Improved findability of datasets in cBioPortal

The Hyve has recently developed and implemented a feature that makes it easier to find private studies in cBioPortal and to request access to those studies. This feature is helpful for internal instances of cBioPortal, where users may need to request access to studies before they can use them.

Background

cBioPortal is an open-access platform for interactive exploration of multidimensional cancer genomics data sets. It currently provides open access to data on more than 170,000 tumor samples from over 350 cancer studies. However, cBioPortal is not limited to the public website; it can be installed locally. In this case, proprietary data can be loaded, and client-specific customizations can be made.

Such internal cBioPortal installations are often paired with identity and access management tools, like Keycloak, to manage access permissions and authorizations for users, including varying levels of rights and restrictions.

The Challenge

For these internal instances of cBioPortal, users may need to request access to studies before they can actually see them. So they need to be aware that these studies exist and know how to request access. In this case, relevant studies may be missed since users can be either unaware of the existence of particular studies or the user may not be able to find them because the studies are listed outside of cBioPortal, for example, on a wiki page.

Our Solution

Our solution is to list all available studies on the front page of cBioPortal. Studies to which a user has access will be shown as usual. However, studies to which the user does not have access will be grayed out. A lock icon will be displayed next to those studies at the end of the line.

CBP_auth1
Figure 1: When a study is available in cBioPortal, but not authorized for a particular user, the study will be grayed out, and a lock icon will be shown to the right.

When a user hovers over the lock icon, a popup will appear with instructions on how to request access. These instructions can, for example, contain email addresses or links to request forms. The instructions can be configured on the portal level with placeholders for study-specific information, such as the name and email address of the person responsible for authorizing users for that particular study.

CBP_auth_2
Figure 2: When the user hovers over the lock icon, information is shown on how to request access to the locked study.

Closing remarks

The Hyve provides services to develop, extend and improve features in cBioPortal, such as the one described in this article. Implemented features are shared with the community via the cBioPortal repository on GitHub. We hope you like this new feature and that it helps many users find more studies relevant to their research in cBioPortal by showing them all studies internally available and by providing instructions on how they can access studies they do not yet have authorization for. For inquiries on cBioPortal feature development projects or other cBioPortal services, feel free to contact us.

Written by

Jessica Singh