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DDBJ launches a new archive database
with analytical tools for next-generation
sequence data
Eli Kaminuma, Jun Mashima, Yuichi Kodama, Takashi Gojobori, Osamu Ogasawara,
Kousaku Okubo, Toshihisa Takagi 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 15, 2009; Accepted September 22, 2009
ABSTRACT
The DNA Data Bank of Japan (DDBJ) (http://www
.ddbj.nig.ac.jp) has collected and released 1 701 110
entries/1 116 138 614 bases between July 2008 and
June 2009. A few highlighted data releases from
DDBJ were the complete genome sequence of
an endosymbiont within protist cells in the termite
gut and Cap Analysis Gene Expression tags for
human and mouse deposited from the Functional
Annotation of the Mammalian cDNA consortium.
In this period, we started a novel user announcement
service using Really Simple Syndication (RSS) to
deliver a list of data released from DDBJ on a daily
basis. Comprehensive visualization of a DDBJ
release data was attempted by using a word cloud
program. Moreover, a new archive for sequencing
data from next-generation sequencers, the ‘DDBJ
Read Archive’ (DRA), was launched. Concurrently,
for read data registered in DRA, a semi-automatic
annotation tool called the ‘DDBJ Read Annotation
Pipeline’ was released as a preliminary step.
The pipeline consists of two parts: basic analysis
for reference genome mapping and de novo
assembly and high-level analysis of structural and
functional annotations. These new services will aid
users’ research and provide easier access to DDBJ
databases.
INTRODUCTION
The DNA Data Bank of Japan (DDBJ) is one of three
databanks that constitute the DDBJ/EMBL-Bank/
GenBank International Nucleotide Sequence Database
(INSD), which was established through close collabora-
tion with the European Bioinformatics Institute (EBI)
in Europe and the National Center for Biotechnology
Information (NCBI) in the USA. DDBJ is administered
by the Center for Information Biology and DDBJ (CIB-
DDBJ) of the National Institute of Genetics (http://www
.nig.ac.jp/index-e.html) with funding endorsement from
the Japanese Ministry of Education, Culture, Sports,
Science and Technology (MEXT). All researchers can
submit their data to one of the three summit databanks
to register it with INSD. The data that are enrolled are
exchanged on every day, so that the three collaborating
databanks share virtually the same data at any given time.
The syntax for the INSD entries is discussed among the
three databanks at an INSD collaborative meeting held
once every year. The agreed rules are reflected in feature
tables that define the common syntax (http://www.ddbj.
nig.ac.jp/FT/full_index.html).
In the last year, we started novel web services that focus
on daily announcements using Really Simple Syndication
(RSS) technology and visualization of DDBJ content
with high readability. Furthermore, a new data archive
database for massive amounts of raw sequencing reads
from next-generation sequencers was officially launched.
The expert annotators of the DDBJ Read Archive
(DRA) issue original accession numbers for submitted
data. Concurrently, there was a preliminary release of
a raw read annotation pipeline tool. This analytical
pipeline tool supports reference genome mapping,
de novo assembly and further annotation analyses, such
as single nucleotide polymorphism (SNP) detection.
The following sections describe three major advancements
of the DDBJ databases, the novel announcement web
services and the new archiving database with analytical
tools for raw sequencing reads.
DEVELOPMENT OF DDBJ DATABASES
We have introduced newly released DDBJ databases,
databases within the framework of INSD and other indi-
vidual databases that have been appended from last year’s
report (1).
*To whom correspondence should be addressed. Tel: +81 55 981 6859; Fax: +81 55 981 6889; Email: yanakamu@genes.nig.ac.jp
Published online 22 October 2009 Nucleic Acids Research, 2010, Vol. 38, Database issue D33–D38
doi:10.1093/nar/gkp847
� The Author(s) 2009. 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/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Datasets contributing to INSD through DDBJ
In the period from July 2008 to June 2009, DDBJ col-
lected and released original data on 1 701 110 entries/
1 116 138 614 bases. More than 90% of the data came
from Japanese researchers and the Japan Patent Office
(JPO) and the rest was mainly from researchers in
China, Korea and Taiwan. We call this dataset the
‘INSD-core data’. It consists of INSD data in traditional
format and includes general sequence data, complete
genomes, expressed sequence tags (ESTs), etc., but
excludes whole-genome shotgun (WGS), mass sequence
for genome annotation (MGA) and third party annota-
tion (TPA). Large sets of contigs (i.e. overlapping reads)
and finished sequences without annotation from an
ongoing genome project can be submitted to INSD as
WGS data. DDBJ has released one WGS entry
(2 878 428 bp) on Staphylococcus aureus ssp. aureus
Mu50-omega and 23 675 009 MGA entries (80 069 915
counts). All of these INSD-core, WGS and MGA data
were collected, reviewed and accessioned by DDBJ.
Another portion of the INSD-core data contains the
complete genome sequence of an endosymbiont within
protist cells in the gut of the termite (Candidatus
Azobacteroides pseudotrichonymphae genomovar. CFP2)
submitted by Institute of Physical and Chemical
Research (RIKEN) and National Institute of Genetics;
full-length cDNA (HTC) and EST entries for the tomato
(Solanum lycopersicum) submitted by Kazusa DNA
Research Institute; Genome Survey Sequences entries for
the rat (Rattus norvegicus LE/Stm) submitted by Kyoto
University; EST entries for rhizomes of Chinese liquorice
(Glycyrrhiza uralensis) submitted by Chiba University,
MGA entries for the human and mouse submitted by
RIKEN Omics Science Center; and MGA entries for
small RNAs of the silkworm (Bombyx mori) submitted
by the University of Tokyo. These data can be obtained
at the DDBJ ftp site (http://www.ddbj.nig.ac.jp/ftp_
soap-e.html). The reader may find it worthwhile to refer
to the two sets of data on the complete genome sequence
of an endosymbiont within protist cells in the termite gut
and the MGA datasets used in Functional annotation of
the mammalian cDNA (FANTOM; http://fantom.gsc
.riken.jp/). This bacterial endosymbiont is widely known
as a model organism for the study of cellulolysis. With
regard to the endosymbiont, functional annotation of
the bacterial genome has revealed that nitrogen fixation
and cellulolysis are coupled within the protist’s cells (2).
An MGA dataset from the FANTOM consortium
identified a large-scale gene network that controls the dif-
ferentiation of the human myeloid leukaemia cell line
THP-1 from monoblast to monocyte by applying next-
generation sequencing technology and the Cap Analysis
Gene Expression (CAGE) method (3).
Datasets released from DDBJ
In Table 1, we summarize numbers of published records
collected and released from DDBJ. A primary database is
a database as originally constructed and a secondary
database is based on a primary database. An MGA is
defined as a sequence that is produced in large quantity
for the purpose of genome annotation, such as CAGE
and 50SAGE. A TPA (4) is a nucleotide sequence data
collection in which each entry is obtained by assembling
primary entries publicized from INSD and/or the Trace
Archive with additional feature annotations determined
by experimental or inferential methods by the TPA
submitter. The DDBJ Trace Archive (DTA) is a perma-
nent repository of DNA sequence chromatograms
(traces), base calls and quality estimates for single-pass
reads from various large-scale sequencing projects.
The DTA has operated since 2008. In 2009, a simple
metadata search system and a viewer of trace data
for DDBJ-accepted data were added. Gene Trek in
Prokaryote Space (GTPS) (5) is a database of prokaryotic
genome data that have been reannotated by analyzing the
original data in various ways. Genome Information
Broker (GIB) (6) is a comprehensive data repository of
complete microbial genomes in the public domain. GIB
distributes genome sequence data and annotation 1 day
after the data are submitted to INSD. The DDBJ
Amino Acid Sequence Database (DAD) is produced by
extracting all translated sequences from the DDBJ period-
ical release, including all INSD (DDBJ/EMBL-Bank/
GenBank) entries. We also support two other databases
by providing maintenance service: Center for Information
Biology gene Expression database (CIBEX) (7) is a public
database for microarray data and stores MIAME-
compliant data in accordance with MGED Society
recommendations; Genomes TO Protein structures and
function (GTOP) (8) is a database consisting of data
Table 1. Datasets released from DDBJ
Type Database name No. of records Released date
Primary DB INSD-core (processed by DDBJ) 17 440 910 entries (1 701 110 entries) 29 May 2009
WGS 1246 513 entries 10 September 2009
MGA 34 740 058 entries 1 June 2009
TPA 593 entries 10 September 2009
DTA 2 submissions 7 July 2008
DRA 12 submissions 11 September 2009
Secondary DB DAD 14 710 673 entries 29 May 2009
GTPS 690 genomes 25 May 2009
GIB 982 genomes 10 September 2009
The number of records represents only published data.
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analyses of proteins identified by various genome projects.
The GTOP database mainly uses sequence homology
analyses and features extensive use of information on
3D structures.
DAILY RELEASE ANNOUNCEMENT AND
COMPREHENSIVE VISUALIZATION OF DDBJ
DATABASES
To deliver up-to-date information from DDBJ to
researchers every day, we started the daily publication of
newly released data from DDBJ by implementing the fol-
lowing two new functions into the DDBJ web services.
The first function is the announcement of RSS feeds
of contents of data released from DDBJ databases each
day (Figure 1). The second function is the visualization
of DDBJ entries as word cloud figures. The following
sections explain these in detail.
Frequent announcement of daily data releases by RSS
The first new function is the RSS publication of daily data
releases by DDBJ. The RSS is a family of web-feed
formats used to publish frequently updated items
such as blog entries and news headlines (9). RSS feeds
are also used by biological databases such as
PubMed Central (http://www.pubmedcentral.nih.gov/)
and ArrayExpress (10). A list of new enhancements in
FLATFILE/WGS/CON/TPA is generated as RSS feeds
every day. The contents of the RSS feeds are generated
in connection with the respective VERSION,
ACCESSION ID, DEFINITION if these are present in
REFERENCE tags. The unit of published content is set
by PROJECT of DBLINK; however, if there are no XML
tags in PROJECT, the TITLE of the REFERENCE tag
and the AUTHOR are substituted for the PROJECT.
Comprehensive visualization of DDBJ entries by
word cloud images
In addition to daily publication of database updates,
information on classified statistics in DDBJ databases
such as species and features is worthwhile for users.
DDBJ already provides several statistics on its web site,
such as the gross numbers of registered entries and of
bases in registered databases, with numerical values and
graphs. However, with conventional media it is difficult to
provide an overview of the features of DDBJ databases
at a glance. Therefore, we apply the word cloud image
program Wordle (http://www.wordle.net/) to statistics
on the frequency of DDBJ database. This program
generates a word cloud image based on the frequency of
keywords appearing in a text document or webpage.
Figure 1. A feed file for RSS 2.0 is published from the DDBJ homepage every day (http://www.ddbj.nig.ac.jp/rss/update_information.xml).
Daily released contents of DDBJ databases can be confirmed via RSS reader programs.
Nucleic Acids Research, 2010, Vol. 38, Database issue D35
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Figure 2 shows word cloud images in which the size of
each word indicates its frequency, using keywords rank-
ing among the top 100. To generate the figures,
frequencies of species names and feature keys were
calculated based on DDBJ release 78 of June 2009.
Among the top 100 species, Homo sapiens occupies most
of the image. On the other hand, the image for feature tags
indicates extremely high frequencies of db_xref key and
moderately high frequencies of product, protein_id, gene
and translation. The keywords codon start, transl_table,
note, mol_type and organism are also highlighted; the
frequent words are feature keys for protein-coding
sequences. These word cloud figures enable us to
comprehensively capture information on the released
DDBJ data at a glance.
DRA: A NEW DATABASE FOR NEXT-GENERATION
SEQUENCERS
Overview of DRA
Next-generation sequencing platforms are revolutionizing
biological science. These instruments are producing
vastly more sequencing data than was ever possible with
capillary technology. In addition, instead of microarrays,
new sequencing platforms are used to measure molecular
abundance because of their higher resolution and
accuracy. In 2007, NCBI started the Short Read Archive
(SRA) to accommodate the data from next-generation
sequencing platforms. Early in 2008, EBI began operating
the European Read Archive (ERA), and late in the same
year DDBJ started to accept sequencing data from next-
generation technologies such as Roche-454 Life Sciences
GS FLX, Illumina Genome Analyzer and Applied
Biosystems SOLiD. Initially, we prepared submission
files at DDBJ and uploaded them to SRA. Since May
2009 we have operated a new repository, the DRA
(http://trace.ddbj.nig.ac.jp/dra/index_e.shtml), to archive
raw output data from new platforms. In June 2009, we
started to issue our own internationally recognized
accession numbers with prefix ‘DR’. Most submissions
are from Japan. DRA has released 12 submissions by
FTP and these data can also be retrieved from SRA.
Considering the number of next-generation machines
running in Japan and other Asian countries, the number
of submissions to DRA is expected to increase.
Data model and validation system for DRA metadata
DRA uses the same metadata formats as SRA and ERA,
and provides common accessions of the Submission
(DRA), Study (DRP), Experiment (DRX), Sample
(DRS) and Run (DRR) metadata objects with the prefix
indicated in parentheses followed by a six-digit number
(e.g. DRA000001). We are developing a submission
system for DRA to improve submission throughput.
As a first step, we have developed a web system,
DRA Meta Checker, to validate metadata in XML file
format (http://trace.ddbj.nig.ac.jp/DRAMetaChecker).
This checker first validates uploaded XML files against
an SRA XML schema, and then validates what cannot
be validated by the schema, such as reference integrity
among the XML documents, and correspondence
between taxonomy ID and organism name. Detailed
error, warning and usage messages are displayed after
the validation process to help users create their metadata
by themselves.
Data submission to DRA
We have released Excel spreadsheets for metadata submis-
sion to DRA, called ‘DRA sheets’ (Figure 3). Submitters
are able to create metadata files by simply filling in the
fields of familiar Excel files. Submitters can use the DRA
sheets for three major platforms: 454, Genome Analyzer
and SOLiD. Every field is explained by pop-up comments,
required and optional fields are distinguished by colour,
and the fixed fields contain entered values. In addition,
these DRA sheets contain an Excel macro to generate
the metadata XML files. Submitters can submit their
metadata either in Excel file format or in XML file
format (they can be validated by the DRA Meta
Checker) as they prefer. For data transfer, submitters
can use the FTP service of DDBJ or send a hard disk by
a return-paid courier service. Once files have been
received, the DRA team validates, issues accessions and
uploads the data to SRA. DRA works with large
sequencing centres producing massive amounts of data
to establish a high-throughput submission pipeline
between the centre and DRA.
Planned development of DRA
At this moment, DRA is developing data release and
retrieval systems, where they are currently supported as
SRA systems. We will integrate the validation, submission
creation and data transfer systems into a single fully
Figure 2. Word cloud images created using a DDBJ database release.
The upper figure uses feature keys ranking among the top 100 for the
total number of nucleotides; similarly, the lower figure uses species
names.
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automated interactive submission system to accommodate
increased numbers of submissions. In May 2009, DDBJ/
EBI/NCBI held its first international collaborative
meeting on sequencing data from next-generation
platforms. At this meeting, three databanks agreed to
position the DRA/ERA/SRA activities within the frame-
work of INSD and to prepare announcement articles for
the research community and journal offices. DRA/ERA/
SRA also discussed and agreed to develop a roadmap for
XML schema releases with proposals for features, to
establish a release policy, and to exchange (at least)
metadata and FASTQ (sequence and quality values)
data. DRA/ERA/SRA will collaborate to archive the
data and share an accession space to provide a worldwide
archive.
DDBJ READ ANNOTATION PIPELINE: AN
ANALYTICAL TOOL FOR DRA
Automatic tools for the analysis of raw sequencing reads
registered in DRA may be convenient and valuable for
experimental biologists. We have developed a read anno-
tation pipeline tool to annotate DRA-registered raw
sequencing reads with high throughput. The ‘DDBJ
Read Annotation Pipeline’ uses input data from
FASTQ-formatted files in the DRA databases. The
pipeline consists of two subprocesses: basic analysis for
reference genome mapping and de novo assembly, and
high-level analysis for combining automatic and manual
annotations, such as SNP detection and expression tag
counts (Figure 4).
The DDBJ Read Annotation Pipeline has the following
three features. First, there is a short cut for the submission
of analytical results to DDBJ databases, which means that
map/assembly outputs are converted to DRA formats
or DDBJ-based INSD formats. The second feature is
high throughput, achieved by the use of a cluster
computing system in DDBJ. The third feature is flexibility
to select appropriate analytical tools from multiple
candidates.
As a preliminary step for high-level annotation, analyt-
ical tools for SNP detection have been implemented in the
current pipeline system. Other annotation tools, such as
the high-level step, will be connected to the basic part.
In general, to analyse massive amounts of raw reads
requires high-level bioinformatics expertise. On the
other hand, the DDBJ Read Annotation Pipeline
enables experimental biologists to obtain results of auto-
matic annotations by simply manipulating a graphical
user interface. Currently, the pipeline only has the
function of automatic annotation. To screen automati-
cally annotated results, manual curation is indispensable
[e.g. (11)]. Therefore, a user support function for further
manual curation will be added to the pipeline tool.
FUTURE DIRECTIONS
In this report, we introduce the new archive database—the
DRA—and an analytical pipeline for massive amounts of
Figure 3. DRA sheets: it contains an Excel macro to generate XML-formatted files for submission of metadata to DRA.
WGS/CON
Basic Analysis Genome
Mapping
reads, metadata
High Level Analysis
INSDDDBJ Read Archive
de novo
Assembly
Structural Annotation
Functional Annotation
map positions
metadata,
annotation
manual
curation
reads, metadata, basic results
Figure 4. Flowchart of DDBJ Read Annotation Pipeline. The files of
analytic results for structural and functional annotations are deposited
in DDBJ databases, DRA and INSD.
Nucleic Acids Research, 2010, Vol. 38, Database issue D37
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