The DNA Data Bank of Japan launches a new
resource, the DDBJ Omics Archive of functional
genomics experiments
Yuichi Kodama, Jun Mashima, Eli Kaminuma, Takashi Gojobori, Osamu Ogasawara,
Toshihisa Takagi, Kousaku Okubo and Yasukazu Nakamura*
Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research
Organization for Information and Systems, Yata, Mishima 411-8510, Japan
Received September 7, 2011; Revised October 17, 2011; Accepted October 18, 2011
ABSTRACT
The DNA Data Bank of Japan (DDBJ; http://www
.ddbj.nig.ac.jp) maintains and provides archival,
retrieval and analytical resources for biological
information. The central DDBJ resource consists
of public, open-access nucleotide sequence data-
bases including raw sequence reads, assembly
information and functional annotation. Database
content is exchanged with EBI and NCBI within the
framework of the International Nucleotide Sequence
Database Collaboration (INSDC). In 2011, DDBJ
launched two new resources: the ‘DDBJ Omics
Archive’ (DOR; http://trace.ddbj.nig.ac.jp/dor) and
BioProject (http://trace.ddbj.nig.ac.jp/bioproject).
DOR is an archival database of functional
genomics data generated by microarray and highly
parallel new generation sequencers. Data are
exchanged between the ArrayExpress at EBI and
DOR in the common MAGE-TAB format. BioProject
provides an organizational framework to access
metadata about research projects and the data
from the projects that are deposited into different
databases. In this article, we describe major
changes and improvements introduced to the
DDBJ services, and the launch of two new
resources: DOR and BioProject.
INTRODUCTION
Since 1987, the DNA Data Bank of Japan (DDBJ;
http://www.ddbj.nig.ac.jp) has been operating public
resources for biological information at the National
Institute of Genetics (NIG) by providing submission,
archive, search, download and analysis services. The
objective of DDBJ is to support and promote the
sharing and use of biological data as a public resource.
The traditional DDBJ archive has collected annotated
nucleotide sequences by collaborating with the EMBL-
Bank at the European Bioinformatics Institute (EBI)
and GenBank at the National Center for Biotechnology
Information (NCBI) as partners in the International
Nucleotide Sequence Database Collaboration (INSDC)
(1). In the late 1990s, automated capillary platforms
were introduced to many sequencing centres, which
began to produce raw data at the genomic scale.
Researchers soon recognized the importance of this
raw data for the qualitative assessment of sequences
and high-level re-analysis such as re-base-calling and
re-assembly. DDBJ therefore installed the Trace Archive
(http://trace.ddbj.nig.ac.jp/dta) to store the DNA
sequence chromatograms (traces), base-calls and quality
estimates from single-pass reads of various large-scale
sequencing projects. More recently, massively parallel
new generation sequencing platforms are producing
biological sequencing data in unprecedented amounts.
To ensure the wider scientific community can access and
use these enormous amounts of data for scientific discov-
ery and application, DDBJ established the ‘Sequence
Read Archive’ (DRA; http://trace.ddbj.nig.ac.jp/dra)
in 2008 to store and disseminate raw next-generation
sequencing data (2). The traditional DDBJ and the
DDBJ Trace and Sequence Read Archives share all
submitted public data with the other members of INSDC.
This year, DDBJ established two new resources: the
‘DDBJ Omics Archive’ (DOR; http://trace.ddbj.nig.ac
.jp/dor) and BioProject (http://trace.ddbj.nig.ac.jp/
bioproject). The new-generation sequencing platforms
produce data from gene expression, epigenomics and vari-
ation studies. In these functional genomics studies, the
new-generation platforms are replacing the microarray
because of their much greater resolving power and
accuracy. These functional genomics data have been
archived by the Gene Expression Omnibus (GEO) at
*To whom correspondence should be addressed. Tel: +81 55 981 6859; Fax: +81 55 981 6889; Email: yanakamu@genes.nig.ac.jp
D38–D42 Nucleic Acids Research, 2012, Vol. 40, Database issue Published online 22 November 2011
doi:10.1093/nar/gkr994
� The Author(s) 2011. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/
by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
NCBI (3) and by the ArrayExpress at EBI (4). DOR is
a resource of high-throughput experimental data for func-
tional genomics generated by sequencing as well as using
microarray platforms. DOR accepts functional genomics
experiments in the MAGE-TAB format used by
ArrayExpress. All public DOR data are exchanged with
ArrayExpress.
As new-generation technologies significantly increase
sequencing throughput, data from a single project can
be dispersed across more than one archival database.
The DDBJ BioProject resource provides an overview of
diverse types of projects and organizes the data from
the projects deposited into the archival databases main-
tained by members of INSDC. The DDBJ submission
portal ‘D-way’ was developed to be a single submission
account to enable users to submit their data to all relevant
DDBJ archival databases (traditional DDBJ, Omics
Archive, Trace Archive, Sequence Read Archive and
BioProject).
The public analysis service of new generation sequences
is provided by the ‘DDBJ Read Annotation Pipeline’
(http://p.ddbj.nig.ac.jp) (2). This pipeline processes the
uploaded raw sequence reads on cloud computers and
supports data submissions to the DDBJ archival data-
bases. DDBJ is developing into a more comprehensive
and integrated public domain resource for biological
research by providing archival databases and analysis
services.
DDBJ ARCHIVAL DATABASES
DDBJ traditional assembled sequence archive
Here we describe the development of the DDBJ database
as a member of INSD during the course of 2011, which is
appended to last year’s report (2). Between July 2010
and June 2011, 18 296 211 entries/13 576 228 536 bp were
released from INSD as core traditional nucleotide flat
files, except for whole-genome shotgun (WGS), mass
sequence for genome annotation (MGA) and third party
annotation (TPA) files (5). DDBJ contributed 12.7% of
the entries and 10% of the base pairs added to the core
nucleotide data of INSD during this period. Most of
the nucleotide data were submitted by Japanese research-
ers; the rest came from China, Korea, Taiwan and other
countries. DDBJ has also continually distributed sequence
data related to patent applications transferred from the
Japan Patent Office (JPO, http://www.jpo.go.jp) and
the Korean Intellectual Property Office (KIPO, http://
www.kipo.go.kr/en). In addition to the core nucleotide
data, DDBJ has released a total of 2 228 313 WGS
entries, 35 271 312 MGA entries, 660 TPA entries, 6374
TPA-WGS entries and 1272 TPA-CON entries as of
15 July 2011.
Noteworthy large-scale data released from DDBJ
are listed in Table 1. The genome data of the vase
tunicate (Ciona intestinalis) has been re-assembled and
re-annotated from the first draft sequences. The first
draft genome of C. intestinalis was published in 2002 by
the international genome sequencing project (6). Main
contributors to the sequencing project were from the US
Department of Energy Joint Genome Institute and
Kyoto University. The international collaboration for
the C. intestinalis genome was discontinued and the
genome sequences reported in INSD remained as the
first version. However, the genome data were updated
by the Kyoto University team independently of the
sequencing collaboration (7). Since the updated version
of the C. intestinalis genome has been used as a standard
in the ascidian research community, it would be useful for
researchers to share the updated genome data through
INSD. Since the Kyoto University team submitted the
updated genome data, DDBJ accepted and released the
Table 1. List of large-scale data released by DDBJ from July 2010 to June 2011
Type Organism Accession number [number of entries, number of base pairs (bp)]
GSS Fission yeast (S. pombe) FT321169-FT434719 (113 551 entries, 55 932 252)
EST Fission yeast (S. pombe) FY072959-FY174037 (101 079 entries, 51 492 242)
EST Kale (Brassica oleracea var. acephala) DK455950-DK575153 (119 204 entries, 93 446 677)
Metagenome Uncultivated thermophilic archaeon
(Candidatus Caldiarchaeum subterraneum)
Fosmid clones: AB201309, AP011633, AP011650, AP011675,
AP011689, AP011708, AP011723, AP011724, AP011727,
AP011745, AP011751, AP011786, AP011796, AP011826-AP011902
(90 entries, 3 092 718)
Scaffold CON: BA000048 (1 entry, 1 680 938)
GSS Uncultivated thermophilic archaeon
(Candidatus Caldiarchaeum subterraneum)
AG993735-AG999698 (5964 entries, 3 194 765)
Genome Jatropha curcas HTG: AP011961-AP011977 (17 entries, 1 356 476)
WGS: BABX01000001-BABX01150417 (150 417 entries, 285 858 490)
GSS Mouse (Mus musculus domesticus) GA000001-GA131507 (131 507 entries, 130 569 356)
GSS Rice (Oryza sativa Japonica Group) FT872362-FT932077 (59 716 entries, 26 152 462)
Full length cDNA Domesticated barley (Hordeum vulgare
subsp. vulgare)
AK353559-AK377172 (23 614 entries, 40 190 236)
GSS African rice (Oryza glaberrima) FT434720-FT872361 (437 642 entries, 206 317 130)
Genome (Chromosome 3H) Domesticated barley (Hordeum vulgare subsp.
vulgare cv. Haruna Nijo)
BACC01000001-BACC01008583 (8583 entries, 28 015 997)
Genome (Re-assemble
and re-annotation)
Vase tunicate (Ciona intestinalis) TPA-WGS: EAAA01000001-EAAA01006374 (6374 entries, 112 163 512)
TPA-scaffold CON: HT000001-HT001272 (1272 entries, 115 226 814)
EST Tammar wallaby (Macropus eugenii) FY469875-FY736474 (265 835 entries, 212 531 387)
Nucleic Acids Research, 2012, Vol. 40, Database issue D39
updated version as its first case of TPA re-assemble. TPA
re-assemble was agreed among INSD partners, GenBank,
EMBL-Bank and DDBJ, as a strategy to accept some im-
portant genomes that were re-assembled by researchers
other than the original submitters. Moreover, DDBJ has
released the following: Expressed sequence tags (EST) and
genome survey sequences (GSS) of fission yeast
(Schizosaccharomyces pombe) submitted by Osaka City
University, Japan; the kale (Brassica oleracea var.
acephala) EST submitted by Kirin Holdings Company,
Ltd, Japan; Metagenome and GSS of an uncultivated
thermophilic archaeon (Candidatus Caldiarchaeum
subterraneum) submitted by Japan Agency for
Marine-Earth Science and Technology, Japan; the
biofuel crop (Jatropha curcas) genome submitted by
Kazusa DNA Research Institute, Japan; the mouse
(Mus musculus domesticus) GSS submitted by the
RIKEN BioResource Center, Japan; GSS of Japanese
rice (Oryza sativa Japonica Group) and African rice
(O. glaberrima) and full length cDNAs of domesticated
barley (Hordeum vulgare subsp. vulgare) submitted by
National Institute of Agrobiological Sciences, Japan;
WGS derived from chromosome 3H of domesticated
barley (H. vulgare subsp. vulgare cv. Haruna Nijo)
submitted by Okayama University, Japan; the tammar
wallaby (Macropus eugenii) EST submitted by National
Institute of Genetics, Japan.
DDBJ Sequence Read Archive
DRA accepts raw sequencing data submissions from
new-generation sequencing platforms (8). New submitters
should contact DRA for the creation of a D-way submis-
sion account and a secure data upload area. Sequencing
data files should then be uploaded into the secure data
upload area. Submitters can prepare and submit all their
information, including study, experiment, sample, run
and analysis metadata associated with the sequenc-
ing data by using the web-based submission tool
‘MetaDefine’. In the MetaDefine intuitive interface,
users can create metadata by simply entering the necessary
pieces of information into the appropriate fields and
can revise the content according to the feedback
given by the metadata validation. Data search and
download services have also been included in DRA
(http://trace.ddbj.nig.ac.jp/DRASearch). Users can
search all the public SRA data of DDBJ/EBI/NCBI
by accession numbers, several other parameters
(e.g. organism and study type) and free-text keywords.
The sequencing data can be downloaded by FTP in
either the SRA toolkit format or fastq format via
ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra. DRA works
closely with several large-sequencing projects. For
example, in the Genome Science Project (http://www
.genome-sci.jp), DRA serves as a data hub to support
data flow from sequencing centres to participant
researchers and the DDBJ Read Annotation Pipeline.
DRA continues to support large-scale and collaborative
projects by coordinating data flow, submission and
analysis.
DDBJ Omics Archive
DDBJ has supported the Center for Information Biology
Gene Expression Database (CIBEX; http://cibex.nig.ac
.jp), which has collected more than 3700 hybridizations
from microarray experiments since 2004 (9). DDBJ has
participated in the Functional Genomics Data (FGED;
http://www.mged.org) society which aims to assure that
the investment in functional genomics data generates
maximum public benefit by defining minimum informa-
tion specifications for reporting data and standards for
biological research data. CIBEX accepts microarray
data compliant with the Minimum Information About a
Microarray Experiment (MIAME) guideline developed by
FGED, which is required to interpret and verify the results
of an experiment (10). Many scientific journals require
the deposition of MIAME-compliant microarray data to
GEO at NCBI and ArrayExpress at EBI or CIBEX before
publication of the relevant paper. In functional genomics
research areas, new-generation sequencers play a key role
in producing data by measuring the abundance of DNA
and RNA molecules. The shift from microarrays to new
generation sequencing platforms for functional genomics
investigations has resulted in much greater resolving
power and accuracy for such experiments. To accommo-
date the increasing volume of high-throughput functional
genomics data from sequencing- and microarray-based
technologies, DDBJ established a new resource called
‘DDBJ Omics Archive’ (DOR; http://trace.ddbj.nig.ac
.jp/dor). DOR accepts functional genomics data (e.g.
gene expression, small RNA profiling and epigenetics,
etc.) in the MAGE-TAB format specified by FGED and
used by ArrayExpress. DOR encourages microarray and
sequencing data submissions compliant with MIAME
and Minimum Information about a high-throughput
SeQuencing Experiment (MINSEQE) guidelines, respect-
ively. Submitters need to prepare the MAGE-TAB
submission files by using spreadsheet applications or
third-party tools until our own submission tool is
released. DOR issues internationally recognized accession
numbers in the E-DORD-n format to the submitted
experiments. Public data are exchanged between
ArrayExpress and DOR. Once new-generation sequencing
data sets are deposited in DOR, the raw sequencing data
are submitted to DRA with the SRA XML metadata
generated from the supplied MAGE-TAB files. CIBEX
will stop accepting new submissions once DOR becomes
fully operational. Access to the data that have been
deposited into CIBEX will be provided. The CIBEX
data will be exported to DOR on the request of the data
owner.
DDBJ BioProject
As new high-throughput sequencing technologies signifi-
cantly increase the volume of data that can be generated,
distinct types of data (e.g. genome, transcriptome and
targeted locus data) from a single project can be deposited
into different archival databases. The BioProject resource
is a redesigned, expanded, replacement of the NCBI
Genome Project resource. The redesign adds tracking of
several data elements including more precise information
D40 Nucleic Acids Research, 2012, Vol. 40, Database issue
about a project’s scope, material, objectives, funding
source and general relevance categories. DDBJ
BioProject issues accession numbers with the prefix
‘PRJD’ to the submitted projects and exchanges the
released data with other members of INSDC. Data
submitted to INSDC-associated databases cross-reference
to the BioProject identifier to support navigation between
the project and the project’s datasets. BioProject enables
users to retrieve a project’s datasets across multiple
archival databases. Related projects can be grouped
under an umbrella project. An umbrella project may
group projects that are part of a single collaborative
effort but represent distinct studies that differ in method-
ology, sample material or resulting data type. The defin-
ition of a set of related data, a ‘project’, is very flexible
and supports the need to define a complex project and
various distinct sub-projects. Registration for a DDBJ
BioProject accession is encouraged for the types of
projects that result in submission of a very large volume
of data, submissions from multiple members of a collab-
oration or submissions to multiple archival databases.
A BioProject accession is required for submissions of
microbial and eukaryotic genomes. At DDBJ, BioProject
unites the records in the traditional DDBJ archive,
Sequence Read Archive, Trace Archive and Omics
Archive.
DDBJ ANALYSIS SERVICES
DDBJ Read Annotation Pipeline
The DDBJ Read Annotation Pipeline (DDBJ Pipeline,
http://p.ddbj.nig.ac.jp) analyzes and annotates raw new-
generation sequencing data and generates a template
metadata file to support submission of analyzed data to
the DDBJ archival databases (2). DDBJ Pipeline is a
cloud computing-based analysis system in which users
can access NIG supercomputers through a web applica-
tion with a graphical user interface. DDBJ Pipeline
consists of two processes: a basic process for reference
sequence mapping and de novo assembly, and a successive
analytical process for structural and functional anno-
tations. In the basic process, popular mapping and
assembly tools are available, and reference sequences can
be retrieved by their INSDC accession numbers from the
DDBJ database using SOAP access (11). Major enhanced
functions are as follows: (i) DRA data import, (ii) New
annotation workflows in the analytical process, (iii)
Deletion policy of query and result data, (iv) MD5
checksum for download files and (v) Usage statistics
information. DDBJ Pipeline implemented an automatic
loader which loads DRA data from the public DDBJ
FTP server in FASTQ file formats for query
(Figure 1A). When loading is complete, the Pipeline
system sends an e-mail notification to users. New
workflows, genomic contig annotation, SNP detection
(Figure 1B) and RNA-seq transcript annotation have
been implemented in the analytical process. To save disk
space for data storage, we set a policy to store query and
result data up to 30 days. To verify the download process,
MD5 checksums have been added to compressed
download files. Usage statistics of job submissions and
web access are displayed on the website.
ADDITIONAL INFORMATION
More information is available on the DDBJ website
at http://www.ddbj.nig.ac.jp. News is delivered by really
simple syndication (RSS), Twitter and mail magazines.
ACKNOWLEDGEMENTS
We gratefully acknowledge the support of all members of
DDBJ for data collection, annotation and release and for
software development. In particular, we thank Dr Hideki
Nagasaki, Dr Satoshi Saruhashi, Takako Mochizuki,
Naoko Sakamoto and Natsuko Sakakura for consult-
ations on DRA and Pipeline, and Prof. Hideaki
Figure 1. (A) DRA query import panel of DDBJ Pipeline. (B) Generated image for genomic locations of SNPs.
Nucleic Acids Research, 2012, Vol. 40, Database issue D41
Sugawara and Prof. Yoshio Tateno for support in the
form of database maintenance and INSD collaboration.
FUNDING
Ministry of Education, Culture, Sports, Science and
Technology of Japan (MEXT) (management expense
grant for National University Cooperation, to DDBJ);
MEXT Grant-in-Aid for Scientific Research on
Innovative Areas ‘Genome Science’ (to DDBJ Sequence
Read Archive and DDBJ Pipeline, partial). Funding for
open access charge: The DDBJ management expenses
grant (from MEXT).
Conflict of interest statement. None declared.
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