{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,23]],"date-time":"2024-08-23T18:27:59Z","timestamp":1724437679869},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Public genomic databases, which are often used to guide genetic studies of human disease, are now being applied to genomic medicine through in silico integrative genomics. These databases, however, often lack tools for systematically determining the experimental origins of the data.<\/jats:p>\n               <jats:p>Results: We introduce a new data provenance model that we have implemented in a public web application, BioQ, for assessing the reliability of the data by systematically tracing its experimental origins to the original subjects and biologics. BioQ allows investigators to both visualize data provenance as well as explore individual elements of experimental process flow using precise tools for detailed data exploration and documentation. It includes a number of human genetic variation databases such as the HapMap and 1000 Genomes projects.<\/jats:p>\n               <jats:p>Availability and implementation: BioQ is freely available to the public at http:\/\/bioq.saclab.net<\/jats:p>\n               <jats:p>Contact: \u00a0ssaccone@wustl.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts117","type":"journal-article","created":{"date-parts":[[2012,3,17]],"date-time":"2012-03-17T00:32:05Z","timestamp":1331944325000},"page":"1189-1191","source":"Crossref","is-referenced-by-count":17,"title":["BioQ: tracing experimental origins in public genomic databases using a novel data provenance model"],"prefix":"10.1093","volume":"28","author":[{"given":"Scott F.","family":"Saccone","sequence":"first","affiliation":[]},{"given":"Jiaxi","family":"Quan","sequence":"additional","affiliation":[]},{"given":"Peter L.","family":"Jones","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2012,3,16]]},"reference":[{"key":"2023012711534511400_B1","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1038\/nature09298","article-title":"Integrating common and rare genetic variation in diverse human populations","volume":"467","author":"Altshuler","year":"2010","journal-title":"Nature"},{"key":"2023012711534511400_B2","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1038\/467401b","article-title":"Disclose all data in publications","volume":"467","author":"Baggerly","year":"2010","journal-title":"Nature"},{"key":"2023012711534511400_B3","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1038\/nature09534","article-title":"A map of human genome variation from population-scale sequencing","volume":"467","author":"Durbin","year":"2010","journal-title":"Nature"},{"key":"2023012711534511400_B4","doi-asserted-by":"crossref","first-page":"D876","DOI":"10.1093\/nar\/gkq963","article-title":"The UCSC Genome Browser database: update 2011","volume":"39","author":"Fujita","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012711534511400_B5","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1038\/nature09764","article-title":"Charting a course for genomic medicine from base pairs to bedside","volume":"470","author":"Green","year":"2011","journal-title":"Nature"},{"key":"2023012711534511400_B6","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1038\/nrg2795","article-title":"Next-generation genomics: an integrative approach","volume":"11","author":"Hawkins","year":"2010","journal-title":"Nat. Rev. Genet."},{"key":"2023012711534511400_B7","doi-asserted-by":"crossref","first-page":"9362","DOI":"10.1073\/pnas.0903103106","article-title":"Potential etiologic and functional implications of genome-wide association loci for human diseases and traits","volume":"106","author":"Hindorff","year":"2009","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012711534511400_B8","doi-asserted-by":"crossref","first-page":"1699","DOI":"10.1056\/NEJMp0808934","article-title":"Genomewide association studies\u2014illuminating biologic pathways","volume":"360","author":"Hirschhorn","year":"2009","journal-title":"N. Engl. J. Med."},{"key":"2023012711534511400_B9","doi-asserted-by":"crossref","first-page":"1127","DOI":"10.1038\/nbt1347","article-title":"The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics","volume":"25","author":"Jones","year":"2007","journal-title":"Nat. Biotechnol."},{"key":"2023012711534511400_B10","doi-asserted-by":"crossref","first-page":"D901","DOI":"10.1093\/nar\/gkq1054","article-title":"New tools and methods for direct programmatic access to the dbSNP relational database","volume":"39","author":"Saccone","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012711534511400_B11","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1038\/469139a","article-title":"Cancer trial errors revealed","volume":"469","author":"Samuel","year":"2011","journal-title":"Nature"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/8\/1189\/48930516\/bioinformatics_28_8_1189.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/8\/1189\/48930516\/bioinformatics_28_8_1189.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T12:24:22Z","timestamp":1674822262000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/8\/1189\/196508"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,3,16]]},"references-count":11,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2012,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts117","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2012,4]]},"published":{"date-parts":[[2012,3,16]]}}}