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DDBJ
No.62 & 63  Sep. 2, 2011
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 "Obon"
obon There is an event called "Obon" from August 13th to the 16th in Japan, during which Japanese worship the spirits of their ancestors. It is believed the spirits return to their families during Obon.
In the season, there are a lot of summer festivals like fireworks show or Obon dances at everywhere in Japan. Summer festivals have developed as an event to console the spirits of the dead.
The Mishima summer festival was held for three days from August 15th to 17th. During the festival the sounds of the musical phrase called "Mishima Shagiri" echo throughout town.
DDBJ issues DDBJ Mail Magazine (No.62 & 63). If you have any questions and suggestions about Mail Magazine, please do not hesitate to write ddbjmag@ddbj.nig.ac.jp . We would like to hear from you.
This photo shows the date of Mishima summer festival → Usually
 DDBJ HP renewal
DDBJ renewed HP in August 1, 2011, and changed the following points.

RSS of "Update information" in the top page was shifted to getentry.
In the top page, a new RSS for the latest news such as "Hot Topics" starts. So, please change settings.

The twitter icon is set up in top page. "Follow", please.

Google Search is applied to the "Site Search".

Thank you for your understanding and cooperation.
 DDBJ will launch a new resource "BioProject"
The BioProject database represents a higher order organization of research projects and the corresponding data which is deposited into several archival databases maintained by members of the INSDC. Data submitted to INSDC-associated databases cross-reference the BioProject identifier to support navigation between the project and the project's datasets. At the DDBJ, records in the following DDBJ archival databases are grouped: DDBJ nucleotide sequence database, Sequence Read Archive and Trace Archive. The BioProject record has information about a project's scope, material, objectives, funding source and general relevance categories. The BioProject resource is a redesigned, expanded, replacement of the NCBI Genome Project resource.
The DDBJ BioProject issues internationally-recognized accession numbers with the prefix 'PRJD' to the submitted projects. Public project data are exchanged with the EBI and NCBI.

* The BioProject resource is released in phases. After the release of interactive submission system, we will start to accept new BioProject submissions.
And a new directory "bioproject" was added under "ddbj_database" of DDBJ anonymous FTP site. All of released data from DDBJ BioProject will be available at the new "bioproject" directory.
About the "ddbj_database" directory and its sub-directories, please refer to the README.TXT in the directory. If you monitor the DDBJ anonymous FTP, please confirm your monitoring program if necessary.
 The fax number changed to "Mandatory" of SAKURA
SAKURA is a nucleotide sequence data submission system through the WWW server at DDBJ.

The input of the fax number changed to "Mandatory(Marked with )" on 15 August 2011. You can't proceed further if you fail to fill up any one of the fields.


Generally, DDBJ contacts submitters via E-mail. However, in case of breakdown of communication via E-mail by any reason, DDBJ would contact submitters via fax.
So, please let us know your fax number, if possible.

Please choose "If you do not have any fax machine, please check it." if you do not have the fax.
Thank you for your understanding and cooperation.
 Directory and file names for quality scores was changed
DDBJ changed directory and file names for quality scores of anonymous FTP, on 23 August 2011.

   FTP server ftp://ftp.ddbj.nig.ac.jp/

   directory name ;
   from /ddbj_database/ddbjnew/qvalue/
   to /ddbj_database/ddbjnew/qscore/

   file name ;
   from DDBJNEWr##.###.qvalue.gz
   to DDBJNEWr##.###.qscore.gz

For details, please see README.TXT.
If you automatically monitor DDBJ anonymous FTP, please confirm your monitoring program if necessary.
 Release of sequence data from DDBJ (Jul. - Aug. 2011)
DDBJ newly released EST data derived from sea squirt (Halocynthia roretzi), which had been submitted by University of Tokushima.

Reference: MAGEST

The accession numbers are as follows ;
  • FY844421-FY896670 (52,250 entries)    (Available by getentry)
DDBJ newly released WGS and scaffold CON data derived from Acropora digitifera, which had been submitted by Okinawa Institute of Science and Technology.

Reference:

The accession numbers are as follows ;
  • WGS                BACK01000001-BACK01053640 (BACK.gz) (53,640 entries)
  • scaffold CON     DF093604-DF097774 (4,171 entries)
DDBJ newly released TSA and EST data derived from Botryococcus braunii, which had been submitted by National Institute for Environmental Studies.

The accession numbers are as follows ;
  • TSA data FX056085-FX112549 (56,465 entries)
  • EST data FY358876-FY368220 ( 9,345 entries)
 Patent column from DDBJ
1. Patent data distribution for Japan Patent Office (JPO)
Hideo Aono
DDBJ Patent Annotator
1. Introduction
In this column, I would like to introduce about patent data exchange in the International Nucleotide Sequence Databases (INSD) and Japan Patent Office (JPO) data.

2. Data distribution from INSD
DDBJ is constructing INSD with EMBL-Bank in EBI (European Bioinformatics Institute) and GenBank in NCBI (National Center for Biotechnology Information).
INSD distributes not only scientific data but also patent data transferring from each patent office as follows.
   *Japan: Japan patent office (JPO) → DDBJ
   *South Korea: Korean Intellectual Property Office (KIPO) → DDBJ
   *USA: United States Patent and Trademark Office (USPTO) → GenBank
   *Europe: European Patent Office (EPO) → EMBL-Bank

Patent data contains nucleotide sequence and amino acid sequence. After distributed nucleotide sequence data, it was exchanged among INSD. However, INSD does not exchanged amino acid data.
DDBJ distributes JPO and KIPO amino acid data on DDBJ anonymous FTP site.

DDBJ anonymous FTP:
   JPO file: jpo_ddbj_aa*.seq.gz (*=file number)
   KIPO file: kipo_ddbj_aa.seq.gz

3. Patent data summary for JPO
3-1) JPO data
DDBJ distributes nucleotide sequence and amino acid data containing publication of unexamined patent applications. Therefore, new distribution sequences do not have the patent right. When you would like to confirm the progression status of patent examination, you need checking the registration status using by retrieval site for IPDL (Industrial Property Digital Library) in Japan.

3-2) Kinds of JPO patent data and distribution frequency
DDBJ receives three kind of patent data from JPO;
  1. Publication of patent applications
  2. International application published under the Patent Cooperation Treaty (PCT)
  3. Japanese translations of PCT international publication for patent applications

DDBJ distributes the regular data at once a month and infrequently irregular data in some cases.

3-3) Patent data contents
JPO data of DDBJ flat file (FF) has enough information such as the front page of patent publication by the following contents; sequence, organism name, invention title, applicant name(s), inventor name(s), publication number, publication date, application number, application date, priority date, comment and sequence's feature information.

  Example: DL000001

3-4) Patent applied sequence submission to DDBJ
If you have sequence(s) for patent application, you do not have to submit to DDBJ. Because JPO transfers those sequences to DDBJ and your sequence(s) will be opened to the public through DDBJ. However, if you need the accession number to submit a paper before apply for a patent, you should care since sequence becomes public knowledge in case of released from DDBJ. In this case, please confirm to JPO before your submission.

4. Author comments
I hope to help understanding about JPO patent data. I will introduce about KIPO data and retrieval method of patent sequence in KIPO related organization at next column.

To be continued.
  ddbjmag@ddbj.nig.ac.jp
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