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DNA Data Bank of Japan

Abbreviation:DDBJ

Recommended

General Information

An annotated collection of all publicly available nucleotide and protein sequences. DDBJ collects sequence data mainly from Japanese researchers, as well as researchers in other countries. DDBJ is part of the International Nucleotide Sequence Database Collaboration (INSDC), which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at the NCBI. These three organizations exchange data on a daily basis.

Homepage https://www.ddbj.nig.ac.jp/ddbj

Countries that developed this resource European Union , Japan , United States

Created in 1987

Taxonomic range

All

Knowledge Domains

Subjects

In the following recommendations:

How to cite this record FAIRsharing.org: DDBJ; DNA Data Bank of Japan; DOI: https://doi.org/10.25504/FAIRsharing.k337f0; Last edited: May 19, 2021, 3:07 p.m.; Last accessed: Jan 27 2022 8:39 a.m.

This record is maintained by Bioinformation and DDBJ Center (ddbjcommon)

Record updated: May 19, 2021, 3:07 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.k337f0' by 'The FAIRsharing Team' at 15:07, 19 May 2021 (not approved):

	'miriam_id' has been modified:
		Before: 
		After: None

	'description' has been modified:
		Before: An annotated collection of all publicly available nucleotide and protein sequences. DDBJ collects sequence data mainly from Japanese researchers, as well as researchers in any other countries. DDBJ is part of the International Nucleotide Sequence Database Collaboration (INSDC), which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at the NCBI. These three organizations exchange data on a daily basis. 
		After: An annotated collection of all publicly available nucleotide and protein sequences. DDBJ collects sequence data mainly from Japanese researchers, as well as researchers in other countries. DDBJ is part of the International Nucleotide Sequence Database Collaboration (INSDC), which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at the NCBI. These three organizations exchange data on a daily basis.

Edits to 'https://fairsharing.org/FAIRsharing.k337f0' by 'The FAIRsharing Team' at 09:48, 23 Feb 2021 (approved):

	'description' has been modified:
		Before: Annotated collection of all publicly available nucleotide and protein sequences. DDBJ collects sequence data mainly from Japanese researchers, as well as researchers in any other countries. DDBJ is part of the International Nucleotide Sequence Database Collaboration (INSDC), which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at the NCBI. These three organizations exchange data on a daily basis. 
		After: An annotated collection of all publicly available nucleotide and protein sequences. DDBJ collects sequence data mainly from Japanese researchers, as well as researchers in any other countries. DDBJ is part of the International Nucleotide Sequence Database Collaboration (INSDC), which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at the NCBI. These three organizations exchange data on a daily basis.

Edits to 'https://fairsharing.org/FAIRsharing.k337f0' by 'The FAIRsharing Team' at 11:44, 05 Feb 2020 (approved):

	'supportLinks' has been modified:
		Before:
			FAQ|https://www.ddbj.nig.ac.jp/faq/en/index-e.html
			blog|https://www.facebook.com/ddbjcenter/
			blog|https://www.ddbj.nig.ac.jp/news/en/index-e.html?db=ddbj
			online documentation|https://www.youtube.com/user/ddbjvideo
			online documentation|https://github.com/ddbj/
			online documentation|https://drive.google.com/drive/u/0/folders/1E0cxLbWV8RGYUdNs0oKfXMij0TzJDQVD
			rss|https://www.ddbj.nig.ac.jp/announcements-e.html
			twitter|@DDBJ_topics
		After:
			FAQ|https://www.ddbj.nig.ac.jp/faq/en/index-e.html
			blog|https://www.facebook.com/ddbjcenter/
			blog|https://www.ddbj.nig.ac.jp/news/en/index-e.html?db=ddbj
			contact form|https://www.ddbj.nig.ac.jp/contact-e.html
			email|ddbj@ddbj.nig.ac.jp
			online documentation|https://github.com/ddbj/
			online documentation|https://drive.google.com/drive/u/0/folders/1E0cxLbWV8RGYUdNs0oKfXMij0TzJDQVD
			online documentation|https://www.youtube.com/user/ddbjvideo
			rss|https://www.ddbj.nig.ac.jp/announcements-e.html
			twitter|@DDBJ_topics
		Added:
			contact form|https://www.ddbj.nig.ac.jp/contact-e.html
			email|ddbj@ddbj.nig.ac.jp
		Removed:

	'description' has been modified:
		Before: Annotated collection of all publicly available nucleotide and protein sequences. In Japan, Bioinformation and DDBJ Center internationally contributes as a member of INSDC to collect and to provide nucleotide sequence data with ENA/EBI in Europe and NCBI in USA. DDBJ collects sequence data mainly from Japanese researchers, as well as researchers in any other countries.
		After: Annotated collection of all publicly available nucleotide and protein sequences. DDBJ collects sequence data mainly from Japanese researchers, as well as researchers in any other countries. DDBJ is part of the International Nucleotide Sequence Database Collaboration (INSDC), which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at the NCBI. These three organizations exchange data on a daily basis. 

	'onto_disciplines' has been modified:
		Before:
			Data Submission, Annotation and Curation
			Life Science
		After:
			Bioinformatics
			Data Management
			Data Submission, Annotation and Curation
			Functional Genomics
			Genomics
			Metagenomics
			Transcriptomics
		Added:
			Bioinformatics
			Data Management
			Functional Genomics
			Genomics
			Metagenomics
			Transcriptomics
		Removed:
			Life Science

	'dataProcesses' has been modified:
		Before:
			Data submission
			DDBJ Nucleotide Sequence Submission System (NSSS)
			Mass Submission System
			Data Updates
			Data release
			Search
			FTP Download
			VecScreen
			Blast
			ClustalW
		After:
			Data submission
			DDBJ Nucleotide Sequence Submission System (NSSS)
			Mass Submission System
			Data Updates
			Data release
			Search (ARSA)
			Download via FTP
			DRA Search
			Search (getentry)
			Search Taxonomy
		Added:
			Search (ARSA)
			Download via FTP
			DRA Search
			Search (getentry)
			Search Taxonomy
		Removed:
			Search
			FTP Download
			VecScreen
			Blast
			ClustalW

	'onto_domains' has been modified:
		Before:
			Annotation
			DNA sequence
			Protein sequence
			genome
			nucleotide
			sequencing assay
		After:
			Annotation
			DNA sequence
			Protein sequence
			Sequence annotation
			data storage
			deoxyribonucleic acid
			genome
			nucleotide
			sequencing assay
		Added:
			Sequence annotation
			data storage
			deoxyribonucleic acid
		Removed:

	'tools' has been modified:
		Before:
		After:
			ClustalW||http://clustalw.ddbj.nig.ac.jp/index.php?lang=en
			BLAST||http://blast.ddbj.nig.ac.jp/blastn?lang=en
			VecScreen||http://ddbj.nig.ac.jp/vecscreen/
		Added:
			ClustalW||http://clustalw.ddbj.nig.ac.jp/index.php?lang=en
			BLAST||http://blast.ddbj.nig.ac.jp/blastn?lang=en
			VecScreen||http://ddbj.nig.ac.jp/vecscreen/
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.k337f0' by 'The FAIRsharing Team' at 10:55, 22 Mar 2019 (approved):

	'organizations' has been modified:
		Before:
			Bioinformation and DDBJ Center|https://www.ddbj.nig.ac.jp|Maintains
		After:
			Bioinformation and DDBJ Center|https://www.ddbj.nig.ac.jp|Maintains
			Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT), Tokyo, Japan|http://www.mext.go.jp/en/|Funds
			Research Organization of Information and Systems (ROIS), Tokyo, Japan|https://www.rois.ac.jp/en/|Funds
			Japan Science and Technology Agency (JST), Tokyo, Japan|http://www.jst.go.jp/EN/|Funds
		Added:
			Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT), Tokyo, Japan|http://www.mext.go.jp/en/|Funds
			Research Organization of Information and Systems (ROIS), Tokyo, Japan|https://www.rois.ac.jp/en/|Funds
			Japan Science and Technology Agency (JST), Tokyo, Japan|http://www.jst.go.jp/EN/|Funds
		Removed:

	'supportLinks' has been modified:
		Before:
		After:
			FAQ|https://www.ddbj.nig.ac.jp/faq/en/index-e.html
			blog|https://www.facebook.com/ddbjcenter/
			blog|https://www.ddbj.nig.ac.jp/news/en/index-e.html?db=ddbj
			online documentation|https://www.youtube.com/user/ddbjvideo
			online documentation|https://github.com/ddbj/
			online documentation|https://drive.google.com/drive/u/0/folders/1E0cxLbWV8RGYUdNs0oKfXMij0TzJDQVD
			rss|https://www.ddbj.nig.ac.jp/announcements-e.html
			twitter|@DDBJ_topics
		Added:
			FAQ|https://www.ddbj.nig.ac.jp/faq/en/index-e.html
			blog|https://www.facebook.com/ddbjcenter/
			blog|https://www.ddbj.nig.ac.jp/news/en/index-e.html?db=ddbj
			online documentation|https://www.youtube.com/user/ddbjvideo
			online documentation|https://github.com/ddbj/
			online documentation|https://drive.google.com/drive/u/0/folders/1E0cxLbWV8RGYUdNs0oKfXMij0TzJDQVD
			rss|https://www.ddbj.nig.ac.jp/announcements-e.html
			twitter|@DDBJ_topics
		Removed:

	'licences' has been modified:
		Before:
		After:
			Policies and Disclaimers|https://www.ddbj.nig.ac.jp/policies-e.html|Data
		Added:
			Policies and Disclaimers|https://www.ddbj.nig.ac.jp/policies-e.html|Data
		Removed:

	'onto_disciplines' has been modified:
		Before:
			Life Sciences
		After:
			Data Submission, Annotation and Curation
			Life Sciences
		Added:
			Data Submission, Annotation and Curation
		Removed:

	'onto_domains' has been modified:
		Before:
			DNA sequence
			Protein sequence
			genome
			nucleotide
			sequencing assay
		After:
			Annotation
			DNA sequence
			Protein sequence
			genome
			nucleotide
			sequencing assay
		Added:
			Annotation
		Removed:

	'contact' has been modified:
		Before: 
		After: Osamu Ogasawara

	'contactEmail' has been modified:
		Before: 
		After: oogasawa@nig.ac.jp

	'grants' has been modified:
		Before:
		After:
			JPMJCR1501
		Added:
			JPMJCR1501
		Removed:

	'publications' has been modified:
		Before:
			DNA Data Bank of Japan: 30th anniversary.|Kodama Y,Mashima J,Kosuge T,Kaminuma E,Ogasawara O,Okubo K,Nakamura Y,Takagi T|Nucleic Acids Res|2017
		After:
			DNA Data Bank of Japan: 30th anniversary.|Kodama Y,Mashima J,Kosuge T,Kaminuma E,Ogasawara O,Okubo K,Nakamura Y,Takagi T|Nucleic Acids Res|2017
			DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data.|Kodama Y,Mashima J,Kosuge T,Ogasawara O|Nucleic Acids Res|2018
		Added:
			DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data.|Kodama Y,Mashima J,Kosuge T,Ogasawara O|Nucleic Acids Res|2018
		Removed:

	'dataProcesses' has been modified:
		Before:
		After:
			Data submission
			DDBJ Nucleotide Sequence Submission System (NSSS)
			Mass Submission System
			Data Updates
			Data release
			Search
			FTP Download
			VecScreen
			Blast
			ClustalW
		Added:
			Data submission
			DDBJ Nucleotide Sequence Submission System (NSSS)
			Mass Submission System
			Data Updates
			Data release
			Search
			FTP Download
			VecScreen
			Blast
			ClustalW
		Removed:

	'accessPoints' has been modified:
		Before:
		After:
			Other|https://www.ddbj.nig.ac.jp/wabi.html|Web API for Biology
		Added:
			Other|https://www.ddbj.nig.ac.jp/wabi.html|Web API for Biology
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.k337f0' by 'ddbjcommon' at 22:06, 15 Jan 2019 (approved):

	'organizations' has been modified:
		Before:
			DDBJ Center, National Institute of Genetics, Research Organization for Information and Systems|https://www.ddbj.nig.ac.jp|Maintains
		After:
			Bioinformation and DDBJ Center|https://www.ddbj.nig.ac.jp|Maintains
		Added:
			Bioinformation and DDBJ Center|https://www.ddbj.nig.ac.jp|Maintains
		Removed:
			DDBJ Center, National Institute of Genetics, Research Organization for Information and Systems|https://www.ddbj.nig.ac.jp|Maintains

	'description' has been modified:
		Before: Annotated collection of all publicly available nucleotide and protein sequences. In Japan, DDBJ Center internationally contributes as a member of INSDC to collect and to provide nucleotide sequence data with ENA/EBI in Europe and NCBI in USA. DDBJ collects sequence data mainly from Japanese researchers, as well as researchers in any other countries. Ninety-nine percent of INSD data from Japanese researchers are submitted through DDBJ.
		After: Annotated collection of all publicly available nucleotide and protein sequences. In Japan, Bioinformation and DDBJ Center internationally contributes as a member of INSDC to collect and to provide nucleotide sequence data with ENA/EBI in Europe and NCBI in USA. DDBJ collects sequence data mainly from Japanese researchers, as well as researchers in any other countries.

Edits to 'https://fairsharing.org/FAIRsharing.k337f0' by 'ddbjcommon' at 13:28, 16 Jun 2018 (approved):

	'name' has been modified:
		Before: The DNA Data Bank of Japan
		After: DNA Data Bank of Japan

In Collections

RDA Covid-19 WG Resources

Data Citation Implementation

Support

General

FAQ	FAQ
blog	DDBJ Facebook
blog	News
contact form	DDBJ Contact Form
support email	DDBJ General Contact
online documentation	DDBJ GitHub
online documentation	DDBJ Google Drive
online documentation	DDBJ YouTube Channel
rss	DDBJ RSS Feed
twitter	@DDBJ_topics

Additional Information

Contact

Osamu Ogasawara

Tools

ClustalW	http://clustalw.ddbj.nig.ac.jp/index.php?lang=en
BLAST	http://blast.ddbj.nig.ac.jp/blastn?lang=en
VecScreen	http://ddbj.nig.ac.jp/vecscreen/

Access / Retrieve Data

Conditions of Use

Applies to: Data use

DDBJ Policies and Disclaimers

Data Release

Data release	No link recorded
Download via FTP	ftp://ftp.ddbj.nig.ac.jp/

Data Curation

Data submission	https://www.ddbj.nig.ac.jp/ddbj/submission-e.html
DDBJ Nucleotide Sequence Submission System (NSSS)	https://www.ddbj.nig.ac.jp/ddbj/websub-e.html
Mass Submission System	https://www.ddbj.nig.ac.jp/ddbj/mss-e.html
Data Updates	https://www.ddbj.nig.ac.jp/ddbj/updt-e.html

Data Access

Search (ARSA)	http://ddbj.nig.ac.jp/arsa/
DRA Search	https://ddbj.nig.ac.jp/DRASearch/
Search (getentry)	http://getentry.ddbj.nig.ac.jp/top-e.html
Search Taxonomy	http://ddbj.nig.ac.jp/tx_search/?lang=en

Other Web Services

Web API for Biology

https://www.ddbj.nig.ac.jp/wabi.html

Publications

DNA Data Bank of Japan: 30th anniversary.

Kodama Y,Mashima J,Kosuge T,Kaminuma E,Ogasawara O,Okubo K,Nakamura Y,Takagi T
Nucleic Acids Res 2017

View Paper (PubMed) View Publication

DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data.

Kodama Y,Mashima J,Kosuge T,Ogasawara O
Nucleic Acids Res 2018

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

Minimum Information about any (x) Sequence

Terminology Artifacts

NCBI Taxonomy

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

Implementing Policies

Credit

Record Maintainer

This record is maintained by Bioinformation and DDBJ Center (ddbjcommon)

Funds

Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT), Tokyo, Japan (Government body)
Research Organization of Information and Systems (ROIS), Tokyo, Japan (Research institute)
Japan Science and Technology Agency (JST), Tokyo, Japan (Government body)

Maintains

Bioinformation and DDBJ Center (Research institute)

Grant Number(s)

JPMJCR1501 (Japan Science and Technology Agency (JST), Tokyo, Japan)

DNA Data Bank of Japan

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