{"id":"https://openalex.org/W4402649394","doi":"https://doi.org/10.1093/database/baae091","title":"Influenza sequence validation and annotation using VADR","display_name":"Influenza sequence validation and annotation using VADR","publication_year":2024,"publication_date":"2024-01-01","ids":{"openalex":"https://openalex.org/W4402649394","doi":"https://doi.org/10.1093/database/baae091","pmid":"https://pubmed.ncbi.nlm.nih.gov/39297389"},"language":"en","primary_location":{"id":"doi:10.1093/database/baae091","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baae091","pdf_url":null,"source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/database/baae091","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032850756","display_name":"Vince D. Calhoun","orcid":"https://orcid.org/0000-0001-9058-0747"},"institutions":[{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vincent C Calhoun","raw_affiliation_strings":["U.S. National Library of Medicine, National Center for Biotechnology Information National Center for Biotechnology Information, , 8600 Rockville Pike, Bethesda, MD 20894, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"U.S. National Library of Medicine, National Center for Biotechnology Information National Center for Biotechnology Information, , 8600 Rockville Pike, Bethesda, MD 20894, United States","institution_ids":["https://openalex.org/I4210109390"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076036084","display_name":"Eneida Hatcher","orcid":null},"institutions":[{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eneida L Hatcher","raw_affiliation_strings":["U.S. National Library of Medicine, National Center for Biotechnology Information National Center for Biotechnology Information, , 8600 Rockville Pike, Bethesda, MD 20894, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"U.S. National Library of Medicine, National Center for Biotechnology Information National Center for Biotechnology Information, , 8600 Rockville Pike, Bethesda, MD 20894, United States","institution_ids":["https://openalex.org/I4210109390"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005905944","display_name":"Linda Yankie","orcid":null},"institutions":[{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Linda Yankie","raw_affiliation_strings":["U.S. National Library of Medicine, National Center for Biotechnology Information National Center for Biotechnology Information, , 8600 Rockville Pike, Bethesda, MD 20894, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"U.S. National Library of Medicine, National Center for Biotechnology Information National Center for Biotechnology Information, , 8600 Rockville Pike, Bethesda, MD 20894, United States","institution_ids":["https://openalex.org/I4210109390"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021155495","display_name":"Eric P. Nawrocki","orcid":"https://orcid.org/0000-0002-2497-3427"},"institutions":[{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Eric P Nawrocki","raw_affiliation_strings":["U.S. National Library of Medicine, National Center for Biotechnology Information National Center for Biotechnology Information, , 8600 Rockville Pike, Bethesda, MD 20894, United States"],"raw_orcid":"https://orcid.org/0000-0002-2497-3427","affiliations":[{"raw_affiliation_string":"U.S. National Library of Medicine, National Center for Biotechnology Information National Center for Biotechnology Information, , 8600 Rockville Pike, Bethesda, MD 20894, United States","institution_ids":["https://openalex.org/I4210109390"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5021155495"],"corresponding_institution_ids":["https://openalex.org/I4210109390"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":1.4157,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.826361,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"2024","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10167","display_name":"Influenza Virus Research Studies","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10167","display_name":"Influenza Virus Research Studies","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9642999768257141,"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/T11243","display_name":"Respiratory viral infections research","score":0.9603000283241272,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"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/annotation","display_name":"Annotation","score":0.7986876964569092},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5737549066543579},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5616318583488464},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.503553569316864},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.34998083114624023},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.33594098687171936},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3002901077270508},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18915557861328125},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09495452046394348}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7986876964569092},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5737549066543579},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5616318583488464},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.503553569316864},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.34998083114624023},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.33594098687171936},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3002901077270508},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18915557861328125},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09495452046394348}],"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007251","descriptor_name":"Influenza, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007251","descriptor_name":"Influenza, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007251","descriptor_name":"Influenza, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007251","descriptor_name":"Influenza, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007251","descriptor_name":"Influenza, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007251","descriptor_name":"Influenza, Human","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D007251","descriptor_name":"Influenza, Human","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D007251","descriptor_name":"Influenza, Human","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D007251","descriptor_name":"Influenza, Human","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D007251","descriptor_name":"Influenza, Human","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D009975","descriptor_name":"Orthomyxoviridae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009975","descriptor_name":"Orthomyxoviridae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009975","descriptor_name":"Orthomyxoviridae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009975","descriptor_name":"Orthomyxoviridae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009975","descriptor_name":"Orthomyxoviridae","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":"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":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/database/baae091","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baae091","pdf_url":null,"source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},{"id":"pmid:39297389","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39297389","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11411204","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11411204","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11411204/pdf/baae091.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Database (Oxford)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/baae091","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baae091","pdf_url":null,"source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1483301458","https://openalex.org/W1536270671","https://openalex.org/W1974962646","https://openalex.org/W2001788095","https://openalex.org/W2015292449","https://openalex.org/W2069831575","https://openalex.org/W2091526576","https://openalex.org/W2134884409","https://openalex.org/W2141152740","https://openalex.org/W2153053964","https://openalex.org/W2158714788","https://openalex.org/W2159734253","https://openalex.org/W2559258718","https://openalex.org/W2789843538","https://openalex.org/W2944708711","https://openalex.org/W2992633765","https://openalex.org/W2998154928","https://openalex.org/W2998449782","https://openalex.org/W3006274289","https://openalex.org/W3028206028","https://openalex.org/W3202634790","https://openalex.org/W4239734004","https://openalex.org/W4309305890","https://openalex.org/W4309908917","https://openalex.org/W4317624906","https://openalex.org/W4381251144","https://openalex.org/W6810378445"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W1533177136","https://openalex.org/W4380994516"],"abstract_inverted_index":{"Tens":[0],"of":[1,3,112],"thousands":[2],"influenza":[4,33,86,100,113,128,134,152],"sequences":[5,93,130],"are":[6,154],"deposited":[7],"into":[8],"the":[9,90,109,150],"GenBank":[10,25,65],"database":[11],"each":[12],"year.":[13],"The":[14],"software":[15,61],"tool":[16,19],"FLu":[17],"ANnotation":[18],"(FLAN)":[20],"has":[21,37],"been":[22,38],"used":[23,63],"by":[24,64],"since":[26],"2007":[27],"to":[28,97,160],"validate":[29],"and":[30,36,59,70,94,103,115,140,149,162],"annotate":[31,99],"incoming":[32],"sequence":[34,57,73],"submissions":[35],"publicly":[39],"available":[40,77,157],"as":[41,46,78,131,133],"a":[42,47,55,79],"webserver":[43],"but":[44],"not":[45],"standalone":[48,80],"tool.":[49,81],"Viral":[50],"Annotation":[51],"DefineR":[52],"(VADR)":[53],"is":[54,76,120],"general":[56],"validation":[58],"annotation":[60],"package":[62],"for":[66,158],"norovirus,":[67],"dengue":[68],"virus":[69,72],"SARS-CoV-2":[71],"processing":[74],"that":[75],"We":[82],"have":[83],"created":[84],"VADR":[85,96,102,119,123,147],"models":[87,153],"based":[88],"on":[89,108],"FLAN":[91,104,145],"reference":[92],"adapted":[95],"accurately":[98,126],"sequences.":[101],"show":[105],"consistent":[106],"results":[107],"vast":[110],"majority":[111],"sequences,":[114,143],"when":[116],"they":[117],"disagree,":[118],"usually":[121],"correct.":[122],"can":[124],"also":[125],"process":[127],"D":[129],"well":[132],"A":[135],"H17,":[136],"H18,":[137],"H19,":[138],"N10":[139],"N11":[141],"subtype":[142],"which":[144],"cannot.":[146],"1.6.3":[148],"associated":[151],"now":[155],"freely":[156],"users":[159],"download":[161],"use.":[163],"Database":[164],"URL:":[165],"https://bitbucket.org/nawrockie/vadr-models-flu.":[166]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
