About DDBJ Center
(May 2-May 6) Correspondence during the Golden Week holidays
INSDC Minimal Specifications
Bioinformation and DDBJ Center (BI-DDBJ) collects nucleotide sequence data as a member of
INSDC(International Nucleotide Sequence Database Collaboration)
and provides freely available nucleotide sequence data and supercomputer system, to support research　activities in life science.
Mission
It is generally accepted that research in biology today requires both
computer and experimental equipment equally well. Information achieved
from enormous exhaustive data have greatly contributed to the paradigm
shift in biology. Biology or life sciences are no longer restricted to
wet-bench experiments. In silico and in vitro / in vivo analyses
together will push back the frontiers of life sciences. In particular,
researchers in life science must rely on computers to analyze nucleotide
sequence data accumulating at a remarkably rapid rate. Actually, this
triggered the birth and development of information biology. BI-DDBJ
is to play a major role in carrying out research in information biology
and to run DDBJ operation in the world.
The principal purpose of BI-DDBJ operations is to improve the quality of
INSD, as public domains. When researchers make their data open to the
public through INSD and
commonly shared in world wide
we at BI-DDBJ make efforts to describe information on the data as rich as possible,
according to the unified rules of INSD, preferably without any stress by using DDBJ.
Nucleotide sequence records organismic evolution more directly than
other biological materials and thus is invaluable not only for research
in life sciences but also human welfare in general. The database is, so
to speak, a common treasure of human beings. With this in mind, we make
the database online accessible to anyone in the world.
Governing Structure
Currently, BI-DDBJ is in operation at
Research Organization of Information and System National Institute of Genetics (NIG)
in Mishima, Japan with endorsement of
MEXT; Japanese Ministry of Education, Culture, Sports, Science and Technology
BI-DDBJ is reviewed and advised by its own advisory board,
DNA Database Advisory Committee (an outside committee of NIG).
A list of current staff of DDBJ.
Major Activities
Construction and Operation of INSDC
In Japan, BI-DDBJ internationally contributes as a member of
INSDC
to collect and to provide nucleotide sequence data.
BI-DDBJ is officially certified to collect nucleotide sequences from researchers and to issue
the internationally recognized accession number
to data submitters.
The accession number issued for each sequence data is unique on the database and internationally
recognized to guarantee the submitter the property of the submitted and
published data. Since BI-DDBJ exchanges the released data with
ENA/EBI and NCBI on a daily basis, the three data centers share
virtually the same data at any given time.
The virtually unified database is called INSD: International Nucleotide Sequence Database.
DDBJ collects sequence data mainly from Japanese researchers, but of
course accepts data and issue the accession numbers to researchers in
any other countries. 99% of INSD data from Japanese researchers are submitted through DDBJ.
Providing nucleotide and amino acid sequence data related to patent applications
INSD
contains nucleotide sequence data related to
patent applications collected by Patent Offices in Japan, Korea, Europe and USA.
BI-DDBJ also provides amino acid sequence data related to patent
applications collected by patent offices in Japan and Korea.
See following links in detail.
Refer to:
Sequence data included in patent applications
Patent, Intellectual Property and Priority
Patent column from DDBJ
Management and operation of the National Institute of Genetics Supercomputer System
The National Institute of Genetics Supercomputer
System
(NIG Supercomputer) is a
large-scale computer utilization site with genome analysis as its
primary focus. The system provides Supercomputing System Services
comprising leading-edge, large-scale cluster-type computers, large-scale
memory-sharing computers, and high-capacity, high-speed disk devices.
Providing services to search and to analyze biological data
Biological database management: tools for depositing and retrieving
We provide databases maintained by BI-DDBJ and others through
web services
or on NIG Supercomputer.
You can collectively download databases from
our FTP site
Providing software tools for analyzing biological
We provide software tools for data analyses developed by BI-DDBJ and others
through
web services
or on NIG Supercomputer.
Training course and publication
BI-DDBJ holds a training course for bioinformatics,
DDBJing
(in Japanese), to teach how to submit
nucleotide sequence data and how to use our services for analyzing life science data.
We announce
the latest information for DDBJ activities
See also
our publications
1980
EMBL data library was organized, and asked international cooperation for nucleotide sequence data bank to Japan.
1982
EMBL and GenBank started international cooperation, and invited Japan to participate their data bank.
1983
Aimed at contribution for international data bank to collect, to evaluate and to provide nucleotide sequence data, trial data loading was started.
1984
NIG; the National Institute of Genetics was reorganized as an Inter-University Research Institute.
DDBJ began to work at NIG.
1986
DNA Database Advisory Committee organized.
1987
DDBJ release 1 was provided.
By this release, we regard this year as official start of DDBJ operation.
1995.04
To operate DDBJ more efficiently, CIB; the Center for Information Biology was established in NIG.
2001.04
CIB was reorganized as CIB-DDBJ; the Center for Information Biology and DNA Data Bank of Japan
2004.04
NIG was reorganized as a member of
ROIS; Research Organization of Information and Systems
. DDBJ has also belonged to ROIS.
2005.05
DDBJ, EMBL-Bank and GenBank agreed to call their collaboration INSDC; International Nucleotide Sequence Database Collaboration; and to call the unified nucleotide sequence database INSD; the International Nucleotide Sequence Database.
2007.04
DBCLS; Database Center for Life Science
was newly founded in ROIS
2009
DDBJ faculty staff have greatly been reshuffled. DDBJ collaborates with DBCLS more closely.
INSDC added a collaborative meeting to deal with huge sequence data produced by the next generation sequencers (Sequence Read Archive)and traces produced by traditional sequencers (Trace Archive).
2012.04
DDBJ, expanding its DNA databank activities, was restructud as one of the Intellectual Infrastructure Project Centers of NIG, being separated from CIB.
2013.10
Collaborating with
NBDC; National Bioscience Database Center
, DJ Center started to operate the archive for all types of individual-level genetic and de-identified phenotypic data from human subjects,
JGA
; Japanese Genotype-phenotype Archive.
2019.01
According to the reorganization of National Institute of Genetics, the center name is changed from “DDBJ Center” to “Bioinformation and DDBJ Center”.
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