Cancer researchers can now store and share data on a free, public-access repository
For Kedar Narayan, a little-known research tool is helping him meet a critical need in his work at the Frederick National Laboratory for Cancer Research.
Narayan is a senior scientist and group lead at the Center for Molecular Microscopy. He investigates urgent problems in cancer biology by using emerging technologies to obtain high-resolution images of tissues and cells. He wants the broader cancer research community to access his work, but traditional repositories are not suited for his data type, limiting his ability to share it.
Enter the Center for Strategic Scientific Initiatives Data Coordinating Center Portal.
The CSSI DCC Portal offers researchers a public-access platform for storing and displaying biomedical data. Anyone can view and download the stored data at no cost, although researchers who wish to upload their data must register for a free account and receive approval from the DCC steering committee. The resource was built and is maintained by the Frederick National Laboratory.
The portal’s mission is to make data available to the greater scientific community. It provides a widely accessible and continuously maintained place to store disparate data that do not conform to more rigid genomics and proteomics repositories.
Creating and launching the CSSI DCC Portal was a team effort among the FNL’s Strategic Pilots Incubator, Advanced Biomedical Computational Science group, and a handful of subject-matter experts. The team built the portal with scientific publishers’ needs in mind— public-access data, scientific transparency, and reproducibility. An increasing number of journals, even those that require a paid subscription, now require researchers to submit their data in the flexible Investigation-Study-Assay (ISA) format and deposit it in a publicly available repository. The portal satisfies both requirements.
“We decided to undertake this project because we felt that the Frederick National Laboratory had the capability and resources to be able to provide this type of durable data repository for public access,” explained Corinne Zeitler, Ph.D., a member of the project team.
Because the portal uses the ISA hierarchical data framework, users can upload a variety of data and file types, such as atomic force microscopy and FIB-SEM (focused ion beam scanning electron microscopy). Uploaders can also link their data files to files in other repositories, making the portal a centralized home for studies that leverage other published data sets or data that are required to be stored in other repositories. This approach gives users the advantage of referencing other shared data sets without duplication.
Narayan said the portal’s team has worked with him to develop meaningful relationships and conventions for the FIB-SEM data that his lab uploads. That has expanded the portal’s functionality and made it easier for him to deposit data later. The portal also lets him give the scientific community access to more data than what his lab publishes in their manuscripts.
If needed, uploaders can obtain a grace period to temporarily protect their data from public release and control its access by other registered users. This feature enables collaborative research among certain users and facilitates the peer review process for embargoed manuscripts with raw data that reviewers need to evaluate but that cannot be shared until publication.
The project team hopes to expand the portal’s functionality in 2019 by adding tools to help users arrange their files in ISA format and modify existing ISA files to match their current needs.
The CSSI DCC Portal is funded by the National Cancer Institute’s Center for Strategic Scientific Initiatives.