{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,8]],"date-time":"2026-03-08T08:51:32Z","timestamp":1772959892835,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,7,14]],"date-time":"2021-07-14T00:00:00Z","timestamp":1626220800000},"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":["WT201535\/Z\/16\/Z"],"award-info":[{"award-number":["WT201535\/Z\/16\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["206194"],"award-info":[{"award-number":["206194"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Australian Genomics Health Alliance [NHMRC","award":["1113531"],"award-info":[{"award-number":["1113531"]}]},{"name":"Australian Medical Research Future Fund"},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["GM128636"],"award-info":[{"award-number":["GM128636"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"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":[[2021,12,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Reference sequences are essential in creating a baseline of knowledge for many common bioinformatics methods, especially those using genomic sequencing.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have created refget, a Global Alliance for Genomics and Health API specification to access reference sequences and sub-sequences using an identifier derived from the sequence itself. We present four reference implementations across in-house and cloud infrastructure, a compliance suite and a web report used to ensure specification conformity across implementations.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The refget specification can be found at: https:\/\/w3id.org\/ga4gh\/refget.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab524","type":"journal-article","created":{"date-parts":[[2021,7,12]],"date-time":"2021-07-12T19:12:28Z","timestamp":1626117148000},"page":"299-300","source":"Crossref","is-referenced-by-count":11,"title":["Refget: standardized access to reference sequences"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8886-4772","authenticated-orcid":false,"given":"Andrew D","family":"Yates","sequence":"first","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus , Hinxton, Cambridge CB10 1SD, UK"},{"name":"Global Alliance for Genomics and Health"}]},{"given":"Jeremy","family":"Adams","sequence":"additional","affiliation":[{"name":"Global Alliance for Genomics and Health"},{"name":"Ontario Institute for Cancer Research , Toronto, ON, Canada"}]},{"given":"Somesh","family":"Chaturvedi","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus , Hinxton, Cambridge CB10 1SD, UK"},{"name":"Google Summer of Code"}]},{"given":"Robert M","family":"Davies","sequence":"additional","affiliation":[{"name":"Global Alliance for Genomics and Health"},{"name":"Wellcome Sanger Institute, Wellcome Genome Campus , Hinxton CB10 1SA, UK"}]},{"given":"Matthew","family":"Laird","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus , Hinxton, Cambridge CB10 1SD, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2639-7187","authenticated-orcid":false,"given":"Rasko","family":"Leinonen","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus , Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Rishi","family":"Nag","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus , Hinxton, Cambridge CB10 1SD, UK"},{"name":"Global Alliance for Genomics and Health"}]},{"given":"Nathan C","family":"Sheffield","sequence":"additional","affiliation":[{"name":"Center for Public Health Genomics, School of Medicine, University of Virginia , Charlottesville, VA 22903, USA"}]},{"given":"Oliver","family":"Hofmann","sequence":"additional","affiliation":[{"name":"Global Alliance for Genomics and Health"},{"name":"University of Melbourne Centre for Cancer Research, University of Melbourne , Melbourne, VIC, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7532-6898","authenticated-orcid":false,"given":"Thomas M","family":"Keane","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus , Hinxton, Cambridge CB10 1SD, UK"},{"name":"Global Alliance for Genomics and Health"}]}],"member":"286","published-online":{"date-parts":[[2021,7,14]]},"reference":[{"key":"2023020108391396200_btab524-B1","doi-asserted-by":"crossref","first-page":"e0239883","DOI":"10.1371\/journal.pone.0239883","article-title":"SeqRepo: a system for managing local collections of biological sequences","volume":"15","author":"Hart","year":"2020","journal-title":"PLoS One"},{"key":"2023020108391396200_btab524-B2","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1101\/gr.114819.110","article-title":"Efficient storage of high throughput DNA sequencing data using reference-based compression","volume":"21","author":"Fritz","year":"2011","journal-title":"Genome Res"},{"key":"2023020108391396200_btab524-B3","doi-asserted-by":"crossref","first-page":"D48","DOI":"10.1093\/nar\/gkx1097","article-title":"The international nucleotide sequence database collaboration","volume":"46","author":"Karsch-Mizrachi","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023020108391396200_btab524-B4","first-page":"D756","article-title":"UCSC Genome Browser enters 20th year","volume":"48","author":"Lee","year":"2020","journal-title":"Nucleic Acids 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Biol"},{"key":"2023020108391396200_btab524-B6","doi-asserted-by":"crossref","first-page":"D726","DOI":"10.1093\/nar\/gkx967","article-title":"EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies","volume":"46","author":"Mitchell","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023020108391396200_btab524-B7","first-page":"D682","article-title":"Ensembl 2020","volume":"48","author":"Yates","year":"2020","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab524\/40304092\/btab524.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/1\/299\/49006376\/btab524.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/1\/299\/49006376\/btab524.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T19:55:08Z","timestamp":1675281308000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/1\/299\/6321456"}},"subtitle":[],"editor":[{"given":"Zhiyong","family":"Lu","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,7,14]]},"references-count":7,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,12,22]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab524","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,1]]},"published":{"date-parts":[[2021,7,14]]}}}