{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T10:53:58Z","timestamp":1740135238886,"version":"3.37.3"},"reference-count":8,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2023,3,3]],"date-time":"2023-03-03T00:00:00Z","timestamp":1677801600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2023,3,3]],"date-time":"2023-03-03T00:00:00Z","timestamp":1677801600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HL133040"],"award-info":[{"award-number":["R01HL133040"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"Abstract<\/jats:title>\n Background<\/jats:title>\n Data archiving and distribution are essential to scientific rigor and reproducibility of research. The National Center for Biotechnology Information\u2019s Database of Genotypes and Phenotypes (dbGaP) is a public repository for scientific data sharing. To support curation of thousands of complex data sets, dbGaP has detailed submission instructions that investigators must follow when archiving their data.<\/jats:p>\n <\/jats:sec>\n Results<\/jats:title>\n We developed dbGaPCheckup, an R package which implements a series of check, awareness, reporting, and utility functions to support data integrity and proper formatting of the subject phenotype data set and data dictionary prior to dbGaP submission. For example, as a tool, dbGaPCheckup ensures that the data dictionary contains all fields required by dbGaP, and additional fields required by dbGaPCheckup; the number and names of variables match between the data set and data dictionary; there are no duplicated variable names or descriptions; observed data values are not more extreme than the logical minimum and maximum values stated in the data dictionary; and more. The package also includes functions that implement a series of minor\/scalable fixes when errors are detected (e.g., a function to reorder the variables in the data dictionary to match the order listed in the data set). Finally, we also include reporting functions that produce graphical and textual descriptives of the data to further reduce the likelihood of data integrity issues. The dbGaPCheckup R package is available on CRAN (https:\/\/CRAN.R-project.org\/package=dbGaPCheckup<\/jats:ext-link>) and developed on GitHub (https:\/\/github.com\/lwheinsberg\/dbGaPCheckup<\/jats:ext-link>).<\/jats:p>\n <\/jats:sec>\n Conclusion<\/jats:title>\n dbGaPCheckup is an innovative assistive and timesaving tool that fills an important gap for researchers by making dbGaP submission of large and complex data sets less error prone.<\/jats:p>\n <\/jats:sec>","DOI":"10.1186\/s12859-023-05200-8","type":"journal-article","created":{"date-parts":[[2023,3,3]],"date-time":"2023-03-03T13:03:02Z","timestamp":1677848582000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["dbGaPCheckup: pre-submission checks of dbGaP-formatted subject phenotype files"],"prefix":"10.1186","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7690-5485","authenticated-orcid":false,"given":"Lacey W.","family":"Heinsberg","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9410-7228","authenticated-orcid":false,"given":"Daniel E.","family":"Weeks","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,3,3]]},"reference":[{"key":"5200_CR1","doi-asserted-by":"publisher","first-page":"D975","DOI":"10.1093\/nar\/gkt1211","volume":"42","author":"KA Tryka","year":"2014","unstructured":"Tryka KA, Hao L, Sturcke A, et al. NCBI\u2019s database of genotypes and phenotypes: dbGaP. Nucleic Acids Res. 2014;42:D975-979. https:\/\/doi.org\/10.1093\/nar\/gkt1211.","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"5200_CR2","doi-asserted-by":"publisher","first-page":"1181","DOI":"10.1038\/ng1007-1181","volume":"39","author":"MD Mailman","year":"2007","unstructured":"Mailman MD, Feolo M, Jin Y, et al. The NCBI dbGaP database of genotypes and phenotypes. Nat Genet. 2007;39(10):1181\u20136. https:\/\/doi.org\/10.1038\/ng1007-1181.","journal-title":"Nat Genet"},{"key":"5200_CR3","unstructured":"dbGaP study submission guide. https:\/\/www.ncbi.nlm.nih.gov\/gap\/docs\/submissionguide\/. Accessed 11 Nov 2022."},{"key":"5200_CR4","unstructured":"Wickham H, Miller E, Smith D. haven: import and export \u201cSPSS\u201d, \u201cStata\u201d and \u201cSAS\u201d files. Published online 2022. https:\/\/CRAN.R-project.org\/package=haven."},{"key":"5200_CR5","unstructured":"Larmarange J. labelled: manipulating labelled data. Published online 2022. https:\/\/CRAN.R-project.org\/package=labelled."},{"key":"5200_CR6","unstructured":"NCBI. GaPTools. https:\/\/github.com\/ncbi\/gaptools. Accessed 7 Feb 2023."},{"key":"5200_CR7","unstructured":"NCBI. Introducing GaPTools, a stand-alone data validation tool for dbGaP submissions. Accessed 7 Feb 2023. https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/05\/26\/gaptools\/."},{"key":"5200_CR8","unstructured":"Final NIH Policy for data management and sharing. https:\/\/grants.nih.gov\/grants\/guide\/notice-files\/NOT-OD-21-013.html."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-023-05200-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-023-05200-8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-023-05200-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,3,3]],"date-time":"2023-03-03T13:05:15Z","timestamp":1677848715000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-023-05200-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,3,3]]},"references-count":8,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2023,12]]}},"alternative-id":["5200"],"URL":"https:\/\/doi.org\/10.1186\/s12859-023-05200-8","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2023,3,3]]},"assertion":[{"value":"22 November 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 February 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 March 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The funders had no role in the design of the study or development of the package. As such, the authors declare no competing interest.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"77"}}