{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:37Z","timestamp":1740185137948,"version":"3.37.3"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2019,8,29]],"date-time":"2019-08-29T00:00:00Z","timestamp":1567036800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["PIC-FAIR OT3 OD025466-01"],"award-info":[{"award-number":["PIC-FAIR OT3 OD025466-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000050","name":"National Heart, Lung, and Blood Institute","doi-asserted-by":"publisher","award":["OT3 HL142480-01"],"award-info":[{"award-number":["OT3 HL142480-01"]}],"id":[{"id":"10.13039\/100000050","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Based on the Genomic Data Sharing Policy issued in August 2007, the National Institutes of Health (NIH) has supported several repositories such as the database of Genotypes and Phenotypes (dbGaP). dbGaP is an online repository that provides access to large-scale genetic and phenotypic datasets with more than 1000 studies. However, navigating the website and understanding the relationship between the studies are not easy tasks. Moreover, the decryption of the files is a complex procedure. In this study we propose the dbgap2x R package that covers a broad range of functions for searching dbGaP studies, exploring the characteristics of a study and easily decrypting the files from dbGaP.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>dbgap2x is an R package with the code available at https:\/\/github.com\/gversmee\/dbgap2x. A containerized version including the package, a Jupyter server and with a Notebook example is available at https:\/\/hub.docker.com\/r\/gversmee\/dbgap2x.<\/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\/btz680","type":"journal-article","created":{"date-parts":[[2019,8,28]],"date-time":"2019-08-28T18:46:49Z","timestamp":1567018009000},"page":"1305-1306","source":"Crossref","is-referenced-by-count":2,"title":["dbgap2x: an R package to explore and extract data from the database of Genotypes and Phenotypes (dbGaP)"],"prefix":"10.1093","volume":"36","author":[{"given":"Gr\u00e9goire","family":"Versm\u00e9e","sequence":"first","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laura","family":"Versm\u00e9e","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mika\u00ebl","family":"Dusenne","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Niloofar","family":"Jalali","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul","family":"Avillach","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,8,29]]},"reference":[{"key":"2023013110144502100_btz680-B1","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1016\/j.tig.2014.12.006","article-title":"NIH\u2019s genomic data sharing policy: timing and tradeoffs","volume":"31","author":"Contreras","year":"2015","journal-title":"Trends Genet"},{"key":"2023013110144502100_btz680-B2","first-page":"87","volume-title":"Positioning and Power in Academic Publishing: Players, Agents and Agendas","author":"Kluyver","year":"2016"},{"key":"2023013110144502100_btz680-B3","doi-asserted-by":"crossref","first-page":"1181","DOI":"10.1038\/ng1007-1181","article-title":"The NCBI dbGaP database of genotypes and phenotypes","volume":"39","author":"Mailman","year":"2007","journal-title":"Nat. Genet"},{"key":"2023013110144502100_btz680-B4","doi-asserted-by":"crossref","first-page":"D975","DOI":"10.1093\/nar\/gkt1211","article-title":"NCBI\u2019s database of genotypes and phenotypes: dbGaP","volume":"42","author":"Tryka","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023013110144502100_btz680-B5","doi-asserted-by":"crossref","first-page":"D819","DOI":"10.1093\/nar\/gkw1139","article-title":"The dbGaP data browser: a new tool for browsing dbGaP controlled-access genomic data","volume":"45","author":"Wong","year":"2017","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\/btz680\/29225215\/btz680.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/4\/1305\/48983119\/btz680.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/4\/1305\/48983119\/btz680.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T20:14:33Z","timestamp":1675196073000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/4\/1305\/5556117"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,8,29]]},"references-count":5,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2020,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz680","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2020,2,15]]},"published":{"date-parts":[[2019,8,29]]}}}