{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T09:38:39Z","timestamp":1774690719672,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2022,8,18]],"date-time":"2022-08-18T00:00:00Z","timestamp":1660780800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"ELIXIR"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,30]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>Beacon v2 is an API specification established by the Global Alliance for Genomics and Health initiative (GA4GH) that defines a standard for federated discovery of genomic and phenotypic data. Here, we present the Beacon v2 Reference Implementation (B2RI), a set of open-source software tools that allow lighting up a local Beacon instance \u2018out-of-the-box\u2019. Along with the software, we have created detailed \u2018Read the Docs\u2019 documentation that includes information on deployment and installation.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The B2RI is released under GNU General Public License v3.0 and Apache License v2.0. Documentation and source code is available at: https:\/\/b2ri-documentation.readthedocs.io.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac568","type":"journal-article","created":{"date-parts":[[2022,8,18]],"date-time":"2022-08-18T12:48:11Z","timestamp":1660826891000},"page":"4656-4657","source":"Crossref","is-referenced-by-count":20,"title":["Beacon v2 Reference Implementation: a toolkit to enable federated sharing of genomic and phenotypic data"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9280-058X","authenticated-orcid":false,"given":"Manuel","family":"Rueda","sequence":"first","affiliation":[{"name":"European Genome-Phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology , Barcelona 08003, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8348-2524","authenticated-orcid":false,"given":"Roberto","family":"Ariosa","sequence":"additional","affiliation":[{"name":"European Genome-Phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology , Barcelona 08003, Spain"}]},{"given":"Mauricio","family":"Moldes","sequence":"additional","affiliation":[{"name":"European Genome-Phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology , Barcelona 08003, Spain"}]},{"given":"Jordi","family":"Rambla","sequence":"additional","affiliation":[{"name":"European Genome-Phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology , Barcelona 08003, Spain"}]}],"member":"286","published-online":{"date-parts":[[2022,8,18]]},"reference":[{"key":"2023041408230120500_","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly (Austin)"},{"key":"2023041408230120500_","doi-asserted-by":"crossref","first-page":"35","DOI":"10.3389\/fgene.2012.00035","article-title":"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program","volume":"3","author":"Cingolani","year":"2012","journal-title":"Front. Genet"},{"key":"2023041408230120500_","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":"2023041408230120500_","doi-asserted-by":"crossref","first-page":"D862","DOI":"10.1093\/nar\/gkv1222","article-title":"ClinVar: public archive of interpretations of clinically relevant variants","volume":"44","author":"Landrum","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023041408230120500_","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1186\/s13073-020-00803-9","article-title":"dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs","volume":"12","author":"Liu","year":"2020","journal-title":"Genome Med"},{"key":"2023041408230120500_","doi-asserted-by":"crossref","first-page":"1749","DOI":"10.1093\/bioinformatics\/btw044","article-title":"BCFtools\/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data","volume":"32","author":"Narasimhan","year":"2016","journal-title":"Bioinformatics"},{"key":"2023041408230120500_","first-page":"791","article-title":"Beacon v2 and Beacon networks: a \u201clingua franca\u201d for federated data discovery in biomedical genomics, and beyond","author":"Rambla","year":"2022","journal-title":"Hum. Mutat"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac568\/45641209\/btac568.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/19\/4656\/49885054\/btac568.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/19\/4656\/49885054\/btac568.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,25]],"date-time":"2023-11-25T22:37:21Z","timestamp":1700951841000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/19\/4656\/6671215"}},"subtitle":[],"editor":[{"given":"Peter","family":"Robinson","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,8,18]]},"references-count":7,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2022,9,30]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac568","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,10,1]]},"published":{"date-parts":[[2022,8,18]]}}}