{"id":"https://openalex.org/W4296577759","doi":"https://doi.org/10.1093/bioinformatics/btac639","title":"Reproducible acquisition, management and meta-analysis of nucleotide sequence (meta)data using q2-fondue","display_name":"Reproducible acquisition, management and meta-analysis of nucleotide sequence (meta)data using q2-fondue","publication_year":2022,"publication_date":"2022-09-19","ids":{"openalex":"https://openalex.org/W4296577759","doi":"https://doi.org/10.1093/bioinformatics/btac639","pmid":"https://pubmed.ncbi.nlm.nih.gov/36130056"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac639","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac639","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/22/5081/47153924/btac639.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/22/5081/47153924/btac639.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037922055","display_name":"Micha\u0142 Ziemski","orcid":"https://orcid.org/0000-0001-6285-8852"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Michal Ziemski","raw_affiliation_strings":["Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Z\u00fcrich , Z\u00fcrich 8092, Switzerland"],"affiliations":[{"raw_affiliation_string":"Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Z\u00fcrich , Z\u00fcrich 8092, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082470569","display_name":"A. K. Adamov","orcid":"https://orcid.org/0000-0002-7506-1583"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Anja Adamov","raw_affiliation_strings":["Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Z\u00fcrich , Z\u00fcrich 8092, Switzerland"],"affiliations":[{"raw_affiliation_string":"Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Z\u00fcrich , Z\u00fcrich 8092, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082545931","display_name":"Lina Kim","orcid":"https://orcid.org/0000-0002-2852-2869"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Lina Kim","raw_affiliation_strings":["Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Z\u00fcrich , Z\u00fcrich 8092, Switzerland"],"affiliations":[{"raw_affiliation_string":"Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Z\u00fcrich , Z\u00fcrich 8092, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058645932","display_name":"Lena Fl\u00f6rl","orcid":"https://orcid.org/0000-0003-4458-4071"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Lena Fl\u00f6rl","raw_affiliation_strings":["Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Z\u00fcrich , Z\u00fcrich 8092, Switzerland"],"affiliations":[{"raw_affiliation_string":"Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Z\u00fcrich , Z\u00fcrich 8092, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000165682","display_name":"Nicholas A. Bokulich","orcid":"https://orcid.org/0000-0002-1784-8935"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Nicholas A Bokulich","raw_affiliation_strings":["Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Z\u00fcrich , Z\u00fcrich 8092, Switzerland"],"affiliations":[{"raw_affiliation_string":"Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Z\u00fcrich , Z\u00fcrich 8092, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5000165682"],"corresponding_institution_ids":["https://openalex.org/I35440088"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.9548,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.73452566,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"38","issue":"22","first_page":"5081","last_page":"5091"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"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":0.9994999766349792,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9940000176429749,"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":0.9939000010490417,"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/metadata","display_name":"Metadata","score":0.7478883266448975},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7470020055770874},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7166756391525269},{"id":"https://openalex.org/keywords/executable","display_name":"Executable","score":0.600472092628479},{"id":"https://openalex.org/keywords/download","display_name":"Download","score":0.5950976014137268},{"id":"https://openalex.org/keywords/data-management","display_name":"Data management","score":0.5105773210525513},{"id":"https://openalex.org/keywords/bloom-filter","display_name":"Bloom filter","score":0.46349120140075684},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.4516512453556061},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4257318377494812},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4171043038368225},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37746962904930115},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.37139177322387695},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.23354721069335938}],"concepts":[{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.7478883266448975},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7470020055770874},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7166756391525269},{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.600472092628479},{"id":"https://openalex.org/C2780154274","wikidata":"https://www.wikidata.org/wiki/Q7126717","display_name":"Download","level":2,"score":0.5950976014137268},{"id":"https://openalex.org/C1668388","wikidata":"https://www.wikidata.org/wiki/Q1149776","display_name":"Data management","level":2,"score":0.5105773210525513},{"id":"https://openalex.org/C147224247","wikidata":"https://www.wikidata.org/wiki/Q885373","display_name":"Bloom filter","level":2,"score":0.46349120140075684},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.4516512453556061},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4257318377494812},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4171043038368225},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37746962904930115},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.37139177322387695},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.23354721069335938},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"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":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac639","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac639","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/22/5081/47153924/btac639.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36130056","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36130056","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9665871","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9665871","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac639","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac639","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/22/5081/47153924/btac639.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4743802784","display_name":null,"funder_award_id":"310030_204275","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4296577759.pdf","grobid_xml":"https://content.openalex.org/works/W4296577759.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W1511524925","https://openalex.org/W1838079655","https://openalex.org/W1989348205","https://openalex.org/W2011301426","https://openalex.org/W2032005977","https://openalex.org/W2036897871","https://openalex.org/W2076381052","https://openalex.org/W2104846587","https://openalex.org/W2113904019","https://openalex.org/W2116041602","https://openalex.org/W2120358246","https://openalex.org/W2129687578","https://openalex.org/W2135323299","https://openalex.org/W2142153593","https://openalex.org/W2144659346","https://openalex.org/W2153627933","https://openalex.org/W2165446840","https://openalex.org/W2302501749","https://openalex.org/W2308634414","https://openalex.org/W2401404581","https://openalex.org/W2406493898","https://openalex.org/W2535055464","https://openalex.org/W2577303777","https://openalex.org/W2585379990","https://openalex.org/W2737371096","https://openalex.org/W2753961085","https://openalex.org/W2766358903","https://openalex.org/W2791681873","https://openalex.org/W2798209956","https://openalex.org/W2807194798","https://openalex.org/W2810419619","https://openalex.org/W2896411436","https://openalex.org/W2911244738","https://openalex.org/W2922146544","https://openalex.org/W2944114814","https://openalex.org/W2944623206","https://openalex.org/W2949631084","https://openalex.org/W2950150251","https://openalex.org/W2952045272","https://openalex.org/W2953236953","https://openalex.org/W2956864158","https://openalex.org/W2963276645","https://openalex.org/W2966125063","https://openalex.org/W2984894304","https://openalex.org/W3088303111","https://openalex.org/W3150635270","https://openalex.org/W3209575515","https://openalex.org/W3209642438","https://openalex.org/W3216588755","https://openalex.org/W4237457671","https://openalex.org/W6658503034","https://openalex.org/W6765784246","https://openalex.org/W6769989246"],"related_works":["https://openalex.org/W2086572746","https://openalex.org/W2604468458","https://openalex.org/W2157216338","https://openalex.org/W121740227","https://openalex.org/W1662107788","https://openalex.org/W3082379938","https://openalex.org/W2135966669","https://openalex.org/W2594143027","https://openalex.org/W2732769800","https://openalex.org/W2924589531"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2}],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
