Getting Started with All of Us Projects

A. Initiating a Project

  1. Get to know All of Us: If you are thinking of doing a project using the All of Us database, start with watching this New User Orientation recording. Watch the first 26 minutes which will introduce you to the All of Us Research Program and types of data available (electronic health records, FitBit data, surveys, genomic data).
  2. Get to know the Researcher Workbench and tools: We access data and perform analyses on a cloud platform called Researcher Workbench. The All of Us Program is currently transitioning to a newer version of the workbench. Watch this video to familiarize with the platform and analysis process.
  3. Explore All of Us: Go to the All of Us Research Hub and look around. In particular, explore data using Data Browser and look at published studies and ongoing projects by searching Publication Directory and Research Project Directory
  4. Explore the larger literature: Now that you have an idea what has been done using the All of Us database, it’s time to consider what areas of research you would like to explore (population, intervention, control, outcome). To do this, you must first understand how your area of research has been explored in the larger body of literature. Using the keywords from step 2, explore larger databases (e.g., PubMed, Web of Science, Google Scholar, Scopus). At this stage, begin drafting your Triple-I research proposal.
  5. Establish a research question: Now that you have started drafting your proposal, let’s further refine what your research question should look like. A great research question is clear, specific, answerable, measurable, relevant, and interesting. Much of what you organized from steps 2 and 3 will inform how best to formulate this question. See here for reference on how to build a research question.
  6. Identify an advisor: While IOURMR Research Core can provide general research support or All of Us-specific technical support, you need to identify an advisor with expertise related to your area of research. Identify and visit with this advisor to discuss your research question, and confirm their willingness to serve as your Principal Investigator (PI) on your Triple-I proposal. Note, your PI may be an IOURMR member depending on your area of research.
  7. Meet with us: Once you have completed the above steps, contact Dr. Nicholas Coombs (ncoombs@uidaho.edu) at IOURMR to arrange a meeting. Come with any questions and a draft of your research proposal.

B. Registering for the Researcher Workbench

You must become a registered user of the All of Us Researcher Workbench in order to access data and work with it. The University of Idaho already has the institutional Data Use and Registration Agreement with All of Us. As an individual user, you must create your own account, undergo training, and sign the Data User Code of Conduct. Go to the All of Us Research Hub. Click on the “REGISTER” button on the top right corner and follow the instructions to verify identity and create an account.

You can choose either “Registered Tier” or “Controlled Tier” level of access. There is an additional training module if you want to access the Controlled Tier level data. Feel free to contact me (yesols@uidaho.edu) if you have questions about appropriate data access levels for your project.

Note:
  • Plan ahead: Plan to spend at least several hours for the registration and training step. Sometimes identity verification can take a long time. Training modules (if completing both parts) also can take awhile.
  • Computational cost: Accessing data and usage of analysis applications incur charges. However, the All of Us Program provides new users an initial credit of $300, which is more than enough for a typical student project that does not use genomic data. The initial credits expire after a year from the date of registration. If your project is not completed before the credits expire, you must set up a personal Google Billing Account in order to continue working in the Researcher Workbench.

C. JupyterLab

The Researcher Workbench provides users with pre-installed analysis tools such as JupyterLab, RStudio, and Visual Studio Code. If you are new to programming and will be attending our workshop where we will use JupyterLab with R, watch the following short videos to familiarize with the environment. (Ignore the installation part.)

  • Jupyter Notebook Basics (Watch until 11:07)
  • JupyterLab (Watch the first 9 minutes or so)

D. Readings

Working with All of Us data can be confusing at first due to the complex data structures and terminologies. Read following support articles which will help with understanding the All of Us data:

E. Hands-on Workshop

I will offer a workshop either in early spring or early summer depending on student needs. The workshop will consist of four 2-hr in-person sessions and they will not be recorded due to the sensitive nature of the All of Us data. However, workshop materials including code examples will be available on the workshop website.


Additional Resources

Official Support

Access the official All of Us User Support Hub and documentation.