3 posts tagged with "Blog posts"

Step-by-step instructions to log into and set up DUOS to access controlled data for analysis in a Terra workspace.

AnVIL users: dbGaP authorization is still applicable to access AnVIL datasetsYou do not have to use DUOS to access controlled data. To enable dbGaP access, link your NIH account in Terra (enables access to controlled data granted by dbGaP in both Terra and the AnVIL Data Explorer). For step-by-step instructions, see Access controlled-data by linking your NIH account in Terra.

Step 1: Request access on DUOS​

1.1. Go to duos.org and click sign-up/sign in using MSFT or Google SSO. Use the same login you use for app.terra.bio. 

1.2. Accept the Terms of service.

1.3. In the Researcher Console, select Your Profile under your name (top right).

1.4. Once you land on the profile page, add your full name and select your institution from the dropdown (start to fill in the name). 

1.5. Link your eRA Commons ID. This will allow you to request access to controlled data.

You’ll be taken to the external NIH page to sign into your eRA Commons account.

1.6. Invite your signing official to duos.org to register and give you a library card. See How to pre-authorize researchers to submit Data Access Requests (DARs) in DUOS for instructions.

1.7. Once you receive a Library Card, login to the DUOS Researcher Console. You should see your library card in the Profile page.

1.8. Go to the Data Library (https://duos.org/datalibrary) and filter/search for the dataset you’re looking for. Note that the example dataset in this doc is GTEx, but the instructions are not specific to that dataset.  

1.9. Select the dataset of interest (circled in screenshot) and click apply for access at the bottom right.

1.10. Fill out your data access request form, with as much detail as possible.

1.11. Make sure to attest to all terms in the library card agreements (screenshot below) by clicking the blue Attest button.

1.12. Submit your DAR by clicking the blue Submit button (bottom left) beneath the addendum summarizing the requested datasets grouped by data use terms.

What to expect​

It will take a few days to a few weeks for your DAR to be approved. You will get a notification in your email when you have access to the dataset.

Step 2: Export snapshot to Terra from the DUOS Library​

2.1. Once your DAR is approved, return to the DUOS Data Library, where you should now see a blue Export link in the View by Dataset tab under Export to Terra (right column) .

2.2. Clicking the button should allow you to export to an existing Terra workspace or to create a new one.

2.3. Note that if you’re accessing controlled data, DUOS will automatically enable additional security on your new or existing workspace. 

What to expect​

DUOS will import the data snapshot to a new or existing workspace.

It will take a few minutes to export the snapshot. You’ll get a green popup (upper right) when data is in your workspace.

Once you refresh your page, you’ll see the data tables containing all the snapshot data and metadata in the Data tab of your workspace. Note the security shield at the top right indicating additional security monitoring.

Sofia Labrecque and Jonathan Lawson
The Broad Institute of MIT and Harvard

NIH Repositories: A Landscape Analysis​

See the full article here: https://papers.ssrn.com/sol3/papers.cfm?abstract_id=5374625

Workshop Reference Graphs​

Total Number of Repositories by Access type
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Total Number of Repositories by Data type

The NIH-Sponsored Repository list will be valuable to principal investigators (PIs)​

1. Those who are looking for secondary data to use for their research.
2. Those who need to identify a repository to submit data to, potentially as a part of their Data Management and Sharing (DMS) plan.

Additional Notes

• The preprint SSRN paper (QR code on reverse) provides an overview of the NIH-sponsored repositories available and can serve as a good starting point in the search for a repository to submit to or to access data for secondary research.
• When submitting data to a repository as part of NIH requirements, identify a repository and contact them early in the grant lifecycle, as you may need to vet multiple repositories and ensure schema alignment with the final chosen repository, and more.

NIH-Supported Scientific Repositories:

https://www.grants.nih.gov/new-to-nih/information-for/researchers/resources-for-research

We’re excited to announce a new SSRN publication co-authored by Bronwyn Walsh, Jonathan Lawson, Sofia Labrecque, and Vasiliki Rahimzadeh, “Where Is All the NIH Data? A Landscape Analysis of the 150 NIH Repositories and the Path Beyond the Mountains.”

This comprehensive study maps out the current NIH-supported data repository ecosystem—spanning roughly 150 domain‑specific and generalist repositories—and evaluates gaps and usability. It provides critical insights into how NIH data is organized, discoverable, and maintained across different platforms, while identifying challenges around access, metadata standardization, and sustainability.

The paper concludes with a forward-looking “path beyond the mountains,” recommending strategic improvements such as enhancing metadata harmonization, strengthening repository integration, and leveraging FAIR and GA4GH standardsto bolster discoverability and ease of datasharing and use across NIH-funded datasets .