Dr. Hideaki Sugawara, Professor of National Institute of Genetics and Director of Center for Information Biology and DNA Data Bank of Japan (CIB-DDBJ) was elected as one of the Honorary Membership of the World Federation for Culture Collections (WFCC) on March 16, 2008, and was presented the inaugural WFCC Medal Award for his long time outstanding contribution to the WFCC activities.

Dr. Sugawara, has been committing to the worldwide activities of the WFCC over many years in particular to Newsletter editing, training, information dissemination, providing statistics on collections worldwide and not least the direction of the World Data Centre for Microorganisms(WDCM). He constructs and maintains the WDCM web site on his own laboratory web site. Through this web site, he continued to provide the scientific community for the microorganism researchers, as well as spread the useful information to all over the world. More recently he also contributed to establishment of OECD Global Biodiversity Information Facility (GBIF)) and the design of OECD Global Biological Resource Centre Network.

Appreciating his contribution to the WFCC for these years, the WFCC decided to elect him to the Honorary Membership of the WFCC and present the WFCC Medal, on the occasion of his retirement from the National Institute of Genetics(NIG). For the presentation ceremony, Dr. Ken-Ichiro Suzuki, Vice-President of the WFCC (and director of National Institute of Technology and Evaluation(NITE)) visited Mishima-city (where NIG is located) on March 24, 2008. Dr. Suzuki read for the message of Dr. David Smith, President of the WFCC, and handed the award medal to Dr. Sugawara. Many DDBJ staffs congratulated his honor at the ceremony, together with his family.
Dr. Suzuki presented the certificate certificate WFCC medal (small red box)

DDBJ Rel. 73 Completed Mar.27, 2008
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 73 on March 27, 2008/. DDBJ Release 73 consists of 83,167,582 entries, and the number of bases reached 86,099,950,395.
The periodical release and the new data are available by FTP download from the "FTP/Web API" page.
 
[Apology for mistaking a part of CON data for PLN division on the DDBJ Rel.72 and DAD Rel.43]
  • DDBJ Rel.72
    • File name: ddbjcon1.seq.gz, ddbjcon1.insd_xml.gz
    • Accession number: reference(3,514 data)
    • Current status: Correction of DDBJ rel.73 (release on March 27,2008)
  • DAD Rel.42
    • File name: ddbjcon1.DAD.gz
    • Accession number: reference(30,434 data)
    • Current status: Correction of DAD rel.43 (release in the first of Aplil,2008)
We apologize very much for your inconvenience, and appreciate your cooperation and understanding.

Release of new rat GSS 331,272 entries Mar.25, 2008
DDBJ newly released rat (Rattus norvegicus) GSS 331,272 entries, which had been submitted by Kyoto University.
The accession numbers are as follows;
DH508174-DH839445 (331,272 entries)
These entries were released as DDBJ daily updates on 3/25.
Anonymous FTP:Rattus_norvegicus_GSS_080325_1.seq.gz

Release of new human small RNAs, MGA 12,134 entries Mar.25, 2008
DDBJ newly released Homo sapiens small RNAs, MGA 12,134 entries,
which had been submitted by RIKEN Genome Sciences Center.
The accession numbers are as follows;
ADAAA0000001-ADAAA0005988 (5,988 Entries)
ADAAB0000001-ADAAB0006146 (6,146 Entries)
These entries were released as DDBJ daily updates on 3/19.
Anonymous FTP: AD_resource_index
Related URL: about MGA entry

NIG network service temporary down Mar. 21, 2008
NIG (National Institute of Genetics) network service will be unavailable at the following schedule, because of the emergency network maintenance. All DDBJ network services and NIG supercomputer (supernig) service will also be unavailable.
Date & Time : Mar 26 (Wed) from 17:00 to 20:00
Thank you very much for your understanding and cooperation.
Maintenance works was finished, and the services are resumed. Thank you for your cooperation.(March 26, 2008 at 19:50)

Correction of the invalid sequence version number for BA000010 and BA000044 Mar. 10, 2008
On 2008/02/19, BA000010 and BA000044 (CON division entries) were distributed with the invalid sequence version number by our operation mistake.
The correct versions were "BA000010.8" and "BA000044.2" respectively, but they appeared as "BA000010.9" and "BA000044.3".
Details are as follows:
  • Relevant accession numbers: BA000010, BA000044
  • Affected DDBJ services and period:
    - getentry /ARSA: 2008/02/19 - 2008/03/05
    - Anonymous FTP site: ftp://ftp.ddbj.nig.ac.jp/ddbj_database/ddbjnew/contig/
    DDBJNEWr72.086.CON.gz: Including the enties with invalid sequence version number ( BA000010.9, BA000044.3 ).
    DDBJNEWr73.014.CON.gz: Including the fixed enties.
  • Cause: A software problem in the flatfile making process.
  • Current status: We have already fixed and deleted the invalid version entries
    in 2008/03/08 on the getentry and annonymous FTP (Daily update).
  • We apologize for our mistake very much.
    [Monthly DDBJ Topic(March, 2008)] The directory of anonymous FTP was changed Mar. 7, 2008
    We DDBJ changed the anonymous FTP structure.The key changes lists are following,
    Changed directory names and structure
    There were divided into ddbj_database (the DDBJ data) and mirror_database (the other databases data) directories though the DDBJ data and the other databases data were put together in the database under a top directory so far.

    ---PAST---
    ftp://ftp.ddbj.nig.ac.jp/database/ :from the DDBJ data and from the other databases
    ---NOW---
    ftp://ftp.ddbj.nig.ac.jp/ddbj_database/ :from the DDBJ data
    ftp://ftp.ddbj.nig.ac.jp/mirror_database/ :from the other databases data

    Kind README
    Detailed data in the ddbj_database¡¤we made README.TXT
    - Notice -
    The Old directory(database) will be maintained one month. When regularaly watch, please change to the new directories.
    Pict1. A top position of anonymous FTP(2008.2.26)

    Pict2. A part of README.TXT
    [Monthly DDBJ Topic(March, 2008)] DDBJ started to release patent DNA by KIPOMar. 7, 2008
    We DDBJ released the patent data as a nucleotide sequence and an amino acid sequence that was accepted by Korean Intellectual Property Office (KIPO) and that being able to distribute. The KIPO's patent data is first time distribution. We released that data at February 21, 2008.

    Number of nucleotide sequence: 168,562 entries (93,982,299 base-pair)
    Number of amino acid sequence: 113,555 entries (16,499,605 amino-acid)

    ---Note---
    Besides the data of KIPO, International Nucleotide Sequence Database (INSD) (collaboration of DDBJ, EMBL and GenBank) distribute other patent data that was accepted by Japan Patent Office (JPO), European Patent Office (EPO) and United States Patent and Trademark Office (USPTO).
    For details, please refer to "Nucleotide Sequences Included Patent Applications" section of Patent, Intellectual Property and Priority page.

    The prefix of the accession number of KIPO patent is "DI". Please refer from the following to the example of the open to the public data.

    (ex) DI000001

    ---Note---
    So, the prefixes for patent related data are;
    JPO: E, BD, DD, DJ
    EPO: A, AX, CQ, CS, FB
    USPTO: I, AR, DZ, EA
    KIPO: DI

    The following figure shows summary of TOP 10 of number of ORGANISM in KIPO entries.

    This announce introduced the applied data from KIPO that distributed first time. In the future, DDBJ and KIPO will build a mechanism that regular acquisition and distribution KIPO data.

    韓国特許出願の塩基配列データが DDBJ より公開 2008.3.3
    DDBJ/EMBL/GenBank 国際塩基配列データベース(現在,DDBJ,EMBL,GenBankの三大データバンクはINSDC(International Nucleotide Sequence Database Collaboration)と呼ばれています。)」には,日本特許庁 (JPO),からの特許データの他に, 欧州特許庁 (EPO),米国特許 商標庁 (USPTO) が受理し公開可能となった特許データも,それぞれ EMBL, GenBank を経由し,公開されています。また,2008年2月より韓国特許庁 (KIPO) からも特許出願に含まれる塩基配列データが,DDBJ に取り込まれ,公開する仕組みが確立されました。
    この度公開された,韓国特許庁 (KIPO) からの特許出願塩基配列データは以下の通りです。
      entry number accession number
    DNA 168,562 DI000001-DI168562
    PROTEIN 113,555 DI500001-DI613555
    TOTAL 282,117  

    どちらも getentry より検索可能です。

    DDBJ started to release patent DNA data by KIPO Mar. 3, 2008
    DDBJ constraucts the International DNA Databases, with EMBL in Europe and GenBank in the USA.

    DDBJ, EMBL, and GenBank take the publishable patent DNA data into the INSD,
    mediating JPO, EPO and USPTO, respectively. And also from this February 2008,DDBJ started to take into and release patent related DNA data by KoreanIntellectual Property Office (KIPO)

    Following DNA and protein data from KIPO was released by DDBJ;
      entry number accession number
    DNA 168,562 DI000001-DI168562
    PROTEIN 113,555 DI500001-DI613555
    TOTAL 282,117  

    These entries are searchable by getentry.

    Note: DDBJ has been functioning as one of the International Nucleotide Sequence
    Database Collaboration, including EBI (European Bioinformatics Institute; responsible
    for the EMBL database) in Europe and NCBI (National Center for Biotechnology).
    Information; responsible for GenBank database) in the USA as the two other members.

    The directory of anonymous FTP was changed Feb. 26, 2008
    The directory structure of anonymous FTP was changed.
    The old directory "database" was divided to "ddbj_database" (DDBJ origin data)
    and "mirror_database" (mirror data of another database).

    For details of "ddbj_database", please see README.TXT in this directory.

    Old directory (database) is maintained for one month, If you watch
    regularlly, please change to new directory.

    GIB is unavailable for the urgent maintenance Feb. 26, 2008
    GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because of the urgent maintenance works, GIB is unavailable now. Resusme will be notified on this DDBJ HP. Thank you for your cooperation.
    The service was resumed at 16:22 on Feb. 26. Thank you for you cooperation.
    [Monthly DDBJ Topic(Feb., 2008)] Releasing millions of entries from DDBJ: What has the new computer system in a year brought with? Feb. 1, 2008
    In February 2007, DDBJ replaced the computer system and upgraded some of the application programs. In the meantime, DDBJ has been required to process millions of entries. The question here is if the new system has been able to satisfy the emerging requirements.

    You might recognize that you can hold your entries in a certain period or until the relevant paper are published. DDBJ should not disclose these Hold-Until-Published entries to the public. To retain them inside DDBJ, DDBJ stores these entries in a separate server from servers for data dissemination, e.g. getentry server.

    In the daily data release procedure shown in the following figure, DDBJ convert entries into the flat file format from the server for in-house data management to transfer them to other servers for such services to the public as getentry, ARSA, homology search and anonymous FTP



    This month (January 2008), DDBJ released about 1,500,000 entries only in two days; about 1,000,000 entries in the first day, and about 500,000 entries in the second day. It is to be noted that this process was completed as smoothly as designed. With the previous system, we were able to process only 350,000 entries in a day, namely, we had to spend more than 4 days to complete 1.5M entries.

    Although the mission was completed this time, we learned some lessons to improve the procedure further. You may claim that "2 days" is not quick enough. The system engineers in charge started the discussion to improve the concordance of several servers to gain higher throughput than ever.

    We would appreciate it very much, if you remember the group of hard working system engineers especially when you see the announcement of massive data release.

    Update of the databases related to the H-Invitational Feb. 1, 2008
    The contents of the databases related to the H-Invitational were
    updated. The main contents of the update are the following.
    • The number of cDNA (HIT; H-Invitational transcript) entry has changed
      from 175,536 to 187,156.
    • The number of LOCUS (HIX; H-Invitational cluster) entry has changed from
      34,699 to 36,073.
    • The version of our mirror H-Invitational Database (H-InvDB) was upgraded
      from "4.6" to "5.0".

    [Databases related to the H-Invitational project]

    ARSA database search (DDBJ, DAD) temporary unavailable Jan. 21, 2008
    ARSA is a high-speed data retrieval system provided by DDBJ through WWW.
    At the following schedule, DDBJ and DAD database search is unavailable for the database update. Details are as follows:
    • Date & Time: January 29, 2008(Tus) 9:00 - 18:00 (resume will be notified on this DDBJ HP)
    • Suspended services:
      • DDBJ and DAD search in ARSA
      • From the TXSearch, link to ARSA
      • From search window item DNA on the DDBJ top page, link to ARSA
    • Note: During the above period, ARSA is still available except for the above 2 databases search.
      If you would like to hasten to the search of the above 2 databases, please substitute SRS.
    • Alteration:In the DDBJ database in the ARSA, amino acid translation in the CDS feature was excluded from the specifiable features from this release72.
      In the ARSA, nucleotide sequense data is also not included in the query values.

    Thank you for your understanding and cooperation.
    Maintenance works finished. Thank you for your cooperation.(Jan. 29, 2008 at 18:00)

    DAD rel. 42.0 was released Jan. 21, 2008
    DDBJ amino acid database (DAD) Release 42 was released on 1. 8, 2008 at DDBJ. DAD Release 42.0 consists of 11,715,518 entries,
    and the total number of residues reached 2,995,558,433.
    FTP site for DB download

    [URGENT] Supernig temporary down Jan. 22, 2008
    Supernig (NIG supercomputer system) is unavailable today,
    because of the emergency network maintenance.
    All DDBJ network services and NIG supercomputer (supernig) service will also be unavailable.
    Date & Time:January 22 (Tue), 2008 from 15:00 to 16:00 (JST)
    Thank you very much for your understanding and cooperation.
    Maintenance works finished, and the services are resumed. Thank you for your cooperation.(21:00)

    Report for DDBJ activicies in NAR Jan. 16, 2008
    The new and significant DDBJ activities of the year 2007 were introduced in the following paper appeared in Nucleic Acids Research Vol.36 Database Issue (Jan, 2008 ).

    "DDBJ with new system and face"
    H. Sugawara, O. Ogasawara, K. Okubo, T. Gojobori and Y. Tateno
    Nucleic Acids Research, 2008, Vol. 36, Database issue D22-D24
    (Summary) DDBJ activitiew of 2007 (Data submissions and release, New Computer System, ARSA(New keyword search system) enhancement, etc).

    NIG and DDBJ network services temporary down Jan. 11, 2008
    NIG (National Institute of Genetics) network service will be unavailable at the following schedule because of the SuperSINET maintenance.
    DDBJ network service and NIG supercomputer (supernig) service will also be unavailable.
    • Date:January 16(W), 2008 at 12:00 - 13:00 JST
      10 minutes interception during the above time

    Thank you very much for your understanding and cooperation.

    [Monthly DDBJ Topic(Jan., 2008)] Releasing millions of entries from DDBJ: What has the new computer system in a year brought with? Feb. 1, 2008
    GIB(Genome Information Broker) started the delivery of update information by RSS. You will be notified whenever new genomes are added or existing genomes are updated, if you register the GIB RSS site by use of an RSS reader.
    What is RSS?
    RSS is a shortened name of Rich Site Summary or Really Simple Syndication, and a number of web site has used to push the information on headline, outline, update date, the link to the web site and so on to the user.
    How to read RSS ?
    You can subscribe to RSS of any Web site by Google, Yahoo! and other portal sites, if you are a registered user of the portal site. Please find the example of subscription in the following in the case of Goole:
    Why you should use RSS?
    You need not visit the site every morning to find what's new. You will be notified by the site that the site is updated. In the case of GIB RSS, the list of new genomes and updated genomes is delivered to you. You click the genome of you interest in the list and you are directly guided to the web page of the genome that you choose.
    How to register to the GIB RSS
    You may want to install a program of RSS reader by yourself, instead of using Google, Yahoo! or other portal sites. We explain the usage of RSS program installed in Windows machine:
    • Install a RSS reader. The following figure is RssReader
    • Register RSS delivery site of GIB(http://gib.genes.nig.ac.jp/rss.php) to the installed RSS reader.
    How to register to the GIB RSS
    You may want to install a program of RSS reader by yourself, instead of using Google, Yahoo! or other portal sites. We explain the usage of RSS program installed in Windows machine:
    1. Install a RSS reader. The following figure is RssReader(http://www.rssreader.com/)。
    2. Register RSS delivery site of GIB(http://gib.genes.nig.ac.jp/rss.php) to the installed RSS reader.
    3. The line of GIB is added.
    4. Select the GIB line (the box 3 in the figure) and the list from GIB is displayed.
    5. Choose one of the genomes in the list (the box 4 in the figure) and you will know if it is updated or newly added.

    Please forward your request to this type of alert system and we will expand RSS to other DDBJ services

    DDBJ Rel. 72 CompletedDec. 25, 2007
    The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 72 in December 25, 2007. DDBJ Release 72 consists of 79,004,098 entries, and the number of bases reached 82,592,245,487.
    The periodical release and the new data are available by FTP download from the "FTP/Web API" page.
    As was already notified, DDBJ proceeded deletion of the both phone and fax numbers, and E-mail address from the flat files of the entries submitted to DDBJ. The retrofit of the all entries was completed by the issue of this release 72. Hereafter, database users become difficult to contact submitters based on the information described in the DDBJ flat files. When you wish to contact to the submitter(s) of an entry of your interest, please contact us using the prescribed inquiry form placed in the DDBJ HP.