Journal:Building infrastructure for African human genomic data management
| Full article title | Building infrastructure for African human genomic data management |
|---|---|
| Journal | Data Science Journal |
| Author(s) | Parker, Ziyaad; Maslamoney, Suresh; Meintjes, Ayton; Botha, Gerrit; Panji, Sumir; Hazelhurst, Scott; Mulder, Nicola |
| Author affiliation(s) | University of Cape Town, University of the Witwatersrand |
| Primary contact | Email: ziyaad dot parker at uct dot ac dot za |
| Year published | 2019 |
| Volume and issue | 18(1) |
| Page(s) | 47 |
| DOI | 10.5334/dsj-2019-047 |
| ISSN | 1683-1470 |
| Distribution license | Creative Commons Attribution 4.0 International |
| Website | https://datascience.codata.org/articles/10.5334/dsj-2019-047/ |
| Download | https://datascience.codata.org/articles/10.5334/dsj-2019-047/galley/894/download/ (PDF) |
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This article should be considered a work in progress and incomplete. Consider this article incomplete until this notice is removed. |
Abstract
Human genomic data are large and complex, and require adequate infrastructure for secure storage and transfer. The National Institutes of Health (NIH) and The Wellcome Trust have funded multiple projects on genomic research, including the Human Heredity and Health in Africa (H3Africa) initiative, and data are required to be deposited into the public domain. The European Genome-phenome Archive (EGA) is a repository for sequence and genotype data where data access is controlled by access committees. Access is determined by a formal application procedure for the purpose of secure storage and distribution, which must be in line with the informed consent of the study participants. H3Africa researchers based in Africa and generating their own data can benefit tremendously from the data sharing capabilities of the internet by using the appropriate technologies. The H3Africa Data Archive is an effort between the H3Africa data generating projects, H3ABioNet, and the EGA to store and submit genomic data to public repositories. H3ABioNet maintains the security of the H3Africa Data Archive, ensures ethical security compliance, supports users with data submission, and facilitates data transfers. The goal is to ensure efficient data flow between researchers, the archive, and the EGA or other public repositories. To comply with the H3Africa data sharing and release policy, nine months after the data is in secure storage, H3ABioNet converts the data into an Extensible Markup Language (XML) format ready for submission to EGA. This article describes the infrastructure that has been developed for African human genomic data management.
Keywords: genomic data, data archive, H3Africa data, African genomic data
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Notes
This presentation is faithful to the original, with only a few minor changes to presentation. In some cases important information was missing from the references, and that information was added. The original paper listed references alphabetically; this wiki lists them by order of appearance, by design. The two footnotes were turned into inline references for convenience.
