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DDBJ Mail Magazine
No.37    May 13, 2008
top Latest version top    backnumber backnumber    ddbjPublished by DDBJ

sakura road sakura-1 From early spring, there are a lot of different kind of cherry blossoms in our institute, and which looks like botanic garden. At the public open day (5th of April, 2008) , many people with family visited us and enjoyed their fine view, and also each research laboratory showed intersting exhibisions. Please come to see our public open day next year which is held in the best cherry blossom season every year. We might amuse you so much.
If you have any questions and suggestions about DDBJmag, please do not hesitate to write ddbjmag@ddbj.nig.ac.jp . We would like to hear from you!!
  DDBJ Released Korean Patent Data
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)
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
So, the prefixes for patent related data are;

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.
 Change the DDBJ anonymous FTP
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.
ftp://ftp.ddbj.nig.ac.jp/database/ :from the DDBJ data and from the other databases
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
Helpful 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
  Dr. Hideaki Sugawara received the WFCC award
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.
sugawara_suzuki WFCCmessage WFCCmessage
Dr. Suzuki presented the certificate certificate WFCC medal (small red box)
 Release of sequence data from DDBJ
Release of new silkworm ( Bombyx mori ) genome sequence data
DDBJ newly released silkworm ( Bombyx mori ) genome sequence data which had been submitted by National Institute of Agrobiological Siences.
The accession numbers and numbers of entreis are as follows;
  • WGS ( Bombyx_mori_WGS_080423_1.seq.gz )
    BABH01000001-BABH01088672 ( 88,672 entries)
  • scaffold CON ( Bombyx_mori_CON_080423_1.seq.gz )
    DF090316-DF092116 ( 1,801 entries)
  • GSS (fosmid end) ( Bombyx_mori_GSS_080423_1.seq.gz )
    DE143284-DE189151 ( 45,868 entries)
    DE246947-DE248527 ( 1,581 entries)
    DE420876-DE647768 ( 226,893 entries)
  • GSS (BAC end) ( Bombyx_mori_GSS_080424_1.seq.gz )
    DE378561-DE420875 ( 42,315 entries)
  • HTG (BAC clone) ( Bombyx_mori_INV_080423_1.seq.gz )
    AP008992-AP009041 ( 50 entries)
    These entries were released as DDBJ daily updates on 4/23 and 4/24.
    FTP site for DB download
  • Release of new rat GSS 331,272 entries
    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
    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
     DDBJ Rel. 73 Completed
    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.
     Update of the H-Invitationa related the databases
    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) entries has changed
    • from 175,536 to 187,156.
    • - The number of LOCUS (HIX; H-Invitational cluster) entries 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]
     The 7th Japan-Korea-China Bioinformatics seminer was held in Korea (March 18-21, 2008)
    From Mar.18 to 21, the 7th Japan-Korea-China Bioinformatics Training Course was held at Jeju University, Korea. From Japan, there were 10 attendees with the Korean and Chinese researchers of Bioinformatics filed and were lectured and joined practical works in English. This training course was targeted to the young Japanese, Korean and Chinese researchers, and also purposed to be used as the social exchange.
    From DDBJ, Prof. Gojobori, Prof.Tateno and Prof. Saitou had served as the lecturers.
     Retirement and leaving of DDBJ staff
    Professor Hideaki Sugawara (director of CIB) and Professor Yoshio Tateno (director of DDBJ) retired on 31st of March 2008. They would continue acting as specially appointed professors.
    Dr.Jun Ogura (Assistant Professor) left DDBJ on 28th of February 2008, and who works as assistant professor in Ochanomizu University. Dr.Yoshiaki Minezaki changed for new section Targeted Proteins Research Program as research associate from 1st of April 2008.
     Errata for DDBJ Entries
    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.

    Published by:
    DNA Data Bank of Japan (DDBJ)
    Center for Information Biology and DNA Data Bank of Japan (CIB-DDBJ)
    National Institute of Genetics (NIG)
    Research Organization of Information and Systems
    1111 Yata, Mishima, Shizuoka 411-8540, JAPAN