{"id":"https://openalex.org/W3092005606","doi":"https://doi.org/10.1093/bioinformatics/btaa857","title":"Automated download and clean-up of family-specific databases for kmer-based virus identification","display_name":"Automated download and clean-up of family-specific databases for kmer-based virus identification","publication_year":2020,"publication_date":"2020-09-23","ids":{"openalex":"https://openalex.org/W3092005606","doi":"https://doi.org/10.1093/bioinformatics/btaa857","mag":"3092005606","pmid":"https://pubmed.ncbi.nlm.nih.gov/33031509"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa857","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa857","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/5/705/37809181/btaa857.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":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/5/705/37809181/btaa857.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019684712","display_name":"Rosa Lundbye Alles\u00f8e","orcid":"https://orcid.org/0000-0002-8085-4473"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]},{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":true,"raw_author_name":"Rosa L Alles\u00f8e","raw_affiliation_strings":["National Food Institute, Technical University of Denmark , DK-2800 Kgs. Lyngby, Denmark","Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen , DK-2200 Copenhagen N, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Food Institute, Technical University of Denmark , DK-2800 Kgs. Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099"]},{"raw_affiliation_string":"Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen , DK-2200 Copenhagen N, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050933706","display_name":"Camilla K. Lemvigh","orcid":"https://orcid.org/0000-0002-5772-8743"},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Camilla K Lemvigh","raw_affiliation_strings":["Department of Health Technology, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark","National Food Institute, Technical University of Denmark , DK-2800 Kgs. Lyngby, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Health Technology, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099"]},{"raw_affiliation_string":"National Food Institute, Technical University of Denmark , DK-2800 Kgs. Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009528251","display_name":"My V. T. Phan","orcid":"https://orcid.org/0000-0002-6905-8513"},"institutions":[{"id":"https://openalex.org/I913958620","display_name":"Erasmus University Rotterdam","ror":"https://ror.org/057w15z03","country_code":"NL","type":"education","lineage":["https://openalex.org/I913958620"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"My V T Phan","raw_affiliation_strings":["Department of Viroscience, Erasmus University Medical Centre , 3000 CA Rotterdam, The Netherlands"],"raw_orcid":"https://orcid.org/0000-0002-6905-8513","affiliations":[{"raw_affiliation_string":"Department of Viroscience, Erasmus University Medical Centre , 3000 CA Rotterdam, The Netherlands","institution_ids":["https://openalex.org/I913958620"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064950341","display_name":"Philip T. L. C. Clausen","orcid":"https://orcid.org/0000-0002-8197-7520"},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Philip T L C Clausen","raw_affiliation_strings":["National Food Institute, Technical University of Denmark , DK-2800 Kgs. Lyngby, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Food Institute, Technical University of Denmark , DK-2800 Kgs. Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045750184","display_name":"Alfred Ferrer Florensa","orcid":"https://orcid.org/0000-0003-0502-3271"},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Alfred F Florensa","raw_affiliation_strings":["National Food Institute, Technical University of Denmark , DK-2800 Kgs. Lyngby, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Food Institute, Technical University of Denmark , DK-2800 Kgs. Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008677339","display_name":"Marion Koopmans","orcid":"https://orcid.org/0000-0002-5204-2312"},"institutions":[{"id":"https://openalex.org/I913958620","display_name":"Erasmus University Rotterdam","ror":"https://ror.org/057w15z03","country_code":"NL","type":"education","lineage":["https://openalex.org/I913958620"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Marion P G Koopmans","raw_affiliation_strings":["Department of Viroscience, Erasmus University Medical Centre , 3000 CA Rotterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Viroscience, Erasmus University Medical Centre , 3000 CA Rotterdam, The Netherlands","institution_ids":["https://openalex.org/I913958620"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071462078","display_name":"Ole Lund","orcid":"https://orcid.org/0000-0003-1108-0491"},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Ole Lund","raw_affiliation_strings":["National Food Institute, Technical University of Denmark , DK-2800 Kgs. Lyngby, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Food Institute, Technical University of Denmark , DK-2800 Kgs. Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050782615","display_name":"Matthew Cotten","orcid":"https://orcid.org/0000-0002-3361-3351"},"institutions":[{"id":"https://openalex.org/I4210146449","display_name":"MRC University of Glasgow Centre for Virus Research","ror":"https://ror.org/03vaer060","country_code":"GB","type":"government","lineage":["https://openalex.org/I4210087105","https://openalex.org/I4210146449","https://openalex.org/I7882870","https://openalex.org/I90344618"]},{"id":"https://openalex.org/I91369620","display_name":"Uganda Virus Research Institute","ror":"https://ror.org/04509n826","country_code":"UG","type":"facility","lineage":["https://openalex.org/I91369620"]},{"id":"https://openalex.org/I913958620","display_name":"Erasmus University Rotterdam","ror":"https://ror.org/057w15z03","country_code":"NL","type":"education","lineage":["https://openalex.org/I913958620"]}],"countries":["GB","NL","UG"],"is_corresponding":false,"raw_author_name":"Matthew Cotten","raw_affiliation_strings":["Department of Viroscience, Erasmus University Medical Centre , 3000 CA Rotterdam, The Netherlands","MRC-University of Glasgow Centre for Virus Research , G61 1QH Scotland, UK","MRC/UVRI and LSHTM Uganda Research Unit , Entebbe, Uganda"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Viroscience, Erasmus University Medical Centre , 3000 CA Rotterdam, The Netherlands","institution_ids":["https://openalex.org/I913958620"]},{"raw_affiliation_string":"MRC-University of Glasgow Centre for Virus Research , G61 1QH Scotland, UK","institution_ids":["https://openalex.org/I4210146449"]},{"raw_affiliation_string":"MRC/UVRI and LSHTM Uganda Research Unit , Entebbe, Uganda","institution_ids":["https://openalex.org/I91369620"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5019684712"],"corresponding_institution_ids":["https://openalex.org/I124055696","https://openalex.org/I2801134892","https://openalex.org/I96673099"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.4824,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.67494712,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"37","issue":"5","first_page":"705","last_page":"710"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.3806000053882599,"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"}},"topics":[{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.3806000053882599,"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/T11495","display_name":"Animal Virus Infections Studies","score":0.0989999994635582,"subfield":{"id":"https://openalex.org/subfields/1103","display_name":"Animal Science and Zoology"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11754","display_name":"SARS-CoV-2 detection and testing","score":0.053599998354911804,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.6994152069091797},{"id":"https://openalex.org/keywords/download","display_name":"Download","score":0.6514796018600464},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6147809624671936},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5581134557723999},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.27287256717681885},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18961074948310852}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6994152069091797},{"id":"https://openalex.org/C2780154274","wikidata":"https://www.wikidata.org/wiki/Q7126717","display_name":"Download","level":2,"score":0.6514796018600464},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6147809624671936},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5581134557723999},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.27287256717681885},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18961074948310852},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":9,"locations":[{"id":"doi:10.1093/bioinformatics/btaa857","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa857","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/5/705/37809181/btaa857.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:33031509","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33031509","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:pure.eur.nl:openaire/6a8e5f3d-c79f-4a09-9ad9-f47f36a530da","is_oa":true,"landing_page_url":"https://pure.eur.nl/en/publications/6a8e5f3d-c79f-4a09-9ad9-f47f36a530da","pdf_url":null,"source":{"id":"https://openalex.org/S4306401266","display_name":"EUR Research Repository (Erasmus University Rotterdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I913958620","host_organization_name":"Erasmus University Rotterdam","host_organization_lineage":["https://openalex.org/I913958620"],"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":"Alles\u00f8e, R L, Lemvigh, C K, Phan, M V T, Clausen, P T L C, Florensa, A F, Koopmans, M P G, Lund, O & Cotten, M 2021, 'Automated download and clean-up of family-specific databases for kmer-based virus identification', Bioinformatics, vol. 37, no. 5, pp. 705-710. https://doi.org/10.1093/bioinformatics/btaa857","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:eprints.gla.ac.uk:231306","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4210235606","display_name":"ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam)","issn_l":"2622-8912","issn":["2622-8912","2622-8920"],"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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Articles"},{"id":"pmh:oai:researchonline.lshtm.ac.uk:4660941","is_oa":false,"landing_page_url":"https://researchonline.lshtm.ac.uk/view/creators/lshmp6.html>;","pdf_url":null,"source":{"id":"https://openalex.org/S4306402527","display_name":"LSHTM Research Online (London School of Hygiene and Tropical Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210089966","host_organization_name":"London School of Hygiene & Tropical Medicine","host_organization_lineage":["https://openalex.org/I4210089966"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"NonPeerReviewed"},{"id":"pmh:oai:pubmedcentral.nih.gov:8097684","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8097684","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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/acb7a9b3-8d89-43d4-8cd8-31ffba26e2c2","is_oa":true,"landing_page_url":"https://researchprofiles.ku.dk/da/publications/acb7a9b3-8d89-43d4-8cd8-31ffba26e2c2","pdf_url":null,"source":{"id":"https://openalex.org/S4306401983","display_name":"Research at the University of Copenhagen (University of Copenhagen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I124055696","host_organization_name":"University of Copenhagen","host_organization_lineage":["https://openalex.org/I124055696"],"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":"Allesoe , R L , Lemvigh , C K , Phan , M V T , Clausen , P T L C , Florensa , A F , Koopmans , M P G , Lund , O & Cotten , M 2021 , ' Automated download and clean-up of family-specific databases for kmer-based virus identification ' , Bioinformatics , vol. 37 , no. 5 , pp. 705-710 . https://doi.org/10.1093/bioinformatics/btaa857","raw_type":"article"},{"id":"pmh:oai:pure.atira.dk:publications/fe4687e6-6990-43f6-86cb-17c92e32751c","is_oa":true,"landing_page_url":"https://orbit.dtu.dk/en/publications/fe4687e6-6990-43f6-86cb-17c92e32751c","pdf_url":null,"source":{"id":"https://openalex.org/S4306400705","display_name":"Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I96673099","host_organization_name":"Technical University of Denmark","host_organization_lineage":["https://openalex.org/I96673099"],"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":"Alles\u00f8e , R L , Lemvigh , C K , Phan , M V T , Clausen , P T L C , Florensa , A F , Koopmans , M P G , Lund , O &amp; Cotten , M 2021 , ' Automated download and clean-up of family specific databases for kmer-based virus identification ' , Bioinformatics , vol. 37 , no. 5 , pp. 705\u2013710 . https://doi.org/10.1093/bioinformatics/btaa857","raw_type":"article"},{"id":"pmh:oai:pure.eur.nl:openaire_cris_publications/6a8e5f3d-c79f-4a09-9ad9-f47f36a530da","is_oa":true,"landing_page_url":"http://www.scopus.com/inward/record.url?scp=85106069852&partnerID=8YFLogxK","pdf_url":null,"source":{"id":"https://openalex.org/S4306401266","display_name":"EUR Research Repository (Erasmus University Rotterdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I913958620","host_organization_name":"Erasmus University Rotterdam","host_organization_lineage":["https://openalex.org/I913958620"],"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":"Alles\u00f8e, R L, Lemvigh, C K, Phan, M V T, Clausen, P T L C, Florensa, A F, Koopmans, M P G, Lund, O & Cotten, M 2021, 'Automated download and clean-up of family-specific databases for kmer-based virus identification', Bioinformatics, vol. 37, no. 5, pp. 705-710. https://doi.org/10.1093/bioinformatics/btaa857","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa857","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa857","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/5/705/37809181/btaa857.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":[{"score":0.4099999964237213,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G2175344253","display_name":null,"funder_award_id":"643476","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G2583336430","display_name":null,"funder_award_id":"874735","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4282887365","display_name":null,"funder_award_id":"NNF14CC0001","funder_id":"https://openalex.org/F4320322436","funder_display_name":"Novo Nordisk"},{"id":"https://openalex.org/G6662978750","display_name":null,"funder_award_id":"NNF14CC0001","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"},{"id":"https://openalex.org/G7842005466","display_name":null,"funder_award_id":"Horizon 2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7896071357","display_name":"Novel PHAge MEthods for improved virus inactivation","funder_award_id":"799417","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320322436","display_name":"Novo Nordisk","ror":"https://ror.org/0435rc536"},{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3092005606.pdf","grobid_xml":"https://content.openalex.org/works/W3092005606.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1482190741","https://openalex.org/W2087080725","https://openalex.org/W2096525273","https://openalex.org/W2108982334","https://openalex.org/W2110015402","https://openalex.org/W2124351063","https://openalex.org/W2137390232","https://openalex.org/W2146225611","https://openalex.org/W2401834729","https://openalex.org/W2793461621","https://openalex.org/W2889178232","https://openalex.org/W2951729100","https://openalex.org/W4243601081"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2183842793","https://openalex.org/W4255676640","https://openalex.org/W2485259751","https://openalex.org/W4236216870","https://openalex.org/W4243876796","https://openalex.org/W2485273903","https://openalex.org/W2482041988"],"abstract_inverted_index":{"SUMMARY:":[0],"Here,":[1],"we":[2,133,178],"present":[3,114,134],"an":[4,81,161],"automated":[5],"pipeline":[6,44,204],"for":[7,100,138,172,192,205],"Download":[8],"Of":[9],"NCBI":[10],"Entries":[11],"(DONE)":[12],"and":[13,76,87,94,107,120,196,207],"continuous":[14],"updating":[15],"of":[16,58,72,148,164,182],"a":[17,56,135,152,183,188,212],"local":[18],"sequence":[19,60,198],"database":[20,26,49,57,71,96,154,185,191],"based":[21],"on":[22],"user-specified":[23,59],"queries.":[24],"The":[25,43,62,202],"can":[27,45],"be":[28,113],"created":[29],"with":[30,53,140],"either":[31],"protein":[32],"or":[33,39],"nucleotide":[34],"sequences":[35,67,101],"containing":[36],"all":[37],"entries":[38,52,65,168],"complete":[40],"genomes":[41],"only.":[42],"automatically":[46,98],"clean":[47],"the":[48,69,95,131,146,173,180],"by":[50,150],"removing":[51],"matches":[54],"to":[55,123,187],"contaminants.":[61],"default":[63],"contamination":[64],"include":[66],"from":[68,79,102],"UniVec":[70],"plasmids,":[73],"marker":[74],"genes":[75,110],"sequencing":[77],"adapters":[78],"NCBI,":[80],"E.coli":[82],"genome,":[83],"rRNA":[84],"sequences,":[85],"vectors":[86],"satellite":[88],"sequences.":[89],"Furthermore,":[90],"duplicates":[91],"are":[92,221],"removed":[93],"is":[97,209],"screened":[99],"green":[103],"fluorescent":[104],"protein,":[105],"luciferase":[106],"antibiotic":[108],"resistance":[109],"that":[111],"might":[112],"in":[115,126,211],"some":[116],"GenBank":[117],"viral":[118],"entries,":[119],"could":[121],"lead":[122],"false":[124],"positives":[125],"virus":[127,153,157],"identification.":[128],"For":[129],"utilizing":[130],"database,":[132],"useful":[136],"opportunity":[137],"dealing":[139],"possible":[141],"human":[142],"contamination.":[143],"We":[144,159],"show":[145],"applicability":[147],"DONE":[149,203],"downloading":[151,206],"comprising":[155],"37":[156,174],"families.":[158,175],"observed":[160],"average":[162],"increase":[163],"16":[165],"776":[166],"new":[167],"downloaded":[169],"per":[170],"month":[171],"In":[176],"addition,":[177],"demonstrate":[179],"utility":[181],"custom":[184],"compared":[186],"standard":[189],"reference":[190],"classifying":[193],"both":[194],"simulated":[195],"real":[197],"data.":[199],"AVAILABILITYAND":[200],"IMPLEMENTATION:":[201],"cleaning":[208],"deposited":[210],"publicly":[213],"available":[214,222],"repository":[215],"(https://bitbucket.org/genomicepidemiology/done/src/master/).":[216],"SUPPLEMENTARY":[217],"INFORMATION:":[218],"Supplementary":[219],"data":[220],"at":[223],"Bioinformatics":[224],"online.":[225]},"counts_by_year":[{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-06-21T07:57:09.225873","created_date":"2025-10-10T00:00:00"}
