Updates to the Kids First Data Resource Portal - April 2019-title-h1
Updates to the Kids First Data Resource Portal - April 2019
Updates to the Kids First Data Research Portal – April 2019
Since the start of the new year, the NIH Common Fund-supported Gabriella Miller Kids First Data Resource Center (Kids First DRC) has continued its steady growth, as three new datasets have become accessible through the Kids First DRC's Data Resource Portal over the last several months.
Along with these new datasets, additional data were added to the Congenital Heart Defects dataset, led by Kids First X01 Principal Investigator (PI) Christine Seidman, MD of Harvard University Medical School, on behalf of the Pediatric Cardiac Genomics Consortium, and the Orofacial Cleft: European Ancestry dataset, led by Kids First X01 PI Mary Marazita, PhD of The University of Pittsburgh School of Dental Medicine.
Added Kids First X01 Datasets & Integration with TARGET Data
On March 26, 2019, the Data Resource Portal released a new dataset on Disorders of Sex Development, related to a study from Kids First X01 PI Eric Vilain, MD, PhD of the University of California, Los Angeles. The dataset contains aligned reads and gVCF data from 300 study participants and 94 families.
On March 29, 2019, the Kids First DRC launched a initial integration with the NCI Framework Services spanning both the Portal and Cavatica. Two sub-studies of NCI TARGET(Therapeutically Applicable Research to Generate Effective Treatments) were selected to pilot this integration were TARGET: Acute Myeloid Leukemia (AML) and TARGET: Neuroblastoma (NBL). These studies were chosen as they scientifically complement data being generated as part of the Kids First X01 projects Genetic Basis of Neuroblastoma Initiation and Progression and Germline and Somatic Variants in Myeloid Malignancies in Children.
Data from TARGET is made available by the NCI's Genomic Data Commons (GDC), part of the National Cancer Institute's Cancer Research Data Commons (NCI CRDC), and the technical integration with Kids First DRC is made possible by the NCI CRDC Framework Services. With the integration of these two NCI TARGET datasets, Portal users will be able to search across both Kids First data and TARGET data, side-by-side, and migrate the data to a common workspace in Cavatica for further analysis. To fully utilize the TARGET data, users must have appropriate access via dbGaP to controlled access data of interest and enable the integration on both the Portal and Cavatica.
New Kids First Data Resource Portal Features
The Kids First DRC is also pleased to share new features added to the Data Resource Portal over the past several months.
Launched in Beta in conjunction with the 2019 Annual Meeting of the American Association for Cancer Research, the Kids First DRC unveiled our new Explore Data area, which allows Data Resource Portal users to create virtual cohorts with basic and advanced filtering across all Kids First datasets. Users can now create multiple queries in an easy-to-use visual interface that incorporates a variety of elements including study information, demographics, clinical data, biospecimens, and various file format types. This new feature keeps a running query history in a user's dashboard and allows users to combine queries to perform set-like operations on queried results. As this feature develops further and moves out of Beta phase, additional functionality including Survival Plots and added search criteria will be incorporated.
During the Beta phase, the Portal's Explore Data feature is a work in progress, and we encourage everyone to help us identify and squash some bugs! If you encounter any issues, such as difficulties in creating queries, or would otherwise like to provide input, you can email us at any time at firstname.lastname@example.org. We are also planning to roll out a new widget which will allow you to provide feedback directly in the Portal. All feedback is welcome!
Additional functional improvements to the Data Resource Portal include new File Entity pages, which provide registered users with detailed views of specific genomic files so that they can explore file properties in a more in-depth manner over the Portal's file browser. Genomic File IDs (represented as GF_####) are now clickable, bringing users to the File Entity page for that file.
Within the File Entity page, users will find:
- Name of the file
- Associated Study (with a hyperlink to the Kids First DRC study release notes)
- Reference Genome
- Harmonized Data
- Experimental Strategy
- Associated Participants and Biospecimens, and information about them
- Whether or not they currently have access to the data
Please visit our page https://kidsfirstdrc.org/portal/portal-features/ to learn more about the Data Resource Portal and its features, and how to access data for your research.