{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,27]],"date-time":"2025-03-27T21:01:09Z","timestamp":1743109269859,"version":"3.37.3"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,10,28]],"date-time":"2021-10-28T00:00:00Z","timestamp":1635379200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["208377\/Z\/17\/Z","201535\/Z\/16\/Z","099131\/Z\/12\/Z","108749\/Z\/15\/Z"],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ELIXIR"},{"DOI":"10.13039\/100013060","name":"European Molecular Biology Laboratory","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"Abstract<\/jats:title>\n The European Variation Archive (EVA; https:\/\/www.ebi.ac.uk\/eva\/) is a resource for sharing all types of genetic variation data (SNPs, indels, and structural variants) for all species. The EVA was created in 2014 to provide FAIR access to genetic variation data and has since grown to be a primary resource for genomic variants hosting >3 billion records. The EVA and dbSNP have established a compatible global system to assign unique identifiers to all submitted genetic variants. The EVA is active within the Global Alliance of Genomics and Health (GA4GH), maintaining, contributing\u00a0and implementing standards such as VCF, Refget\u00a0and Variant Representation Specification (VRS). In this article, we describe the submission and permanent accessioning services along with the different ways the data can be retrieved by the scientific community.<\/jats:p>","DOI":"10.1093\/nar\/gkab960","type":"journal-article","created":{"date-parts":[[2021,10,15]],"date-time":"2021-10-15T23:40:58Z","timestamp":1634341258000},"page":"D1216-D1220","source":"Crossref","is-referenced-by-count":80,"title":["The European Variation Archive: a FAIR resource of genomic variation for all species"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5626-270X","authenticated-orcid":false,"given":"Timothe","family":"Cezard","sequence":"first","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7445-2419","authenticated-orcid":false,"given":"Fiona","family":"Cunningham","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8350-1235","authenticated-orcid":false,"given":"Sarah E","family":"Hunt","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK"}]},{"given":"Baron","family":"Koylass","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK"}]},{"given":"Nitin","family":"Kumar","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK"}]},{"given":"Gary","family":"Saunders","sequence":"additional","affiliation":[{"name":"ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK"}]},{"given":"April","family":"Shen","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK"}]},{"given":"Andres\u00a0F","family":"Silva","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK"}]},{"given":"Kirill","family":"Tsukanov","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK"}]},{"given":"Sundararaman","family":"Venkataraman","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3897-7955","authenticated-orcid":false,"given":"Paul","family":"Flicek","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK"}]},{"given":"Helen","family":"Parkinson","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7532-6898","authenticated-orcid":false,"given":"Thomas\u00a0M","family":"Keane","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK"}]}],"member":"286","published-online":{"date-parts":[[2021,10,28]]},"reference":[{"key":"2022010507404737400_B1","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1101\/gr.9.8.677","article-title":"dbSNP\u2014database for single nucleotide polymorphisms and other classes of minor genetic variation","volume":"9","author":"Sherry","year":"1999","journal-title":"Genome Res"},{"key":"2022010507404737400_B2","doi-asserted-by":"crossref","first-page":"D936","DOI":"10.1093\/nar\/gks1213","article-title":"dbVar and DGVa: public archives for genomic structural variation","volume":"41","author":"Lappalainen","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2022010507404737400_B3","doi-asserted-by":"crossref","first-page":"D1186","DOI":"10.1093\/nar\/gkaa1005","article-title":"Genome Variation Map: a worldwide collection of genome variations across multiple species","volume":"49","author":"Li","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2022010507404737400_B4","doi-asserted-by":"crossref","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR guiding principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. Data"},{"key":"2022010507404737400_B5","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btab524","article-title":"Refget: standardised access to reference sequences","author":"Yates","year":"2021","journal-title":"Bioinformatics"},{"key":"2022010507404737400_B6","doi-asserted-by":"crossref","DOI":"10.1101\/2021.01.15.426843","article-title":"The GA4GH variation representation specification (VRS): a computational framework for the precise representation and federated identification of molecular variation","author":"Wagner","year":"2021"},{"key":"2022010507404737400_B7","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"2022010507404737400_B8","doi-asserted-by":"crossref","first-page":"D121","DOI":"10.1093\/nar\/gkaa967","article-title":"The international nucleotide sequence database collaboration","volume":"49","author":"Arita","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2022010507404737400_B9","doi-asserted-by":"crossref","first-page":"D1172","DOI":"10.1093\/nar\/gky1061","article-title":"BioSamples database: an updated sample metadata hub","volume":"47","author":"Courtot","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2022010507404737400_B10","first-page":"D70","article-title":"The European Nucleotide Archive in 2019","volume":"48","author":"Amid","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2022010507404737400_B11","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1186\/s13059-016-0974-4","article-title":"The Ensembl Variant Effect Predictor","volume":"17","author":"McLaren","year":"2016","journal-title":"Genome Biol"},{"key":"2022010507404737400_B12","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1038\/s41587-019-0046-x","article-title":"Federated discovery and sharing of genomic data using Beacons","volume":"37","author":"Fiume","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"2022010507404737400_B13","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1093\/bioinformatics\/bty492","article-title":"htsget: a protocol for securely streaming genomic data","volume":"35","author":"Kelleher","year":"2019","journal-title":"Bioinformatics"},{"key":"2022010507404737400_B14","doi-asserted-by":"crossref","first-page":"4325","DOI":"10.1073\/pnas.1720115115","article-title":"Earth BioGenome Project: Sequencing life for the future of life","volume":"115","author":"Lewin","year":"2018","journal-title":"Proc. Natl. Acad. Sci"},{"key":"2022010507404737400_B15","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1146\/annurev-animal-090414-014900","article-title":"The genome 10K project: a way forward","volume":"3","author":"Koepfli","year":"2015","journal-title":"Annu. Rev. Anim. Biosci."},{"key":"2022010507404737400_B16","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1146\/annurev-animal-022516-022811","article-title":"Bat biology, genomes, and the Bat1K project: to generate chromosome-level genomes for all living bat species","volume":"6","author":"Teeling","year":"2018","journal-title":"Annu. Rev. Anim. Biosci."},{"key":"2022010507404737400_B17","doi-asserted-by":"crossref","first-page":"giaa051","DOI":"10.1093\/gigascience\/giaa051","article-title":"An improved pig reference genome sequence to enable pig genetics and genomics research","volume":"9","author":"Warr","year":"2020","journal-title":"GigaScience"},{"key":"2022010507404737400_B18","doi-asserted-by":"crossref","first-page":"1574","DOI":"10.1038\/s41588-018-0223-8","article-title":"Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci","volume":"50","author":"Lilue","year":"2018","journal-title":"Nat. Genet."},{"key":"2022010507404737400_B19","doi-asserted-by":"crossref","first-page":"aae0344","DOI":"10.1126\/science.aae0344","article-title":"Long-read sequence assembly of the gorilla genome","volume":"352","author":"Gordon","year":"2016","journal-title":"Science"},{"key":"2022010507404737400_B20","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1186\/s13059-020-02168-z","article-title":"The design and construction of reference pangenome graphs with minigraph","volume":"21","author":"Li","year":"2020","journal-title":"Genome Biol"},{"key":"2022010507404737400_B21","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1146\/annurev-genom-120120-081921","article-title":"The need for a human pangenome reference sequence","volume":"22","author":"Miga","year":"2021","journal-title":"Annu. Rev. Genomics Hum. Genet."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/D1\/D1216\/42058491\/gkab960.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/D1\/D1216\/42058491\/gkab960.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,5]],"date-time":"2022-01-05T08:20:19Z","timestamp":1641370819000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/50\/D1\/D1216\/6413605"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,10,28]]},"references-count":21,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2021,10,28]]},"published-print":{"date-parts":[[2022,1,7]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkab960","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"type":"print","value":"0305-1048"},{"type":"electronic","value":"1362-4962"}],"subject":[],"published-other":{"date-parts":[[2022,1,7]]},"published":{"date-parts":[[2021,10,28]]}}}