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DDBJ
No.64 & 65  Nov. 2, 2011
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 "Sesame"

I grew sesame(Sesamum indicum) and harvested it. As for the photograph, the fruit of the sesame is shown. You can find sesame in this fruit as seed. This plant could be grown everywhere and does not require time and effort. However, the sesame consumed in Japan is imported in 99.9%.
The sesame which just gathered a harvested is a good aroma. Let's challenge cultivation of sesame.
DDBJ issues DDBJ Mail Magazine (No.64 & 65). If you have any questions and suggestions about Mail Magazine, please do not hesitate to write to us. We would like to hear from you.
 (11/11-14) DDBJ network services are unavailable for power outage of the NIG
DDBJ network services will be unavailable at the following schedule because of the electric power outage of the NIG(National Institute of Genetics). Please note that the suspended period depends on the service.
Services Scheduled (JST)
DDBJ Read Annotation Pipeline Nov. 11 (Fri) 12:00 - Nov. 14 (Mon) 12:00
SAKURA Nov. 11 (Fri) 13:00 - Nov. 14 (Mon) 12:00
D-way, DRA, DTA, BioProject, CIBEX,
getentry, ARSA,
BLAST, ClustalW,
TXSearch, Vector Screening System,
GIB, Anonymous-FTP, WAGI
Nov. 11 (Fri) 15:00 - Nov. 14 (Mon) 12:00
DDBJ HP Nov. 11 (Fri) 17:00 - Nov. 12 (Sat) 18:00
Thank you for your cooperation and understanding.
 DDBJ starts BioProject services
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 INSDC. Data submitted to INSDC-associated databases cross-reference the BioProject identifier to support navigation between the project and the project's datasets.
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.

You need to obtain an account of DDBJ submission portal 'D-way' to submit your project data. Please obtain an account according to the submission account manual and submit your project data from the D-way website.

D-way Submission Account Manual (Japanese)
D-way Submission Account Manual (English)

If you have questions, please contact us.
 The Report for the 24th International Collaborators Meeting
International Nucleotide Sequence Database Collaboration (INSDC), consisted of DDBJ, EBI and NCBI, hold the international collaborators meeting every year.

In 2011, the meeting was held at Osaka in Japan, 23-27 May, to discuss practical matters to maintain and update nucleotide sequence data archives; DDBJ, EMBL-Bank, GenBank, Sequence Read Archive (SRA) and Trace Archive.
Though there were still aftermaths of the Great East Japan Earthquake, DDBJ could host ICM2011 with understanding and cooperation of NCBI and EBI.
The outcomes of the meeting are summarized here.
 DDBJ Rel. 87.0, DAD (DDBJ amino acid database) Rel. 57.0 Completed
DDBJ Rel. 87.0
DAD (DDBJ amino acid database) Rel. 57.0
  • Date: Sep. 26, 2011
  • 21,596,317 entries    6,173,068,786 aa (total number of residues)
  • DAD Release Note
 Resumed GIB
GIB has been resumed since October 3, 2011.
For electricity conservation, we stopped and kept you waiting for a long time.
Please use it.
 Release of sequence data from DDBJ (Sep.- Oct. 2011)
DDBJ newly released WGS and scaffold CON data derived from sake yeast (Saccharomyces cerevisiae Kyokai no. 7), which had been submitted by National Research Institute of Brewing.

   Reference: Sake yeast genome database (SYGD)

The accession numbers are as follows;
  • WGS: BABQ01000001 - BABQ01000705 (BABQ.gz) ( 705 entries)
  • scaffold CON: DG000037 - DG000052 ( 14 entries)
  • mitochondrion: AP012028
DDBJ newly released EST and full length cDNA sequence data derived from silkworm (Bombyx mori), which had been submitted by National Institute of Agrobiological Sciences.

  Reference: Silkworm Genome Research Program (SGP)

The accession numbers are as follows;
EST:
FS724152 - FS939542 ( 215,391 entries)
FY736910 - FY762881 ( 25,972 entries)

full length cDNA (including HTC):
AK377185 - AK388575 ( 11,160 entries; 231 entries dropped)
DDBJ newly released WGS and scaffold CON data derived from a liver fluke (Clonorchis sinensis), which had been submitted by Sun Yat-sen University (China).

The accession numbers are as follows ;
  • WGS: BADR01000001 - BADR01060778 (BADR.gz) ( 60,778 entries)
  • scaffold CON: DF126616 - DF142827 ( 16,212 entries)
DDBJ newly released WGS and scaffold CON data derived from a liver fluke (Clonorchis sinensis), which had been submitted by Sun Yat-sen University (China).

The accession numbers are as follows ;
  • WGS: BADR02000001 - BADR02006190 (BADR.gz) ( 6,190 entries)
  • scaffold CON: DF142828 - DF145382 ( 2,555 entries)
 Patent column from DDBJ
2. Patent data distribution for Korean Intellectual Property Office (KIPO)

Hideo Aono
DDBJ Patent Annotator
Introduction
In previous column, I introduced about patent data for Japan Patent Office (JPO). In this column, I would like to introduce about patent data of Korean Intellectual Property Office (KIPO) and data search service in DDBJ.
DDBJ has just distributed some of KIPO data. Therefore, I would like to introduce also search service of patent applied sequence at Korean Bioinformation Center (KOBIC) and Korea Intellectual Property Rights Information Service (KIPRIS) as KIPO related organization.

Summary of KIPO data
DDBJ has provided the nucleotide sequence and amino acid sequence containing publication of unexamined patent applications from KIPO since March 2008.

KIPO data is transferred to DDBJ as follows;
  1. KIPO sends the patent sequence data to KOBIC.
  2. By cooperation of Dr. Byungwook Lee in KOBIC, KIPO submission files are made by him and transferred
      from KOBIC to DDBJ.
  3. DDBJ exchanges the data format and distributes KIPO data.

DDBJ distributed the following 282,161 entries assigned the prefix "DI" of KIPO accession number, until now.
KIPO data submission is suspended by the problem of submission format from April 2009. Therefore DDBJ is discussing about efficient method for data exchange with KOBIC and KIPO.

Nucleotide sequence data : DI000001 - DI168562 (168,562 entries)
Amino acid sequence data : DI500001 - DI613599 (113,599 entries)

Please see Data example of Fig.1 and Fig.2.
Fig.1, DI000001 (nucleotide sequence)


Fig.2, DI500001 (amino acid sequence)

Data search for KIPO data
[DDBJ]
DDBJ provides the search service for KIPO nucleotide and amino acid sequence (Table.1).

Table.1, KIPO data of DDBJ search services
  getentry
  ARSA   BLAST  File ftp service
 Nucleotide sequence     Ο
    Ο
    Ο  PAT division files (*1) in DDBJ release
 Amino acid sequence     Ο     ×
    Ο  Cumulated file on DDBJ anonymous site (*2)
  *1 KIPO nucleotide data is contained in PAT division files (ddbjpat[N].seq.gz) .  [N]:  File number
  *2 Cumulated file (kipo_ddbj_aa.seq.gz) has all KIPO amino acid data.


[Korean Bioinformation Center (KOBIC)]
PATOME@Korea is Koran patent database for nucleotide and amino acid sequence in KOBIC. "PatSeq DB search" can search by application number, applicant name, invention title in English. In addition, PATOME@Korea provides the similarity search for DNA and protein against patent applied sequences in Korea (Please see Fig.3).

Fig.3, Top page of PATOME@Korea;

[Korea Intellectual Property Rights Information Service (KIPRIS)]
KIPRIS is the search system of Korean patent publication. PATOME@Korea can search the patent publication in Korean. In contrast, "KPA (Korean Patent Abstracts)" search of KIPRIS can refer the front page and abstract of patent publication in English retrieved by keyword, application number, publication number, applicant name and inventor name (Please see Fig.4). K2E-PAT (Korean to English Patent Automatic Translation) has pay service for the provision of full text by English machine translation.

Fig.4, "KPA" search page of KIPRIS;

Author comments
KIPO suspends their submission to DDBJ. We will restart KIPO submission as soon as possible.
At next column, I will introduce about the structure of DDBJ Flat Files (FF) for JPO patent data.

To be continued.
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