Data Download

Last updated: a year ago (view history), Time to read: 4 mins

New Feature

Visualization Community has collaborated with ProteinPaint to implement a new feature. A clinical data set from the Childhood Cancer Survivor Study and St. Jude Life Data Access Units have made a download feature available within the Cancer Survivorship Community.

In order to gain access, you must 1) have an approved Data Access Agreement (DAA) from both CCSS and SJLIFE Data Access Units (DAU) and 2) be signed in to Visualization Community.

SJLIFE and CCSS DAA approval

tip
  • You can read more about the Childhood Cancer Survivor Study which consists of germline-only whole genome sequencing samples of childhood cancer survivors. The following data set is included within CCSS.
  • You can read more about St. Jude Life which contains germline-only whole genome and whole exome sequencing data focused on studying the long-term adverse outcomes associated with cancer and cancer-related therapy. The following data set is included within SJLIFE.

First, navigate here to St. Jude Cloud’s Genomics Platform which is already pre-selected for both CCSS and SJLIFE data sets. If you want to custom select then you must go to Studies and manually select your data sets.

Next, click Log In (at the bottom) and sign in using the St. Jude SSO option. You must use the St. Jude Auth0 to sign on in order for the permissions to be accepted. If you are a SJ employee, you can use the first option, otherwise you can use the alternative GitHub, Gmail, or email options.

To read more about Genomics Platform go here, to learn more about creating a DNAnexus account or setting up billing go here.

Then, you must complete the DAA. To read more about making a DAA request go here, or if you have any questions about filling out the DAA, please read more here.

tip

On page 10 of the DAA, you must address in the Contemplated Use section that you are interested in accessing the portal data. An example would be: I am a researcher in the Yu Lab at Brown University and we are studying factors for modifying cardiovascular system late effects in pediatric cancer survivors with cardiac toxic cancer treatments. I need access to the SJLIFE/CCSS cohort with this information (treatment and late effects), as well as demographics, lifestyle exposure, and genetic factors.

warning

Your DAA must be approved before you have access to the download feature. You will be notified via email if/when the committee approves the request. This process typically takes less than 2 weeks.

Accessing the portal

First, sign in to VisCom. If you need help creating an account or signing in please follow these guidelines.

Once you are signed in, you will navigate to the Cancer Survivorship Community. Here, is where you can begin to explore the Clinical Browser .

Next, you will want to click Charts.

Now you can access the data download button to begin selecting the terms for downloading.

tip

If you are not signed in, you will be prompted to sign-in to VisCom.

warning

If you get a Requires Sign-in error after you have signed in already, please clear your cache to clear out your stale credentials and sessions.