If you are a researcher transitioning from downloading UK Biobank (UKB) data to accessing it via the UKB-Research Analysis Platform (UKB-RAP), you might have questions about how this new process works and how to best integrate your data into this platform. Researchers may need to change to UKB-RAP access for many reasons, such as when requesting new or restricted data. This is because the UKB-RAP environment allows UKB to provide better security and protection over our data. This article will cover the steps that need to be taken when you begin using the UKB-RAP after initially starting your project via download, and how your project will look when starting on the UKB-RAP.
To get started, you will first need to complete the researcher training courses. This will provide you with information on how to start analysing data on the platform. You may also be interested in reading some of our relevant community forum posts and resources, such as:
If you have downloaded data via an exemption request, you will still be allowed to access your previously downloaded data. However, all access to any new or updated data must be within UKB-RAP. On the other hand, researchers who have downloaded the data before the UKB-RAP was introduced will need to delete all previously downloaded data when migrating over to the UKB-RAP. A 3-month grace period is provided to help researchers upload their necessary data into the UKB-RAP.
Once you are in the UKB-RAP, you will be able to access all UKB data under your given tier of access directly on the platform. However, you can also upload your own files to the UKB-RAP (e.g. files of derived data fields) which will allow you to analyse all your data within the platform. Uploading your files can be done in a few different ways:
Command line interface (CLI)
If you are comfortable with using the CLI, you can get started with using the dx client to login to the UKB-RAP platform. To upload files to the UKB-RAP you can use the dx upload command followed by the file path you wish to upload. For example:
$ dx upload /Users/folder/my_file
For more information on how to use dx upload, you can see the DNAnexus documentation as well as the dx command index.
Graphical user interface (GUI)
For researchers less comfortable with the CLI, you may wish to use the GUI. You can upload data by clicking the button in your project directory, and selecting the
option in the dropdown menu. This will allow you to navigate to the file you wish to upload or drag and drop your local files into the UKB-RAP.
Whilst you can upload all data to the UKB-RAP, you cannot download any individual level data from the UKB-RAP under any circumstance.
When you transition your project onto the UKB-RAP, all of your EIDs (participant identifiers) will match up between your downloaded data and UKB-RAP project. This is true only if you are using the same application. If you are using a different application, please be aware that your EIDs will no longer match up between your downloaded data and the UKB-RAP.
Once all of the researchers on your application have taken the researcher training courses and understood how to access and dispense data into your UKB-RAP project, check out our UK Biobank GitHub. This serves as a great starting point to look at examples of coding and data analysis on the platform to support effective research. Some further resources you may be interested in include the Transitional Credit Programme, which is a UK Biobank fund that allows early career and international researchers to have their access fees and computing costs covered.
Transition checklist:
- Request UKB-RAP access by submitting a ticket to the UK Biobank access team
- Complete the UKB-RAP training courses.
- This will provide you with information on how to create your account, enter your billing information, dispense data into your UKB-RAP project, add collaborators, and so on.
- Register on UKB-RAP and link your account to your AMS profile.
- Dispense data into a UKB-RAP project and enter your billing information as directed in the training videos.
- Upload any derived variables or personal data files you wish to access on the UKB-RAP.
- Delete your local copies of UKB data (if applicable).
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