{"id":"https://openalex.org/W3107086932","doi":"https://doi.org/10.1093/database/baaa105","title":"ncVarDB: a manually curated database for pathogenic non-coding variants and benign controls","display_name":"ncVarDB: a manually curated database for pathogenic non-coding variants and benign controls","publication_year":2020,"publication_date":"2020-01-01","ids":{"openalex":"https://openalex.org/W3107086932","doi":"https://doi.org/10.1093/database/baaa105","mag":"3107086932"},"language":"en","primary_location":{"id":"doi:10.1093/database/baaa105","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baaa105","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baaa105/34612123/baaa105.pdf","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"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baaa105/34612123/baaa105.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111598459","display_name":"Harry Biggs","orcid":null},"institutions":[{"id":"https://openalex.org/I80281795","display_name":"University of Otago","ror":"https://ror.org/01jmxt844","country_code":"NZ","type":"education","lineage":["https://openalex.org/I80281795"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Harry Biggs","raw_affiliation_strings":["Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand","institution_ids":["https://openalex.org/I80281795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052282064","display_name":"Padmini Parthasarathy","orcid":null},"institutions":[{"id":"https://openalex.org/I80281795","display_name":"University of Otago","ror":"https://ror.org/01jmxt844","country_code":"NZ","type":"education","lineage":["https://openalex.org/I80281795"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Padmini Parthasarathy","raw_affiliation_strings":["Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand","institution_ids":["https://openalex.org/I80281795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040438451","display_name":"Alexandra Gavryushkina","orcid":"https://orcid.org/0000-0002-1885-1108"},"institutions":[{"id":"https://openalex.org/I80281795","display_name":"University of Otago","ror":"https://ror.org/01jmxt844","country_code":"NZ","type":"education","lineage":["https://openalex.org/I80281795"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Alexandra Gavryushkina","raw_affiliation_strings":["Bio-Protection Research Centre, University of Otago, PO Box 56, Dunedin 9054, New Zealand","Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand"],"affiliations":[{"raw_affiliation_string":"Bio-Protection Research Centre, University of Otago, PO Box 56, Dunedin 9054, New Zealand","institution_ids":["https://openalex.org/I80281795"]},{"raw_affiliation_string":"Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand","institution_ids":["https://openalex.org/I80281795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067459027","display_name":"Paul P. Gardner","orcid":"https://orcid.org/0000-0002-7808-1213"},"institutions":[{"id":"https://openalex.org/I80281795","display_name":"University of Otago","ror":"https://ror.org/01jmxt844","country_code":"NZ","type":"education","lineage":["https://openalex.org/I80281795"]}],"countries":["NZ"],"is_corresponding":true,"raw_author_name":"Paul P Gardner","raw_affiliation_strings":["Bio-Protection Research Centre, University of Otago, PO Box 56, Dunedin 9054, New Zealand","Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand"],"affiliations":[{"raw_affiliation_string":"Bio-Protection Research Centre, University of Otago, PO Box 56, Dunedin 9054, New Zealand","institution_ids":["https://openalex.org/I80281795"]},{"raw_affiliation_string":"Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand","institution_ids":["https://openalex.org/I80281795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5067459027"],"corresponding_institution_ids":["https://openalex.org/I80281795"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":1.7936,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.85870416,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"2020","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11642","display_name":"Genomics and Rare Diseases","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11482","display_name":"RNA modifications and cancer","score":0.9965999722480774,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.6626291275024414},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5763293504714966},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5630459785461426},{"id":"https://openalex.org/keywords/human-genome","display_name":"Human genome","score":0.5318806767463684},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5307579040527344},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5183135271072388},{"id":"https://openalex.org/keywords/indel","display_name":"Indel","score":0.47345536947250366},{"id":"https://openalex.org/keywords/1000-genomes-project","display_name":"1000 Genomes Project","score":0.4585009515285492},{"id":"https://openalex.org/keywords/intergenic-region","display_name":"Intergenic region","score":0.4548013210296631},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4523686468601227},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.41582101583480835},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.35959911346435547},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.14410269260406494}],"concepts":[{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.6626291275024414},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5763293504714966},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5630459785461426},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.5318806767463684},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5307579040527344},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5183135271072388},{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.47345536947250366},{"id":"https://openalex.org/C97425143","wikidata":"https://www.wikidata.org/wiki/Q164786","display_name":"1000 Genomes Project","level":5,"score":0.4585009515285492},{"id":"https://openalex.org/C195139083","wikidata":"https://www.wikidata.org/wiki/Q3463539","display_name":"Intergenic region","level":4,"score":0.4548013210296631},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4523686468601227},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.41582101583480835},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.35959911346435547},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.14410269260406494}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/database/baaa105","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baaa105","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baaa105/34612123/baaa105.pdf","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":"pmh:oai:pubmedcentral.nih.gov:7706182","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7706182","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":"Database (Oxford)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/baaa105","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baaa105","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baaa105/34612123/baaa105.pdf","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":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3107086932.pdf","grobid_xml":"https://content.openalex.org/works/W3107086932.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W19051162","https://openalex.org/W142807026","https://openalex.org/W1507593999","https://openalex.org/W1912672559","https://openalex.org/W2002861821","https://openalex.org/W2011582941","https://openalex.org/W2017818880","https://openalex.org/W2032838501","https://openalex.org/W2054185647","https://openalex.org/W2108871359","https://openalex.org/W2114478923","https://openalex.org/W2117446594","https://openalex.org/W2124410686","https://openalex.org/W2128016314","https://openalex.org/W2135388003","https://openalex.org/W2137297899","https://openalex.org/W2148105023","https://openalex.org/W2154866190","https://openalex.org/W2160995259","https://openalex.org/W2168817344","https://openalex.org/W2169567789","https://openalex.org/W2171777347","https://openalex.org/W2198606573","https://openalex.org/W2612091911","https://openalex.org/W2725988230","https://openalex.org/W2741137565","https://openalex.org/W2751686252","https://openalex.org/W2768145059","https://openalex.org/W2783098129","https://openalex.org/W2885727518","https://openalex.org/W2905452503","https://openalex.org/W2949945261","https://openalex.org/W2951624434","https://openalex.org/W2967059818","https://openalex.org/W2980128108"],"related_works":["https://openalex.org/W2529614973","https://openalex.org/W2247766769","https://openalex.org/W2187917240","https://openalex.org/W2295325708","https://openalex.org/W2395068850","https://openalex.org/W1989130879","https://openalex.org/W2366650996","https://openalex.org/W1544691147","https://openalex.org/W2156272823","https://openalex.org/W2160515792"],"abstract_inverted_index":{"Abstract":[0],"Variants":[1],"within":[2],"the":[3,22,51,59,72,82,94,98,120,167,175],"non-coding":[4,16,29,45,79,90,178],"genome":[5,47],"are":[6],"frequently":[7],"associated":[8],"with":[9,138,162],"phenotypes":[10],"in":[11,21,81,174],"genome-wide":[12],"association":[13],"studies.":[14],"These":[15,127],"regions":[17],"may":[18],"be":[19],"involved":[20],"regulation":[23],"of":[24,43,58,77,88,100,116,171,177],"gene":[25],"expression,":[26],"encode":[27],"functional":[28,101],"RNAs,":[30],"or":[31,152,169],"influence":[32],"splicing":[33],"and":[34,148],"other":[35],"cellular":[36],"functions.":[37],"We":[38,103],"have":[39,69,104,112],"curated":[40,160],"a":[41,113,159,163],"list":[42],"characterized":[44],"human":[46],"variants":[48,91],"based":[49],"on":[50],"published":[52,83,95],"evidence":[53,74,99],"that":[54,111],"indicates":[55],"phenotypic":[56],"consequences":[57],"variation.":[60],"In":[61],"order":[62],"to":[63,93],"minimize":[64],"annotation":[65,141],"errors,":[66],"two":[67],"curators":[68],"independently":[70],"verified":[71],"supporting":[73],"for":[75,131,166],"pathogenicity":[76],"each":[78],"variant":[80,149,179],"literature.":[84],"The":[85,154],"database":[86,124],"consists":[87],"721":[89],"linked":[92],"literature":[96],"describing":[97],"consequences.":[102],"also":[105],"sampled":[106,129],"7228":[107],"covariate-matched":[108],"benign":[109],"controls,":[110],"population":[114],"frequency":[115],"over":[117],"5%,":[118],"from":[119],"single":[121],"nucleotide":[122],"polymorphism":[123],"(dbSNP151)":[125],"database.":[126],"were":[128],"controlling":[130],"potential":[132,164],"confounding":[133],"factors":[134],"such":[135],"as":[136],"linkage":[137],"pathogenic":[139],"variants,":[140],"type":[142,150],"(untranslated":[143],"region,":[144],"intron,":[145],"intergenic,":[146],"etc.)":[147],"(substitution":[151],"indel).":[153],"dataset":[155],"presented":[156],"here":[157],"represents":[158],"repository,":[161],"use":[165],"training":[168],"evaluation":[170],"algorithms":[172],"used":[173],"prediction":[176],"functionality.":[180],"Database":[181],"URL:":[182],"https://github.com/Gardner-BinfLab/ncVarDB.":[183]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
