Introduction of DDBJ
What is DDBJ?
DNA Data Bank of Japan (DDBJ) is the sole nucleotide sequence data bank in Asia, which is officially certified to collect nucleotide sequences from researchers and to issue the internationally recognized accession number to data submitters. Since we exchange the collected data with EMBL-Bank/EBI (European Bioinformatics Institute) and GenBank/NCBI (National Center for Biotechnology Information) on a daily basis, the three data banks share virtually the same data at any given time. The virtually unified database is called "the International Nucleotide Sequence Database (INSD)". DDBJ collects sequence data mainly from Japanese researchers, but of course accepts data and issue the accession number to researchers in any other countries.
DDBJ is organized by the Center for Information Biology and DNA Data Bank of Japan (CIB-DDBJ) of the National Institute of Genetics (NIG) with endorsement of The Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT). 99% of INSD data from Japanese researchers are submitted through DDBJ.
The principal purpose of 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 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.
In detail, following items about DDBJ are briefly explained.
- International Collaboration Framework of Nucleotide Sequence Database Construction
- Governing Structure of DDBJ
- Major Activities of DDBJ
- Governing Structure of DDBJ
International Collaboration Framework of Nucleotide Sequence Database Construction
From the beginning, DDBJ has been functioning as one of the international nucleotide sequence databases, including EMBL-Bank/EBI in Europe and GenBank/NCBI in the USA as the two other members.
DDBJ/EMBL-Bank/GenBank collects the nucleotide sequence data experimentally determined, and constructs the database in accordance with the rule agreed with the three databanks (i.e. (Feature Table: Definition and agrrements in International Collaborative Meeting).
The database is a collection of "entry" which is the unit of the data. Each entry includes nucleotide sequence and the information of submitters, references, source organisms, and the biological nature such as gene function and other property of the sequence, etc.
The database also includes the data from Japan Patent Office (JPO), European Patent Office (EPO), United States Patent and Trademark Office (USPTO), and Korean Intellectual Property Office (KIPO).
Nucleotide sequence records organismic evolution more directly than other biological meterials 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 databaase online accesible to anyone in the world.
Consequently, we have been collaborating with the two data banks through exchanging data and information on internet and by regularly holding two meetings, the International Advisory Committee and the International Collaborative Meeting. The operations of DDBJ/EMBL-Bank/GenBank and ICM subscribe to advice from IAC.
International Advisory Committee (IAC)
International Advisory Committee consists of nine members, each of 3 members selected from Europe, US, or Japan. The committee meeting to advice in fairness to maintenance and future plan of INSDC is held once a year.
International Collaborative Meeting (ICM)
International Collaborative Meeting consists of working-level participants of INSDC and its fundamental principle is international collaboration. The meeting to discuss practical matters to maintain and update INSDC is held once a year.
International Nucleotide Sequence Database Collaboration (INSDC)
In 2005, DDBJ, EMBL-Bank and GenBank agreed to call their collaboration "International Nucleotide Sequence Database Collaboration (INSDC)"; and to call the unified nucleotide sequence database "the International Nucleotide Sequence Database (INSD)". The agreement was approved by IAC in May 2005.
In 2009, INSDC added a coraborative meeting to deal with mass sequence data produced by the "next" generation sequencers (Short Read Archive) and traces produced by traditional sequencers (Trace Archive).
- Short Read Archive
- DRA; DDBJ Read Archive
- ERA; European Read Archive (EBI)
- Short Read Archive (NCBI)
- ERA; European Read Archive (EBI)
A schematic view of INSDC is shown below.
Governing Structure of DDBJ
DDBJ is in operation at the Center for Information Biology and DNA Data Bank of Japan, the National Institute of Genetics in Mishima, Japan.
DDBJ began data bank activities in earnest in 1986 at NIG with the endorsement of the Ministry of Education, Science, Sport and Culture. To operate DDBJ more efficiently, the Center for Information Biology (CIB) was established in NIG in 1995.
CIB was reorganized as the Center for Information Biology and DNA Data Bank of Japan (CIB-DDBJ) in 2001. CIB-DDBJ is to play a major role in carrying out research in information biology and to run DDBJ operation in the world. It is generally accepted that research in biology today requires both computer and experimental equipment equally well. In particular, we 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.
In April 2004, NIG was reorganised as a member of The Research Organization of Information and Systems (ROIS). DDBJ has also belonged to ROIS.
The Database Center for Life Science (DBCLS) was newly founded in ROIS in April 2007.
In 2009, DDBJ faculty staff have greatly been reshuffled. DDBJ collaborates with DBCLS more closely.
Major Activities of DDBJ
- 1. One of the members of INSDC
- 2. Bioinformatics databases management
- 3. Developing software tools for analyzing biological data
- 4. Holding a course to teach begineners: How to analyze biological data
1. One of the members of INSDC
DDBJ is officially certified to collect nucleotide sequences from researchers and to issue the internationally recognized accession number to data submitters. Since DDBJ exchanges the collected data with EMBL-Bank and GenBank on a daily basis, the three data banks share virtually the same data at any given time.
See following links in detail.
Nucleotide Sequence Submission
Current Scheme of the Sequence Data Transition
Collective Download from FTP site
Search and Analysis of sequence data
2. Bioinformatics databases management: tools for depositing and retrieving
Our databases and sequence retrival tools have greatly contributed to the paradigm shift in biology. Biology or life sciences are no longer restricted to wet-bentch experiments. In silico and in vitro / in vivo analyses together will push back the frontiers of life sciences.
See following links in detail about databases provided and maintained by at DDBJ and others.
All-round Retrieval of Sequence and Annotation (ARSA)
Search and Analysis
collective download from FTP site
Link to DDBJ/CIB web pages on Information Biology
3. Developing software tools for analyzing biological data
We also provide many tools for data analyses developed by at DDBJ and others.
See following links in detail.
Web API for Biology (WABI)
Search and Analysis
4. Holding a course to teach begineners: How to analyze biological data
DDBJ holds a course Bioinformatics Training Course, to teach how to analyze biological data.
- DNA Data Bank of Japan (DDBJ)
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Postal Address:
Center for Information Biology and DNA Data Bank of Japan
National Institute of Genetics
1111 Yata, Mishima, 411-8540, Japan
Fax: +81-55-981-6849
