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Abstract
The DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) has been providing public data services for thirty years (since 1987). We are collecting nucleotide sequence data from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org), in collaboration with the US National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EBI). The DDBJ Center also services Japanese Genotype-phenotype Archive (JGA), with the National Bioscience Database Center to collect human-subjected data from Japanese researchers. Here, we report our database activities for INSDC and JGA over the past year, and introduce retrieval and analytical services running on our supercomputer system and their recent modifications. Furthermore, with the Database Center for Life Science, the DDBJ Center improves semantic web technologies to integrate and to share biological data, for providing the RDF version of the sequence data.
Highlights
The DNA Data Bank of Japan (DDBJ, http://www.ddbj. nig.ac.jp) [1] is a public database of nucleotide sequences established at the National Institute of Genetics (NIG)
Since 1987, the DDBJ has been collecting annotated nucleotide sequences as its traditional database service. This endeavor has been conducted in collaboration with GenBank [2] at the National Center for Biotechnology Information (NCBI) and with European Nucleotide Archive (ENA) [3] at the European Bioinformatics Institute (EBI)
Within the INSDC framework, the DDBJ Center services the DDBJ Sequence Read Archive (DRA), BioProject for sequencing project metadata and BioSample for sample information to facilitate the acceptance of largescale data generated from next-generation sequencing platforms [5,6,7]
Summary
The DDBJ Center services the Japanese Genotype-phenotype Archive Our web services, including submission systems, data retrieval systems, Web API, DDBJ Read Annotation Pipeline, and backend databases are performed on the NIG supercomputer system. D26 Nucleic Acids Research, 2017, Vol 45, Database issue scribed here are available from http://www.ddbj.nig.ac.jp and most of the archival data can be downloaded at ftp: //ftp.ddbj.nig.ac.jp.
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