Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, USA.
Center for Translational Data Science, The University of Chicago, Chicago, IL, USA.
Bioinformatics. 2019 Jun 1;35(11):1971-1973. doi: 10.1093/bioinformatics/bty925.
Large biobanks, such as UK Biobank with half a million participants, are changing the scale and availability of genotypic and phenotypic data for researchers to ask fundamental questions about the biology of health and disease. The breadth of the UK Biobank data is enabling discoveries at an unprecedented pace. However, this size and complexity pose new challenges to investigators who need to keep the accruing data up to date, comply with potential consent changes, and efficiently and reproducibly extract subsets of the data to answer specific scientific questions. Here we propose a tool called ukbREST designed for the UK Biobank study (easily extensible to other biobanks), which allows authorized users to efficiently retrieve phenotypic and genetic data. It exposes a REST API that makes data highly accessible inside a private and secure network, allowing the data specification in a human readable text format easily shareable with other researchers. These characteristics make ukbREST an important tool to make biobank's valuable data more readily accessible to the research community and facilitate reproducibility of the analysis, a key aspect of science.
It is implemented in Python using the Flask-RESTful framework for the API, and it is under the MIT license. It works with PostgreSQL and a Docker image is available for easy deployment. The source code and documentation is available in Github: https://github.com/hakyimlab/ukbrest.
大型生物库，如拥有 50 万名参与者的英国生物库，正在改变基因型和表型数据的规模和可及性，使研究人员能够提出关于健康和疾病生物学的基本问题。英国生物库数据的广度正在以前所未有的速度带来发现。然而，这种规模和复杂性给研究人员带来了新的挑战，他们需要使不断积累的数据保持最新，遵守潜在的同意变更，并有效地和可重复地提取数据的子集来回答特定的科学问题。在这里，我们提出了一个名为 ukbREST 的工具，它是为英国生物库研究设计的（很容易扩展到其他生物库），允许授权用户高效地检索表型和遗传数据。它公开了一个 REST API，使数据在私有和安全的网络中高度可访问，允许以人类可读的文本格式指定数据，以便与其他研究人员轻松共享。这些特性使 ukbREST 成为一个重要的工具，可以使生物库的有价值的数据更容易被研究社区访问，并促进分析的可重复性，这是科学的一个关键方面。
它是使用 Flask-RESTful 框架在 Python 中实现的，用于 API，并遵循 MIT 许可证。它与 PostgreSQL 一起使用，并且提供了一个 Docker 映像，便于部署。源代码和文档可在 Github 上获得：https://github.com/hakyimlab/ukbrest。
