DDBJ update: streamlining submission and access of human data

Abstract

The Bioinformation and DDBJ Center (DDBJ Center, https://www.ddbj.nig.ac.jp) provides databases that capture, preserve and disseminate diverse biological data to support research in the life sciences. This center collects nucleotide sequences with annotations, raw sequencing data, and alignment information from high-throughput sequencing platforms, and study and sample information, in collaboration with the National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI). This collaborative framework is known as the International Nucleotide Sequence Database Collaboration (INSDC). In collaboration with the National Bioscience Database Center (NBDC), the DDBJ Center also provides a controlled-access database, the Japanese Genotype-phenotype Archive (JGA), which archives and distributes human genotype and phenotype data, requiring authorized access. The NBDC formulates guidelines and policies for sharing human data and reviews data submission and use applications. To streamline all of the processes at NBDC and JGA, we have integrated the two systems by introducing a unified login platform with a group structure in September 2020. In addition to the public databases, the DDBJ Center provides a computer resource, the NIG supercomputer, for domestic researchers to analyze large-scale genomic data. This report describes updates to the services of the DDBJ Center, focusing on the NBDC and JGA system enhancements.

Figure 1.

The processes of data submission and data use at NBDC and JGA. For data submission, users submit applications to NBDC. After the applications have been approved by the DAC of NBDC, users can upload data to JGA. For data use, users submit applications to NBDC. After the applications have been approved by the DAC of NBDC, users can download data from JGA. Users can carry out all processes in the common login platform.

Figure 2.

The groups of data submitters and users. (A) The application to NBDC and data submission to JGA are managed by the data submitter group. Similarly, the application to NBDC and data download from JGA are managed by the data user group. The principal investigator (PI) and researchers are able to manage the data without sharing their accounts. The PI can manage data from multiple projects by creating groups with different project members (for example, one with the researcher A and the other with the researcher B). (B) The researchers A and B can access only the data associated as group members, while the PI can access all the data.