{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T14:15:55Z","timestamp":1778163355247,"version":"3.51.4"},"reference-count":5,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2013,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>The Sequence Read Archive (SRA) is the largest public repository of sequencing data from the next generation of sequencing platforms including Illumina (Genome Analyzer, HiSeq, MiSeq, .etc), Roche 454 GS System, Applied Biosystems SOLiD System, Helicos Heliscope, PacBio RS, and others.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>SRAdb is an attempt to make queries of the metadata associated with SRA submission, study, sample, experiment and run more robust and precise, and make access to sequencing data in the SRA easier. We have parsed all the SRA metadata into a SQLite database that is routinely updated and can be easily distributed. The SRAdb R\/Bioconductor package then utilizes this SQLite database for querying and accessing metadata. Full text search functionality makes querying metadata very flexible and powerful. Fastq files associated with query results can be downloaded easily for local analysis. The package also includes an interface from R to a popular genome browser, the Integrated Genomics Viewer.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>SRAdb Bioconductor package provides a convenient and integrated framework to query and access SRA metadata quickly and powerfully from within R.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-14-19","type":"journal-article","created":{"date-parts":[[2013,1,17]],"date-time":"2013-01-17T07:14:20Z","timestamp":1358406860000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":107,"title":["SRAdb: query and use public next-generation sequencing data from within R"],"prefix":"10.1186","volume":"14","author":[{"given":"Yuelin","family":"Zhu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert M","family":"Stephens","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul S","family":"Meltzer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sean R","family":"Davis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2013,1,17]]},"reference":[{"key":"5631_CR1","unstructured":"The NCBI Sequence Read Archive[http:\/\/www.ncbi.nlm.nih.gov\/sra]"},{"key":"5631_CR2","volume-title":"R: A Language and Environment for Statistical Computing","author":"R Core Team","year":"2012","unstructured":"R Core Team: R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria; 2012. [. [ISBN 3-900051-07-0] http:\/\/www.R-project.org\/] []. [ISBN 3-900051-07-0]"},{"issue":"10","key":"5631_CR3","doi-asserted-by":"publisher","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","volume":"5","author":"R Gentleman","year":"2004","unstructured":"Gentleman R, Carey V, Bates D, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al.: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004,5(10):R80. 10.1186\/gb-2004-5-10-r80","journal-title":"Genome Biol"},{"key":"5631_CR4","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1038\/nbt.1754","volume":"29","author":"J Robinson","year":"2011","unstructured":"Robinson J, Thorvaldsd\u00f3ttir H, Winckler W, Guttman M, Lander E, Getz G, Mesirov J: Integrative genomics viewer. Nat Biotechnol 2011, 29: 24-26. 10.1038\/nbt.1754","journal-title":"Nat Biotechnol"},{"key":"5631_CR5","volume-title":"RSQLite: SQLite interface for R","author":"DA James","year":"2012","unstructured":"James DA, Falcon S: RSQLite: SQLite interface for R. 2012. . [R package version 0.11.2] http:\/\/CRAN.R-project.org\/package=RSQLite . [R package version 0.11.2]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-19.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T18:34:31Z","timestamp":1630521271000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-19"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,1,17]]},"references-count":5,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2013,12]]}},"alternative-id":["5631"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-14-19","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,1,17]]},"assertion":[{"value":"28 September 2012","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 January 2013","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 January 2013","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"19"}}