Literature DB >> 33156332

DDBJ update: streamlining submission and access of human data.

Asami Fukuda1, Yuichi Kodama1, Jun Mashima1, Takatomo Fujisawa1, Osamu Ogasawara1.   

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.
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

Entities:  

Year:  2021        PMID: 33156332     DOI: 10.1093/nar/gkaa982

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  10 in total

1.  The European Nucleotide Archive in 2021.

Authors:  Carla Cummins; Alisha Ahamed; Raheela Aslam; Josephine Burgin; Rajkumar Devraj; Ossama Edbali; Dipayan Gupta; Peter W Harrison; Muhammad Haseeb; Sam Holt; Talal Ibrahim; Eugene Ivanov; Suran Jayathilaka; Vishnukumar Kadhirvelu; Simon Kay; Manish Kumar; Ankur Lathi; Rasko Leinonen; Fabio Madeira; Nandana Madhusoodanan; Milena Mansurova; Colman O'Cathail; Matt Pearce; Stéphane Pesant; Nadim Rahman; Jeena Rajan; Gabriele Rinck; Sandeep Selvakumar; Alexey Sokolov; Swati Suman; Ross Thorne; Prabhat Totoo; Senthilnathan Vijayaraja; Zahra Waheed; Ahmad Zyoud; Rodrigo Lopez; Tony Burdett; Guy Cochrane
Journal:  Nucleic Acids Res       Date:  2022-01-07       Impact factor: 16.971

2.  Database resources of the national center for biotechnology information.

Authors:  Eric W Sayers; Evan E Bolton; J Rodney Brister; Kathi Canese; Jessica Chan; Donald C Comeau; Ryan Connor; Kathryn Funk; Chris Kelly; Sunghwan Kim; Tom Madej; Aron Marchler-Bauer; Christopher Lanczycki; Stacy Lathrop; Zhiyong Lu; Francoise Thibaud-Nissen; Terence Murphy; Lon Phan; Yuri Skripchenko; Tony Tse; Jiyao Wang; Rebecca Williams; Barton W Trawick; Kim D Pruitt; Stephen T Sherry
Journal:  Nucleic Acids Res       Date:  2022-01-07       Impact factor: 19.160

3.  Data from expressed sequence tags from the organs and embryos of parthenogenetic Haemaphysalis longicornis.

Authors:  Rika Umemiya-Shirafuji; Jinlin Zhou; Min Liao; Badgar Battsetseg; Damdinsuren Boldbaatar; Takeshi Hatta; Thasaneeya Kuboki; Takeshi Sakaguchi; Huey Shy Chee; Takeharu Miyoshi; Xiaohong Huang; Naotoshi Tsuji; Xuenan Xuan; Kozo Fujisaki
Journal:  BMC Res Notes       Date:  2021-08-25

4.  ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments.

Authors:  Fayrouz Hammal; Pierre de Langen; Aurélie Bergon; Fabrice Lopez; Benoit Ballester
Journal:  Nucleic Acids Res       Date:  2022-01-07       Impact factor: 16.971

5.  InsectBase 2.0: a comprehensive gene resource for insects.

Authors:  Yang Mei; Dong Jing; Shenyang Tang; Xi Chen; Hao Chen; Haonan Duanmu; Yuyang Cong; Mengyao Chen; Xinhai Ye; Hang Zhou; Kang He; Fei Li
Journal:  Nucleic Acids Res       Date:  2022-01-07       Impact factor: 16.971

6.  RPS: a comprehensive database of RNAs involved in liquid-liquid phase separation.

Authors:  Mengni Liu; Huiqin Li; Xiaotong Luo; Jieyi Cai; Tianjian Chen; Yubin Xie; Jian Ren; Zhixiang Zuo
Journal:  Nucleic Acids Res       Date:  2022-01-07       Impact factor: 16.971

7.  DNA Data Bank of Japan (DDBJ) update report 2021.

Authors:  Toshihisa Okido; Yuichi Kodama; Jun Mashima; Takehide Kosuge; Takatomo Fujisawa; Osamu Ogasawara
Journal:  Nucleic Acids Res       Date:  2022-01-07       Impact factor: 16.971

8.  Next-generation sequencing of endoscopically obtained tissues from patients with all stages of pancreatic cancer.

Authors:  Shinichi Takano; Mitsuharu Fukasawa; Hiroko Shindo; Ei Takahashi; Yoshimitsu Fukasawa; Satoshi Kawakami; Hiroshi Hayakawa; Natsuhiko Kuratomi; Makoto Kadokura; Tatsuya Yamaguchi; Taisuke Inoue; Shinya Maekawa; Nobuyuki Enomoto
Journal:  Cancer Sci       Date:  2022-01-10       Impact factor: 6.716

9.  GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy.

Authors:  Donovan H Parks; Maria Chuvochina; Christian Rinke; Aaron J Mussig; Pierre-Alain Chaumeil; Philip Hugenholtz
Journal:  Nucleic Acids Res       Date:  2022-01-07       Impact factor: 16.971

10.  IMGT®Homo sapiens IG and TR Loci, Gene Order, CNV and Haplotypes: New Concepts as a Paradigm for Jawed Vertebrates Genome Assemblies.

Authors:  Marie-Paule Lefranc; Gérard Lefranc
Journal:  Biomolecules       Date:  2022-02-28
  10 in total

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