Published online 24 October 2016 Nucleic Acids Research, 2017, Vol. 45, Database issue D25–D31
doi: 10.1093/nar/gkw1001
DNA Data Bank of Japan
Jun Mashima1,*
, Yuichi Kodama1
, Takatomo Fujisawa1
, Toshiaki Katayama2
,
Yoshihiro Okuda1
, Eli Kaminuma1
, Osamu Ogasawara1
, Kousaku Okubo1
,
Yasukazu Nakamura1
and Toshihisa Takagi1,3,*
1
DDBJ Center, National Institute of Genetics, Shizuoka 411-8540, Japan, 2
Database Center for Life Science, Chiba
277-0871, Japan and 3
National Bioscience Database Center, Japan Science and Technology Agency, Tokyo
102-8666, Japan
Received September 16, 2016; Revised October 13, 2016; Editorial Decision October 14, 2016; Accepted October 15, 2016
ABSTRACT
The DNA Data Bank of Japan (DDBJ) (http://www.
ddbj.nig.ac.jp) has been providing public data services
for thirty years (since 1987). We are collecting
nucleotide sequence data from researchers as
a member of the International Nucleotide Sequence
Database Collaboration (INSDC, http://www.insdc.
org), in collaboration with the US National Center
for Biotechnology Information (NCBI) and European
Bioinformatics Institute (EBI). The DDBJ Center also
services Japanese Genotype-phenotype Archive
(JGA), with the National Bioscience Database Center
to collect human-subjected data from Japanese
researchers. Here, we report our database activities
for INSDC and JGA over the past year, and introduce
retrieval and analytical services running on our supercomputer
system and their recent modifications.
Furthermore, with the Database Center for Life Science,
the DDBJ Center improves semantic web technologies
to integrate and to share biological data, for
providing the RDF version of the sequence data.
INTRODUCTION
The DNA Data Bank of Japan (DDBJ, http://www.ddbj.
nig.ac.jp) (1) is a public database of nucleotide sequences
established at the National Institute of Genetics (NIG).
Since 1987, the DDBJ has been collecting annotated nucleotide
sequences as its traditional database service. This
endeavor has been conducted in collaboration with GenBank
(2) at the National Center for Biotechnology Information
(NCBI) and with European Nucleotide Archive
(ENA) (3) at the European Bioinformatics Institute (EBI).
The collaborative framework is called the International Nucleotide
Sequence Database Collaboration (INSDC, http:
//www.insdc.org/) (4) and the product database from this
framework is called the International Nucleotide Sequence
Database (INSD).
Within the INSDC framework, the DDBJ Center also
services the DDBJ Sequence Read Archive (DRA), BioProject
for sequencing project metadata and BioSample for
sample information to facilitate the acceptance of largescale
data generated from next-generation sequencing platforms
(5–7). The comprehensive resource of nucleotide
sequences and associated information complies with the
INSDC policy that guarantees free and unrestricted access
to data archives (8). In 2016, the advisors of INSDC published
an open letter to remind scientists to submit their sequence
data to the INSDC (9,10).
In addition, the DDBJ Center services the Japanese
Genotype-phenotype Archive (JGA, http://trace.ddbj.nig.
ac.jp/jga) in collaboration with the National Bioscience
Database Center (NBDC, http://biosciencedbc.jp/en/) of
the Japan Science and Technology Agency (5,11). This
database stores personal genotype and phenotype data
from individuals who have signed consent agreements authorizing
data release only for specific research use. The
data access is strictly controlled, similar to the data access
policy of the database of Genotypes and Phenotypes
at the NCBI (12) and the European Genome-phenome
Archive at the EBI (13). NBDC provides the guideline and
policies for sharing human-derived data (http://humandbs.
biosciencedbc.jp/en/guidelines) and also reviews data submission
and usage requests.
The DDBJ Center, a part of NIG, is funded as a supercomputing
center. Our web services, including submission
systems, data retrieval systems, Web API, DDBJ Read Annotation
Pipeline, and backend databases are performed on
the NIG supercomputer system. The current commoditybased
cluster was implemented in 2012 (14).
The present article reports the update of the above services
at the DDBJ Center. A highlight is the semantic web
services developed in collaboration with the Database Center
for Life Science (DBCLS, http://dbcls.rois.ac.jp/en) and
the virtualization of annotation pipeline. All resources de*To
whom correspondence should be addressed. Tel: +81 55 981 6839; Fax: +81 55 981 6849; Email: jmashima@nig.ac.jp
Correspondence may also be addressed to Toshihisa Takagi. Tel: +81 4 7136 3981; Fax: +81 4 7136 3975; Email: tt@nig.ac.jp
C The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which
permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
D26 Nucleic Acids Research, 2017, Vol. 45, Database issue
scribed here are available from http://www.ddbj.nig.ac.jp
and most of the archival data can be downloaded at ftp:
//ftp.ddbj.nig.ac.jp.
THE DDBJ ARCHIVAL DATABASES
Data contents: traditional DDBJ and the DRA
In 2015, most of nucleotide data directly submitted to the
DDBJ (3826 times; 75.3%) were made by Japanese research
groups, with the remainder originating from Iran
(238 times; 4.7%), India (188 times; 3.7%), Thailand (154
times; 3.0%), China (111 times; 2.2%), and other countries
and regions (563 times; 11.1%).
Between June 2015 and May 2016, the DDBJ periodical
release increased by 10 317 427 entries and 20 978 161 726
base pairs. The periodical release does not include wholegenome
shotgun (WGS), large parts of transcriptome shotgun
assembly (TSA) or third party data (TPA) files (15).
The DDBJ has continuously distributed sequence data in
published patent applications from the Japan Patent Office
(JPO, http://www.jpo.go.jp) and the Korean Intellectual
Property Office (KIPO, http://www.kipo.go.kr/en). The
JPO directly transferred its data to the DDBJ, whereas
the KIPO transferred its data via an arrangement with
the Korean Bioinformation Center. The DDBJ contributed
19.20% of the entries and 12.84% of the total base pairs
added to the core nucleotide data of the INSD. A detailed
statistical breakdown of the number of records is
shown on the DDBJ homepage (http://www.ddbj.nig.ac.jp/
breakdown stats/prop ent-e.html). In addition to the above
data, the DDBJ has released a total of 11 909 516 WGS entries
(1694 genomes), 1 505 087 contig/constructed (CON)
entries, 1 313 171 TSA entries (18 projects), 786 TPA entries,
6374 TPA-WGS entries (one genome) and 1272 TPA-CON
entries as of 27 May 2016.
In the period between June 2015 and May 2016, nextgeneration
sequencing data of 23,974 runs have been registered
to the DRA.
Notable datasets released from the DDBJ sequence
databases are listed in Table 1. In particular, we accepted
and released the latest sequence data of the reference
genome of rice (16), with the annotation performed by the
Rice Annotation Project (17) that has been anticipated by
many researchers.
Japanese genotype-phenotype archive
The JGA is a permanent archiving service for genotype and
phenotype data of human individuals (11). The JGA accepts
data that are de-identified by submitters. Upon submission,
the JGA team will archive the original data files
in encrypted form in the secure database. As of 1 September
2016, the JGA has archived 57 studies (23.5 TB) of
individual-level human datasets submitted by Japanese researchers.
Archived studies include ‘development of molecular
targeted therapy for small cell lung cancer by comprehensive
genome analysis’ (18), ‘transcriptome analysis
of adolescents and young adults with Acute Lymphoblastic
Leukemia’ (19) and ’Japanese Alzheimer’s disease neuroimaging
initiative’ (20). Submission of these studies has
been reviewed and approved by the Data Access Committee
at the NBDC. The summaries of 37 studies are available
to the public both on the JGA (https://ddbj.nig.ac.
jp/jga/viewer/view/studies) and NBDC (http://humandbs.
biosciencedbc.jp/en/data-use/all-researches) websites. To
access individual-level data of these public studies, users
are required to apply data access requests to the NBDC
(http://humandbs.biosciencedbc.jp/en/data-use). The DAC
ensures that the stated research purposes are compatible
with participant consent and that the principal investigator
and institution will abide by the NBDC guideline and the
specific terms and conditions imposed to a given dataset.
Once access has been granted by DAC, datasets with access
permission can be downloaded with a secure software tool.
It is required for users to establish a secure computing facility
for local use of the downloaded data according to the
NBDC security guideline.
DDBJ SYSTEM UPDATE
Update registration systems for the DDBJ traditional assembled
sequence archives
We provide two systems for data submission to the traditional
DDBJ database: (i) the Nucleotide Sequence Submission
System (NSSS; 5) and (ii) the Mass Submission
System (MSS; 21). The NSSS is an interactive application
facilitating the entry of all items via a web-based form,
http://www.ddbj.nig.ac.jp/sub/websub-e.html. The MSS is
a procedure to directly send large data files, http://www.
ddbj.nig.ac.jp/sub/mss flow-e.html. Both systems were enhanced
to apply the new rules of feature and qualifier
usages (see http://www.ddbj.nig.ac.jp/insdc/icm2015-e.
html#ft). As mentioned above, the data volume of TSA submissions
to the DDBJ was dramatically increased, with individual
submissions of 100 000 sequences. Therefore, we
decided to improve the DDBJ accession number assignment
system to accept such bulk TSA submissions. Since
October 2015, the DDBJ has assigned accession numbers
with four letter prefixes for TSA data submitted to the
DDBJ, similar to the WGS data. During November 2015,
the DDBJ released TSA data with a four letter prefix IAAA
(IAAA01000001–IAAA01132843) for the first time (Table
1). See also the anonymous FTP site of TSA data, ftp:
//ftp.ddbj.nig.ac.jp/ddbj database/tsa/.
Sequence analytical services
The NIG supercomputer as a sequence analytical platform.
The DDBJ Center operates the NIG supercomputer which
specializes in analysis of large-scale sequence data. The
NIG supercomputer offers computational infrastructure
for the construction of DDBJ databases and analysis services,
and provides researchers with a large-scale data analysis
and supercomputing environment. The NIG supercomputer
is currently composed of two computer systems: (i)
the Phase 1 system which was introduced in 2012 and (ii)
the Phase 2 system which went into production in 2014. The
Phase 1 system consists of calculation nodes for generalpurpose
(352 thin-nodes, each with 64 GB memory; Intel
Xeon E5-2670 5632 cores, 117.14 Tflops peak performance
of CPUs in total) and memory-intensive tasks, including de
Nucleic Acids Research, 2017, Vol. 45, Database issue D27
Table 1. List of notable data sets released from the DNA Data Bank of Japan (DDBJ) sequence databases from June 2015 to May 2016
Data type Organism
Accession numbers for annotated sequences (number of
entries) Accession numbers for raw reads
Genome Radish (Raphanus sativus cv. Aokubi S-h) WGS: BAOO01000001-BAOO01072909 (72 909 entries)
scaffold CON: DF196826-DF236948 (40,123 entries)
DRR012610-DRR012624
Soybean (Glycine max cv. Enrei) BBNX02000001-BBNX02108601 (108 601 entries) DRR021740-DRR021744
Common marmoset (Callithrix jacchus) WGS: BBXK01000001-BBXK01109198 (109 198 entries)
scaffold CON: DG000097-DG000120 (24 entries) GSS:
LB274659-LB427105 (152 447 entries)
DRR036754-DRR036764
Rice (Oryza sativa Japonica Group cv.
Nipponbare)
chromosome: AP014957-AP014968 (12 entries) unanchored:
AP014969-AP015011 (43 entries)
n/a
Hawaiian acornworm (Ptychodera flava) WGS: BCFJ01000001-BCFJ01317432 (317 432 entries)
scaffold CON: LD342582-LD560836 (218 255 entries)
DRR027930-DRR027956
Azuki bean (Vigna angularis var. angularis) chromosome: AP015034-AP015044 (11 entries) scaffold:
AP015045-AP017294 (2,250 entries)
DRR031705 DRR031878-DRR031883
DRR032984-DRR033067
Taiwan habu (Protobothrops mucrosquamatu) WGS: BCNE010000001-BCNE011421934 (1 421 934 entries) DRR049668, DRR049669
WGS: BCNE02000001-BCNE02167851 (167 851 entries)
scaffold CON: LD636650-LD688929 (52 280 entries)
DRR049668, DRR049669
Acropora digitifera WGS: BACK02000001-BACK02054400 (54 400 entries)
scaffold CON: DF970692-DF973111 (2420 entries)
DRR001380-DRR001433
Zoysia japonica cv. Nagirizaki WGS: BCLF01000001-BCLF01011786 (11 786 entries) DRR047281-DRR047283, DRR047291
Zoysia matrella cv. Wakaba WGS: BCLG01000001-BCLG01013609 (13 609 entries) DRR047287, DRR047289
Zoysia pacifica cv. Zanpa WGS: BCLH01000001-BCLH01011428 (11 428 entries) DRR047288, DRR047290
A bacterium that degrades and assimilates PET,
Ideonella sakaiensis
WGS: BBYR01000001-BBYR01000227 (227 entries) n/a
Luminous mushroom (Mycena chlorophos) WGS: BAYG01000001-BAYG01025660 (25 660 entries)
scaffold CON: DF837679-DF850034 (12 356 entries)
DRR018497-DRR018504
Ohi’a lehua (Metrosideros polymorpha var.
glaberrima)
WGS: BCNH01000001-BCNH01036376 (36 376 entries) n/a
Matsutake (Tricholoma matsutake) WGS: BDDP01000001-BDDP01088884 (88 884 entries) n/a
Common buckwheat (Fagopyrum esculentum) WGS: BCYN01000001-BCYN01387594 (387 594 entries) DRR046985-DRR046993
Mushroom (Hypsizygus marmoreus) WGS: BDDV01000001-BDDV01010694 (10 694 entries) n/a
Transcriptome Radish (Raphanus sativus cv. Aokubi S-h) n/a DRR010353-DRR010355
DRR014743-DRR014781
Soybean (Glycine max cv. Enrei) n/a DRR031435
Common house spider (Parasteatoda tepidariorum) IAAA01000001-IAAA01132843 (132 843 entries) DRR047015-DRR047017
Ayu (Plecoglossus altivelis altivelis) thrombocyte LA715952-LA738445 (22 494 entries) neutrophil
LA738446-LA761178 (22 733 entries) B lymphocyte
LA761179-LA777683 (16 505 entries)
DRR024801 DRR025094 DRR024802
Taiwan habu (Protobothrops mucrosquamatu) IAAC01000001-IAAC01112307 (112 307 entries) DRR049635-DRR049665
California harvester ant (Pogonomyrmex
californicus)
IAAD01000001-IAAD01311730 (311 730 entries) DRR048539-DRR048582
Ant (Formica aquilonia) LH381539-LH513652 (132 114 entries) DRR042077-DRR042082 (DRA003820)
Ant (Formica cinerea) LH513653-LH652103 (138 451 entries) DRR042083-DRR042088 (DRA003820)
Ant (Formica exsecta) LH652104-LH973351 (321 248 entries) DRR042089-DRR042092 (DRA003820)
Ant (Formica fusca) LI000001-LI121692 (121 692 entries) DRR042093-DRR042098 (DRA003820)
Ant (Formica pratensis) LI121693-LI219804 (98 112 entries) DRR042099-DRR042104 (DRA003820)
Ant (Formica pressilabris) LI219805-LI349988 (130 184 entries) DRR042105-DRR042110 (DRA003820)
Ant (Formica truncorum) LI349989-LI476587 (126 599 entries) DRR042111-DRR042116 (DRA003820)
Ant (Lasius neglectus) LI476588-LI563515 (86 928 entries) DRR042123-DRR042128 (DRA003820)
Ant (Lasius turcicus) LI563516-LI670604 (107 089 entries) DRR042129-DRR042134 (DRA003820)
Ant (Linepithema humile) LI670605-LI795928 (125 324 entries) DRR042117-DRR042122 (DRA003820)
Ant (Monomorium chinense) LI795929-LI926639 (130 711 entries) DRR042135-DRR042140 (DRA003820)
Ant (Monomorium pharaonis) LJ000001-LJ120855 (120 855 entries) DRR042141-DRR042146 (DRA003820)
Ant (Myrmica rubra) LJ120856-LJ206166 (85 311 entries) DRR042147-DRR042152 (DRA003820)
Ant (Myrmica ruginodis) LJ206167-LJ284088 (77 922 entries) DRR042153-DRR042158 (DRA003820)
Ant (Myrmica sulcinodis) LJ284089-LJ356044 (71 956 entries) DRR042159-DRR042164 (DRA003820)
Red fire ant (Solenopsis invicta) monogynous LJ356045-LJ530869 (174 825 entries) DRR042165-DRR042170 (DRA003820)
Red fire ant (Solenopsis invicta) polygynous LJ530870-LJ707314 (176 445 entries) DRR042171-DRR042176 (DRA003820)
Tausch’s goatgrass (Aegilops tauschii) Strain AT76: IAAN01000001-IAAN01045723 (45 723 entries) DRR058959
Strain KU-2003: IAAO01000001-IAAO01055813 (55 813
entries)
DRR058960
Strain KU-2025: IAAP01000001-IAAP01033680 (33 680
entries)
DRR058961
Strain KU-2075: IAAQ01000001-IAAQ01065447 (65 447
entries)
DRR058962
Strain KU-2078: IAAR01000001-IAAR01060884 (60 884
entries)
DRR058963
Strain KU-2087: IAAS01000001-IAAS01065827 (65 827
entries)
DRR058964
Strain KU-2093: IAAT01000001-IAAT01053474 (53 474
entries)
DRR058965
Strain KU-2124: IAAU01000001-IAAU01060479 (60 479
entries)
DRR058966
Strain KU-2627: IAAV01000001-IAAV01060547 (60 547
entries)
DRR058967
Strain PI499262: IAAW01000001-IAAW01055848 (55 848
entries)
DRR058968
D28 Nucleic Acids Research, 2017, Vol. 45, Database issue
novo assembly of sequencing reads: two medium nodes, each
with 2 TB of memory (HP DL980G7: Intel Xeon E7-4870
160 cores 1.22 Tflops in total), and one fat node with 10 TB
of memory (SGI UV1000: Intel Xeon E7-8837 762 cores,
8.17 Tflops). In the general-purpose thin calculation nodes,
64 thin nodes contain NVIDIA Tesla M2090 GPGPU. The
Phase 2 incorporates 202 thin nodes, each with 64 GB of
memory (Intel Xeon E5-2680v2 4040 cores, 90 Tflops in total)
and eight medium nodes (identical to Phase 1).
The calculation nodes in each system are interconnected
with InfiniBand (QDR in Phase 1 and FDR in Phase 2)
by a complete bisection fat-tree topology. To support massive
I/O in the big-data analysis, the NIG supercomputer
is equipped with 7 PB of the Lustre parallel distributed file
system (http://www.lustre.org). The 5.5 PB MAID system
is used for archiving of the Sequence Read Archive data,
including the DRA and JGA (11). The number of NIG Supercomputer
users increased from 2016 in 1 June 2015 to
2532 by 31 May 2016. The criteria for issuing a user login
account are shown on the web page (https://sc.ddbj.nig.ac.
jp/index.php/en/criteria-for-issuing-user-login-accounts).
Supported analytical tools and public datasets in the NIG
Supercomputer. Many popular bioinformatics tools and
libraries were installed in the system for the convenience
of the login users of the NIG supercomputer, as listed on
the NIG supercomputer home page (http://sc.ddbj.nig.ac.
jp/index.php/ja-avail-oss). To help reproduce previously executed
analysis flow, different versions of the analytical
tools are installed in different directory paths. Pre-installed
datasets in the NIG supercomputer for those analytical
tools are listed on the web page (http://sc.ddbj.nig.ac.jp/
index.php/ja-availavle-dbs).
Web BLAST, ClustalW, VecScreen, ARSA and Web API for
Bioinformatics (WABI). The DDBJ Center has provided
the Web BLAST (22), ClustalW (23,24) and VecScreen
(http://www.ncbi.nlm.nih.gov/tools/vecscreen/univec) services,
which receive requests from web interfaces. The
DDBJ Center also provides the Web API for Bioinformatics
(WABI) (25–27) for large scale data analysis and
the RESTful Web API service that can process requests
from computer programs. The WABI service includes
BLAST, VecScreen, ClustalW, MAFFT (28,29), getentry
data retrieval system via accession numbers and the ARSA
keyword search system for the DDBJ flat files (14). The
WABI service recently incorporated a new feature of
MAFFT version 7 (–add, –addfragments, –addprofile, and
–addfull options), which allow the addition of unaligned
sequences into an existing alignment (29).
TXSearch to retrieve NCBI taxonomy index. TXSearch
(http://ddbj.nig.ac.jp/tx search/) is an NCBI Taxonomy
browsing system in the DDBJ. This browsing system allows
data submitters to find authentic scientific names used
in the INSDC for the purpose of vocabulary control. Due
to the replacement of the NIG supercomputer in 2012,
we re-implemented most of our services on open source
middleware for accommodation on the new system. The
TXSearch system was built on the Apache Solr full text
search system and MySQL. The RESTful Web API service
is also provided. The data in the TXSearch are updated on a
daily basis by downloading the NCBI Taxonomy database
(30) from the NCBI FTP site (ftp://ftp.ncbi.nih.gov/pub/
taxonomy). Currently, viral records of TXSearch contain
links to records of Virus Taxonomy: 2015 Release (31), released
from the International Committee on the Taxonomy
of Viruses (ICTV http://www.ictvonline.org/) as shown in
Figure 1.
A virtual machine image for the DDBJ Pipeline. The DDBJ
Read Annotation Pipeline (DDBJ Pipeline, http://p.ddbj.
nig.ac.jp) is a high-throughput web annotation system of
next-generation sequencing reads running on the NIG supercomputer
(32). The pipeline’s basic component facilitates
reference genome mapping and de novo assembly,
and subsequent components such as structural and functional
annotation analyses with a Galaxy interface (33).
During 2016, the subsequent component of DDBJ Pipeline
was moved from a web service on the NIG supercomputer
to a software distribution service for both the local Oracle
VirtualBox and Pitagora-Galaxy community web server
(http://www.pitagora-galaxy.org/) organized by Dr Ryota
Yamanaka. Users are required to operate the virtual machine
on their own local environment or flexible cloud computing
environment. Thus, computational resources in the
NIG supercomputer for the DDBJ Pipeline service was concentrated
from both basic and succeeding components into
only the basic component, which often requires heavy memory
usages and comprises time intensive tasks.
Semantic Representation of DDBJ Annotated Sequence
Records. To improve reusability of the sequence annotation
data, we have developed a system to make the DDBJ
records into the Resource Description Framework (RDF)
version in collaboration with DBCLS (11,34,35). To semantically
represent the DDBJ nucleotide sequence annotation,
we have developed a DDBJ taxonomy ontology for describing
taxonomic information of the source organism and a
DDBJ annotated nucleotide sequence ontology for describing
metadata such as submitters and references, and biological
feature annotations (http://ddbj.nig.ac.jp/ontologies/).
Besides semantic information based on those ontologies,
the RDF dataset contains the semantic relations expressed
using FALDO ontology (36), Semanticscience Integrated
Ontology (37), Sequence Ontology (38) and Relation Ontology
(39) for illustrating all the information in the existing
DDBJ entries and INSDC resources. The RDF version of
the DDBJ annotated sequence records are available at the
DDBJ FTP site (ftp://ftp.ddbj.nig.ac.jp/rdf/).
FUTURE DIRECTION
In the present report, we introduced updates of the DDBJ
datasets, data submissions, and analytical systems during
the past year. We plan to develop a unified submission portal
for all database systems, along with a semi-automatic annotation
and curation system. The key technology is RDF,
and the effort to translate DDBJ sequence records into
RDF is under way.
The current focuses at DDBJ Center are as follows: (i)
improved network security and data management for JGA;
Nucleic Acids Research, 2017, Vol. 45, Database issue D29
B
A
Figure 1. Improvement to link ICTV records on the viral taxonomic records of TXSearch tool. (A) Schematic diagram of data flow to insert links to ICTV
records into NCBI Taxonomy records. (B) Screenshot of a viral record on TXSearch tool. The red arrow shows a link to the ICTV record.
(ii) virtualization of computing infrastructure for better
development and analysis on the HPC environment and
(iii) restructuring of data processes for updating INSDC
databases. In addition, to enhance research productivity on
the NIG supercomputer, we are constructing an experimental
system to enable not only the operation of HPC oriented
software systems (MPI, grid engine) and big-data oriented
systems (Spark, YARN) but also the operation of
Linux containers (Docker etc.) which allow users to build,
re-distribute, and run a set of analysis programs in various
kinds of calculation environments.
ACKNOWLEDGEMENTS
We gratefully acknowledge the support of Koji Watanabe,
Chiharu Kawagoe, and all members of DDBJ Center for
D30 Nucleic Acids Research, 2017, Vol. 45, Database issue
their assistance in data collection, annotation, release and
software development. We are thankful to Mari T. Minowa,
Minae Kawashima, Kazunori Miyazaki and Nobutaka
Mitsuhashi of NBDC as collaborators of the JGA project;
Yasuhiro Tanizawa, Takako Mochizuki, Shota Morizaki
for the DDBJ Pipeline updates; Tazro Ohta of DBCLS and
Ryota Yamanaka of Oracle Corporation Japan for the virtual
machine collaboration; Jerven Bolleman of UniProt;
MicrobeDB.jp project members; Norio Kobayashi and Hiroshi
Masuya of RIKEN BRC Institute; and domestic BioHackathon
organizers of DBCLS for development of RDF
applications. We also would like to thank Kento Aida,
Shigetoshi Yokoyama, Nobuyoshi Masatani of National Institute
of Information and Shinichi Miura and Satoshi Matsuoka
of Tokyo Institute of Technology for the computational
infrastructure of the NIG supercomputer.
FUNDING
Ministry of Education, Culture, Sports, Science and Technology
of Japan (MEXT) via a management Expense grant
for Inter-University Research Institute Corporation (to
DDBJ); Grant-in-Aid for Scientific Research on Innovative
Areas (Genome Science) (to DDBJ, DRA); JGA has
been supported by NBDC of Japan Science and Technology
Agency (JST). Funding for open access charge: MEXT
management expense grant to DDBJ.
Conflict of interest statement. None declared.
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