All of Us Researcher Workbench

Researchers invited to give feedback on initial dataset & tools

In partnership with its participants, the All of Us Research Program is working to build one of the world’s largest and most diverse datasets to advance precision medicine research. UW-Madison, with UW Health, has been continuously engaged in AoU recruitment and enrollment in Madison and Milwaukee since 2017. Now, the program has opened its research platform, the All of Us Researcher Workbench, for beta testing. Once approved, researchers can begin using the initial dataset and tools in studies and report on what’s working and what can be improved. This moment is an important step in the program’s effort to accelerate new discoveries.

Bioinformatics and health services researchers will likely find the most value in the initial dataset, particularly for studies that evaluate the frequency of certain diseases or conditions. Research with a focus on health disparities and underrepresented populations will find the current dataset useful, given its size and diversity. This early version of the Researcher Workbench includes data generously shared with us from over 270,000 participants, over 80% of whom are from communities that are historically underrepresented in research, and more than 50% are of diverse races and ethnicities.

All of Us is committed to serving researchers of all kinds, and workshops and user studies are planned to gather more input from additional research communities, including citizen and community scientists and researchers in the private sector. Currently, researchers with NIH eRA Commons accounts may apply for access.  UW Madison has completed the signed data use agreement with the program.

All of Us also adopted a “data passport” model to make the data broadly accessible. After researchers register with the program, agree to the rules, and complete the training on the responsible conduct of research, they will be granted permission to explore All of Us data for a wide range of studies, rather than determining access for all studies on a project-by-project basis. Ultimately, All of Us is expected to support thousands of studies on many different aspects of health and disease, leading to more individualized treatments and prevention strategies in the future.

We extend a warm welcome to researchers interested in exploring the Researcher Workbench.  We want to design this platform with you, to make it the best resource it can be. Your comments and suggestions are central to that effort. Thank you in advance for being generous with feedback so we can improve.

– Dr. Josh Denny, CEO, All of Us Research Program

Features and Limitations of the Beta Platform

Researchers will find information from electronic health records (leveraging the OMOP Common Data Model); six initial surveys covering demographics, lifestyle factors, and overall health; and baseline physical measurements taken by program staff.

The platform uses a Jupyter Notebook environment to power in-depth analyses, with tools to help researchers set up collaborative workspaces and build customized cohorts. At this time, researchers (or their team members) will need experience with R or Python programming languages to conduct analyses on the platform. All of Us does not yet support integrations with other statistical programs or software, but the program is working to expand analysis tools for future iterations of the Researcher Workbench.

The platform will grow more robust over time with additional data and tools, including genomics, wearable device data, and linkages to other datasets. Regular releases of new data are planned.

The current version of the platform has some key limitations. Because participants take part in the program at different paces and enrollment is still active, variables don’t exist for all participants; in particular, survey completion rates vary, and the collection and harmonization of electronic health record data remain a work in progress. Some preliminary testing occurred on the biological plausibility of the data; other curation efforts are still underway.

In addition, some of the data are blurred to protect participant privacy. While names and other identifiers are stripped out from participant data at the outset, additional adjustments have been made in the curation process. These include shifting dates and hiding or grouping the records of small clusters of participants to further reduce the risks of reidentification. These modifications may pose challenges for epidemiological studies or research on specific subcategories of people.

As another privacy measure, researchers are required to analyze data within the secure cloud-based All of Us platform. Researchers may never download individual-level program data on local computers.

As with any beta testing period, there will be technical bugs, and the program will work through them. All of Us relies on researchers’ feedback to help identify usability issues, improve the data and tools, and plan future enhancements.

Researcher Access

Currently, researchers with NIH eRA Commons accounts may apply for access if their institutions have signed a data use agreement with the program. Right now, any U.S.-based academic, nonprofit, or health care organization can enter into an All of Us data use agreement.

Bioinformatics and health services researchers will likely find the most value in the initial dataset, particularly for studies that evaluate the frequency of certain diseases or conditions. Researchers with a focus on health disparities and underrepresented populations will also find the current dataset useful, given its size and diversity.

After this initial beta phase, other means of identity verification will be added beyond eRA Commons and open the platform more broadly. All of Us is committed to serving researchers of all kinds, and workshops and user studies are planned to gather more input from additional research communities, including citizen and community scientists and researchers in the private sector.

Learn More

If you’d like to learn more about the Researcher Workbench, please visit ResearchAllofUs.org. There you’ll get full details about the initial dataset and tools, along with more information about the data access process. You can also sign up for our Research Hub newsletter to receive regular emails on the Workbench and other news from the All of Us Data and Research Center.

Thanks for your support and stay tuned for more updates ahead!