,267,345],"are":[60,111],"generated":[61],"using":[62],"two":[63,105,176],"next":[64],"generation":[65],"sequencing":[66,106],"technologies,":[67,107],"i.e.":[68],"whole":[69],"genome":[70],"shotgun":[71,88],"(WGS)":[72],"and":[73,109,150,186,209,250,284,343],"amplicon":[74],"(AMP);":[75],"typically,":[76],"former":[78],"filtered":[80],"obtain":[82],"short-reads":[83],"belonging":[84],"(SG),":[89],"whereas":[90,259],"latter":[92],"take":[93],"into":[94,169,322],"account":[95],"only":[96],"some":[97],"specific":[98],"hypervariable":[100],"regions.":[101],"The":[102],"above":[103],"mentioned":[104],"SG":[108,149,342],"AMP,":[110],"used":[112,338],"alternatively,":[113],"this":[115,118,270,315],"reason":[116],"work":[119],"we":[120,146,159,174,210,272],"propose":[121],"deep":[123,178,187,285],"learning":[124,179,286],"approach":[125,309,318],"taxonomic":[127,237],"data,":[131],"that":[132],"can":[133,335],"employed":[135],"both":[137,148,240,248,341],"them.":[139],"RESULTS:":[140],"To":[141],"test":[142],"proposed":[144,201,273,304],"pipeline,":[145],"simulated":[147],"AMP":[151,257,344],"short-reads,":[152,258],"1000":[154],"full-length":[156],"sequences.":[157],"Then,":[158],"adopted":[160],"k-mer":[162,282],"representation":[163,283],"map":[165],"sequences":[166,277],"vectors":[168],"numerical":[171],"space.":[172],"Finally,":[173],"trained":[175,193],"different":[177],"architecture,":[180,287],"i.e.,":[181],"convolutional":[182],"neural":[183],"network":[184,189],"(CNN)":[185],"belief":[188],"(DBN),":[190],"obtaining":[191],"model":[194],"each":[196,236,290],"taxon.":[197],"We":[198,230],"tested":[199],"our":[200,212,317],"methodology":[202],"find":[204],"best":[206],"parameters":[207],"configuration,":[208],"compared":[211],"results":[213,301],"against":[214],"performances":[217],"provided":[218],"by":[219],"reference":[221],"classifier":[222,234,261],"identification,":[225],"known":[226],"RDP":[228,233,260],"classifier.":[229],"outperformed":[231],"level":[238],"with":[239,256,264],"architectures.":[241],"For":[242],"instance,":[243],"CNN":[249],"DBN":[251],"reached":[252],"91.3%":[253],"accuracy":[255],"obtained":[262,332],"83.8%":[263],"same":[266],"CONCLUSIONS:":[268],"In":[269],"work,":[271],"technique":[279],"based":[280],"on":[281],"which":[289],"taxon":[291],"(from":[292],"phylum":[293],"genus)":[295],"generates":[296],"model.":[299],"Experimental":[300],"confirm":[302],"pipeline":[305],"valid":[308],"classifying":[311,340],"sequences;":[313],"reason,":[316],"integrated":[321],"most":[324],"common":[325],"tools":[326],"analysis.":[329],"According":[330],"results,":[333],"successfully":[337]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":19},{"year":2024,"cited_by_count":23},{"year":2023,"cited_by_count":14},{"year":2022,"cited_by_count":16},{"year":2021,"cited_by_count":19},{"year":2020,"cited_by_count":35},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":4}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
