{"id":"https://openalex.org/W3047675315","doi":"https://doi.org/10.1186/s12859-020-03666-4","title":"SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis","display_name":"SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis","publication_year":2020,"publication_date":"2020-08-10","ids":{"openalex":"https://openalex.org/W3047675315","doi":"https://doi.org/10.1186/s12859-020-03666-4","mag":"3047675315","pmid":"https://pubmed.ncbi.nlm.nih.gov/32778056"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-020-03666-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03666-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03666-4","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/s12859-020-03666-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014147774","display_name":"Stevenn Volant","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Stevenn Volant","raw_affiliation_strings":["Hub de Bioinformatique et Biostatistique - D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France","Hub de Bioinformatique et Biostatistique \u2013 D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hub de Bioinformatique et Biostatistique - D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France","institution_ids":["https://openalex.org/I157536573","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Hub de Bioinformatique et Biostatistique \u2013 D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France","institution_ids":["https://openalex.org/I157536573","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078128888","display_name":"P Lechat","orcid":"https://orcid.org/0000-0003-1050-5582"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Pierre Lechat","raw_affiliation_strings":["Hub de Bioinformatique et Biostatistique - D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France","Hub de Bioinformatique et Biostatistique \u2013 D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hub de Bioinformatique et Biostatistique - D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France","institution_ids":["https://openalex.org/I157536573","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Hub de Bioinformatique et Biostatistique \u2013 D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France","institution_ids":["https://openalex.org/I157536573","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037495563","display_name":"Perrine Woringer","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Perrine Woringer","raw_affiliation_strings":["Hub de Bioinformatique et Biostatistique - D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France","Hub de Bioinformatique et Biostatistique \u2013 D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hub de Bioinformatique et Biostatistique - D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France","institution_ids":["https://openalex.org/I157536573","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Hub de Bioinformatique et Biostatistique \u2013 D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France","institution_ids":["https://openalex.org/I157536573","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064507849","display_name":"Laurence Motreff","orcid":null},"institutions":[{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Laurence Motreff","raw_affiliation_strings":["Biomics - D\u00e9partement G\u00e9nomes et G\u00e9n\u00e9tique, Institut Pasteur, 28 Rue du Docteur Roux, Paris, 75015, France","Biomics \u2013 D\u00e9partement G\u00e9nomes et G\u00e9n\u00e9tique, Institut Pasteur, 28 Rue du Docteur Roux, Paris, 75015, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomics - D\u00e9partement G\u00e9nomes et G\u00e9n\u00e9tique, Institut Pasteur, 28 Rue du Docteur Roux, Paris, 75015, France","institution_ids":["https://openalex.org/I157536573"]},{"raw_affiliation_string":"Biomics \u2013 D\u00e9partement G\u00e9nomes et G\u00e9n\u00e9tique, Institut Pasteur, 28 Rue du Docteur Roux, Paris, 75015, France","institution_ids":["https://openalex.org/I157536573"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113448610","display_name":"Pascal Campagne","orcid":"https://orcid.org/0000-0001-7018-1896"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Pascal Campagne","raw_affiliation_strings":["Hub de Bioinformatique et Biostatistique - D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France","Hub de Bioinformatique et Biostatistique \u2013 D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hub de Bioinformatique et Biostatistique - D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France","institution_ids":["https://openalex.org/I157536573","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Hub de Bioinformatique et Biostatistique \u2013 D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France","institution_ids":["https://openalex.org/I157536573","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070536515","display_name":"Christophe Malabat","orcid":"https://orcid.org/0000-0003-2551-2355"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Christophe Malabat","raw_affiliation_strings":["Hub de Bioinformatique et Biostatistique - D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France","Hub de Bioinformatique et Biostatistique \u2013 D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hub de Bioinformatique et Biostatistique - D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France","institution_ids":["https://openalex.org/I157536573","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Hub de Bioinformatique et Biostatistique \u2013 D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France","institution_ids":["https://openalex.org/I157536573","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039721313","display_name":"Sean Kennedy","orcid":"https://orcid.org/0000-0002-3932-8922"},"institutions":[{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Sean Kennedy","raw_affiliation_strings":["Biomics - D\u00e9partement G\u00e9nomes et G\u00e9n\u00e9tique, Institut Pasteur, 28 Rue du Docteur Roux, Paris, 75015, France","Biomics \u2013 D\u00e9partement G\u00e9nomes et G\u00e9n\u00e9tique, Institut Pasteur, 28 Rue du Docteur Roux, Paris, 75015, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomics - D\u00e9partement G\u00e9nomes et G\u00e9n\u00e9tique, Institut Pasteur, 28 Rue du Docteur Roux, Paris, 75015, France","institution_ids":["https://openalex.org/I157536573"]},{"raw_affiliation_string":"Biomics \u2013 D\u00e9partement G\u00e9nomes et G\u00e9n\u00e9tique, Institut Pasteur, 28 Rue du Docteur Roux, Paris, 75015, France","institution_ids":["https://openalex.org/I157536573"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079120219","display_name":"Amine Ghozlane","orcid":"https://orcid.org/0000-0001-7670-6235"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Amine Ghozlane","raw_affiliation_strings":["Biomics - D\u00e9partement G\u00e9nomes et G\u00e9n\u00e9tique, Institut Pasteur, 28 Rue du Docteur Roux, Paris, 75015, France. amine.ghozlane@pasteur.fr","Hub de Bioinformatique et Biostatistique - D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France. amine.ghozlane@pasteur.fr","Biomics \u2013 D\u00e9partement G\u00e9nomes et G\u00e9n\u00e9tique, Institut Pasteur, 28 Rue du Docteur Roux, Paris, 75015, France"],"raw_orcid":"https://orcid.org/0000-0001-7670-6235","affiliations":[{"raw_affiliation_string":"Biomics - D\u00e9partement G\u00e9nomes et G\u00e9n\u00e9tique, Institut Pasteur, 28 Rue du Docteur Roux, Paris, 75015, France. amine.ghozlane@pasteur.fr","institution_ids":["https://openalex.org/I157536573"]},{"raw_affiliation_string":"Hub de Bioinformatique et Biostatistique - D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France. amine.ghozlane@pasteur.fr","institution_ids":["https://openalex.org/I157536573","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Biomics \u2013 D\u00e9partement G\u00e9nomes et G\u00e9n\u00e9tique, Institut Pasteur, 28 Rue du Docteur Roux, Paris, 75015, France","institution_ids":["https://openalex.org/I157536573"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5014147774"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I157536573"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":3.4179,"has_fulltext":true,"cited_by_count":75,"citation_normalized_percentile":{"value":0.93661741,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"21","issue":"1","first_page":"345","last_page":"345"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.6265000104904175,"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/T10066","display_name":"Gut microbiota and health","score":0.6265000104904175,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.1306000053882599,"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":0.1200999990105629,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.8104606866836548},{"id":"https://openalex.org/keywords/shamanism","display_name":"Shamanism","score":0.7417545318603516},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.7127082943916321},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7052090167999268},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4317423701286316},{"id":"https://openalex.org/keywords/raw-data","display_name":"Raw data","score":0.41643112897872925},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3982032537460327},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3936137557029724},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.22154486179351807},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13969078660011292},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08653140068054199}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8104606866836548},{"id":"https://openalex.org/C512209198","wikidata":"https://www.wikidata.org/wiki/Q42042","display_name":"Shamanism","level":2,"score":0.7417545318603516},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.7127082943916321},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7052090167999268},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4317423701286316},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.41643112897872925},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3982032537460327},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3936137557029724},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.22154486179351807},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13969078660011292},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08653140068054199},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001826","descriptor_name":"Body Fluids","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D001826","descriptor_name":"Body Fluids","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D001826","descriptor_name":"Body Fluids","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D002675","descriptor_name":"Child, Preschool","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002675","descriptor_name":"Child, Preschool","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002675","descriptor_name":"Child, Preschool","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002965","descriptor_name":"Classification","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002965","descriptor_name":"Classification","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002965","descriptor_name":"Classification","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005243","descriptor_name":"Feces","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D005243","descriptor_name":"Feces","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D005243","descriptor_name":"Feces","qualifier_ui":"Q000382","qualifier_name":"microbiology","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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","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":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","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":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},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-020-03666-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03666-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03666-4","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:32778056","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32778056","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:pubmedcentral.nih.gov:7430814","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7430814","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:HAL:pasteur-02951458v1","is_oa":true,"landing_page_url":"https://pasteur.hal.science/pasteur-02951458","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, 2020, 21 (1), pp.345. &#x27E8;10.1186/s12859-020-03666-4&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:doaj.org/article:a2a8777a27094f67921552464b51d244","is_oa":true,"landing_page_url":"https://doaj.org/article/a2a8777a27094f67921552464b51d244","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 21, Iss 1, Pp 1-15 (2020)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-020-03666-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03666-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03666-4","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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3047675315.pdf","grobid_xml":"https://content.openalex.org/works/W3047675315.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W1791491556","https://openalex.org/W1846216853","https://openalex.org/W1964027278","https://openalex.org/W1988925586","https://openalex.org/W1999813764","https://openalex.org/W2004014148","https://openalex.org/W2007703905","https://openalex.org/W2026006003","https://openalex.org/W2032066134","https://openalex.org/W2056279562","https://openalex.org/W2061177996","https://openalex.org/W2072970694","https://openalex.org/W2074335138","https://openalex.org/W2075563069","https://openalex.org/W2084443943","https://openalex.org/W2084590843","https://openalex.org/W2085926377","https://openalex.org/W2088833470","https://openalex.org/W2091922579","https://openalex.org/W2105329815","https://openalex.org/W2108718991","https://openalex.org/W2112320611","https://openalex.org/W2114104545","https://openalex.org/W2115875921","https://openalex.org/W2119812663","https://openalex.org/W2122698216","https://openalex.org/W2122796622","https://openalex.org/W2124985265","https://openalex.org/W2127303481","https://openalex.org/W2128711701","https://openalex.org/W2130725058","https://openalex.org/W2130731460","https://openalex.org/W2141637710","https://openalex.org/W2152885278","https://openalex.org/W2160378127","https://openalex.org/W2165909549","https://openalex.org/W2170024099","https://openalex.org/W2179438025","https://openalex.org/W2270107170","https://openalex.org/W2328023807","https://openalex.org/W2347061404","https://openalex.org/W2401404581","https://openalex.org/W2474169383","https://openalex.org/W2513506562","https://openalex.org/W2748261468","https://openalex.org/W2774551105","https://openalex.org/W2804419420","https://openalex.org/W2807194798","https://openalex.org/W2888423719","https://openalex.org/W2892206041","https://openalex.org/W2917207851","https://openalex.org/W2946378187","https://openalex.org/W2950976944","https://openalex.org/W2952615074","https://openalex.org/W2964312306","https://openalex.org/W4245615750"],"related_works":["https://openalex.org/W2382161274","https://openalex.org/W2234483980","https://openalex.org/W3177536641","https://openalex.org/W2591129611","https://openalex.org/W110498564","https://openalex.org/W2082359500","https://openalex.org/W2375219300","https://openalex.org/W4241133622","https://openalex.org/W2326526832","https://openalex.org/W1480144363"],"abstract_inverted_index":{"BACKGROUND:":[0],"Comparing":[1],"the":[2,76,95,102,125,188,206],"composition":[3],"of":[4,9,44,78,98,124,190,217],"microbial":[5],"communities":[6],"among":[7,101],"groups":[8],"interest":[10],"(e.g.,":[11],"patients":[12],"vs":[13],"healthy":[14],"individuals)":[15],"is":[16,37,109,118,136,161,166],"a":[17,42,80,87,130,147,151,180,195,210],"central":[18],"aspect":[19],"in":[20,56,72,163,192],"microbiome":[21],"research.":[22],"It":[23],"typically":[24],"involves":[25],"sequencing,":[26],"data":[27,53],"processing,":[28],"statistical":[29,89],"analysis":[30,36,216],"and":[31,55,91,142,156,165,179],"graphical":[32],"display.":[33],"Such":[34],"an":[35,66,121],"normally":[38],"obtained":[39],"by":[40],"using":[41],"set":[43],"different":[45,126,173],"applications":[46,103],"that":[47,104,212],"require":[48],"specific":[49],"expertise":[50],"for":[51,83,112],"installation,":[52],"processing":[54],"some":[57],"cases,":[58],"programming":[59],"skills.":[60],"RESULTS:":[61],"Here,":[62],"we":[63,70,186,202],"present":[64],"SHAMAN,":[65,201],"interactive":[67,99],"web":[68],"application":[69,135,149],"developed":[71],"order":[73],"to":[74,93,119],"facilitate":[75],"use":[77,120],"(i)":[79],"bioinformatic":[81],"workflow":[82],"metataxonomic":[84,197],"analysis,":[85],"(ii)":[86],"reliable":[88],"modelling":[90],"(iii)":[92],"provide":[94],"largest":[96],"panel":[97],"visualizations":[100],"are":[105],"currently":[106],"available.":[107],"SHAMAN":[108,191],"specifically":[110],"designed":[111],"non-expert":[113],"users.":[114],"A":[115],"strong":[116],"benefit":[117],"integrated":[122],"version":[123],"analytic":[127],"steps":[128],"underlying":[129],"proper":[131],"metagenomic":[132,184,218],"analysis.":[133,198],"The":[134,158],"freely":[137],"accessible":[138],"at":[139,168,204],"http://shaman.pasteur.fr/":[140],",":[141],"may":[143],"also":[144],"work":[145],"as":[146],"standalone":[148],"with":[150,209],"Docker":[152],"container":[153],"(aghozlane/shaman),":[154],"conda":[155],"R.":[157],"source":[159],"code":[160],"written":[162],"R":[164],"available":[167],"https://github.com/aghozlane/shaman":[169],".":[170],"Using":[171],"two":[172],"datasets":[174],"(a":[175],"mock":[176],"community":[177,208],"sequencing":[178],"published":[181],"16S":[182],"rRNA":[183],"data),":[185],"illustrate":[187],"strengths":[189],"quickly":[193],"performing":[194],"complete":[196],"CONCLUSIONS:":[199],"With":[200],"aim":[203],"providing":[205],"scientific":[207],"platform":[211],"simplifies":[213],"reproducible":[214],"quantitative":[215],"data.":[219]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":16},{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":18},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":5}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
