Newswise — The National Institutes of Health (NIH) Common Fund sponsors many big programs, including the 4D Nucleome, which studies the three-dimensional organization of the nucleus in space and time (the 4th dimension), and HubMAP, which is working on a 3D map or human atlas, at the cellular level. Currently, all the projects are independent and each one has a data coordinating center (DCC).
The Common Fund Data Ecosystem (CFDE) was established to provide the infrastructure needed to help solve key challenges facing DCCs. The CFDE portal, which is now live and open for data submissions, links multiple data platforms that have been established through Common Fund programs. By connecting the data and making them more accessible, the CFDE is intended to enable novel scientific research that was not possible before, including hypothesis generation, discovery, and validation. Currently the eleven participating DCCs manage over 900 projects, containing information on more than 425,000 bio samples collected from over 6,600 human and non-human subjects.
Globus services have been integrated into the portal to simplify and automate many of the portal’s data management processes. Submissions are initiated by DCC personnel who have locally installed the cfde-submit CLI tool developed by the University of Chicago. That tool in turn uses Globus Flows to process the submissions and deliver them to the DERIVA-based CFDE Portal. CFDE's flow uses a Globus Connect Server-hosted collection and either Globus Connect Personal (GCP) or HTTPS upload to get the data off the submitter's local system and into the CFDE AWS-hosted system for subsequent processing and loading into DERIVA's database tables for review & approval. Access control for the flow, the Globus Connect Server (GCS) collection, and for DCC permissions in the CFDE Portal are managed using Globus Groups. Each submission is a complete inventory of a DCC's data holdings, including a complete file listing and research-relevant metadata.
The CFDE multi-institutional team is led by the University of Maryland, and includes the University of Chicago, University of Southern California Information Sciences Institute, University of California-Davis, RTI International, University of Oxford, and the Icahn School of Medicine at Mount Sinai.
The CFDE Portal--currently includes submissions from seven DCCs. and is available at https://app.nih-cfde.org/
* Contact us to get early access to the Globus Flows service.
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