DDBJ Mail Magazine No.66 & 67


No. 66 & 67   Jan. 23, 2012
Latest version    Backnumber    Published by DDBJ


Kunozan Toshogu Shrine
The Kunozan Toshogu shrine is located in the city of Shizuoka.
It was founded by Tokugawa Hidetada to enshrine Ieyasu based on the last wishes of Tokugawa Ieyasu. It is the oldest one among the Toshogu Shrine of the country.
The buildings were built with the state of arts technology and the highest level of artistry during the Edo period. It is a part of national treasures in December 2010.
They are located at the top of Mt. Kuno and can command a whole view of the Suruga Bay. You can enjoy the great view of Mt. Fuji on a fine day.

DDBJ issues DDBJ Mail Magazine (No.66 & 67). 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.
DDBJ Rel. 88.0, DAD (DDBJ amino acid database) Rel. 58.0 Completed
DDBJ Rel. 88.0 - Since DDBJ is planning to improve its systems substantially, during the first quarter in 2012, DDBJ will skip to make up its next periodical release in March 2012.
So, DDBJ periodical release 89 will be prepared in June 2012.

DAD (DDBJ amino acid database) Rel. 58.0 - Since DDBJ is planning to improve its systems substantially, during the first quarter in 2012, DDBJ will skip to make up the next periodical release of DAD in March 2012.
So, DAD periodical release 59 will be prepared in June 2012.
DDBJ/EMBL/GenBank Feature Table Definition revised
Feature Table Definition (FT-Doc) is the common annotation manual among the three banks (DDBJ, EMBL-Bank, GenBank) for the construction of the DDBJ/EMBL/GenBank International Nucleotide Sequence Database. Feature Table Definition was revised in December 2011. Version is 10.0.
Report for DDBJ activities in NAR
DDBJ activities were introduced in the following papers appeared in Nucleic Acids Research Vol.40 Database Issue.

"The International Nucleotide Sequence Database Collaboration"
Ilene Karsch-Mizrachi, Yasukazu Nakamura, and Guy Cochrane on behalf of the International Nucleotide Sequence Database Collaboration
Nucl. Acids Res. 2012 40: D33-D37; doi:10.1093/nar/gkr1006.

"The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments"
Yuichi Kodama, Jun Mashima, Eli Kaminuma, Takashi Gojobori, Osamu Ogasawara, Toshihisa Takagi, Kousaku Okubo, and Yasukazu Nakamura
Nucl. Acids Res. 2012 40: D38-D42; doi:10.1093/nar/gkr994.

"The sequence read archive: explosive growth of sequencing data"
Yuichi Kodama, Martin Shumway, and Rasko Leinonen on behalf of the International Nucleotide Sequence Database Collaboration
Nucl. Acids Res. 2012 40: D54-D56; doi:10.1093/nar/gkr854.
Release of sequence data from DDBJ (Nov. 2011 – Jan. 2012)
DDBJ newly released full length enriched cDNA sequence (HTC) data derived from pig (Sus scrofa), which had been submitted by National Institute of Agrobiological Sciences.   (Available by getentry )

The accession numbers are as follows ;

  • AK389169 - AK401026 ( 11,858 entries)
DDBJ newly released WGS and scaffold CON data derived from Hitomebore rice (Oryza sativa Japonica Group cv. Hitomebore), which had been submitted by Iwate Biotechnology Research Center.

The accession numbers are as follows ;

  • WGS                BACJ01000001 - BACJ01064745 (BACJ.gz) ( 64,745 entries)
  • scaffold CON     DG000053 - DG000064 ( 12 entries)
DDBJ newly released 5'SAGE tags, MGA data, derived from human (Homo sapiens), which had been submitted by University of Tokyo.

The accession numbers are as follows;

  AEAAA0000001-AEAAA0026367 (26,367 entries)
  AEAAB0000001-AEAAB0012114 (12,114 entries)
  AEAAC0000001-AEAAC0021096 (21,096 entries)
  AEAAD0000001-AEAAD0024262 (24,262 entries)
  AEAAE0000001-AEAAE0023437 (23,437 entries)
  AEAAF0000001-AEAAF0030485 (30,485 entries)
  AEAAG0000001-AEAAG0021798 (21,798 entries)
  AEAAH0000001-AEAAH0040734 (40,734 entries)
  AEAAI0000001-AEAAI0029614 (29,614 entries)
  AEAAJ0000001-AEAAJ0030206 (30,206 entries)

Anonymous FTP: AE_resource_index
Related site: About Mass sequence Genome for Sequence (MGA) entry
Patent column from DDBJ
3. Flat File structure for Japan Patent Office (JPO) -First part-

Hideo Aono
DDBJ Patent Annotator

Introduction
I introduced about patent data of Japan Patent Office (JPO) in first column and Korean Intellectual Property Office (KIPO) in second column. In this time, I would like to explain about Flat File (FF) structure for JPO nucleotide and amino acid sequence data as two parts. I will introduce about JPO data property, summary of FF structure and relationship between patent application contents and description part on FF in first part.

1. Property of JPO data FF
JPO data FF has fundamental application information of patent publication compared with FF for United States Patent and Trademark Office (USPTO) and European Patent Office (EPO). Because JPO makes the submission file (Fig. 1) containing application information based on WIPO (World Intellectual Property Organization) ST 25 format submitted from applicants. Thereafter, DDBJ makes FF reflected almost contents of JPO submission file (Fig. 2).

Fig.1 Example of JPO submission file


2. FF structure and description contents
I showed FF structure for nucleotide sequence data dividing by six parts (LOCUS Block, SOURCE Block, REFERENCE Block, COMMENT Block, Feature Block and Sequence Block) as different color with sample data and description contents in Fig. 2.

Fig. 2 Correspondence relation of JPO nucleotide sequence data

Each Block name of symbol alphabet is as follows;
[A] LOCUS Block, [B] SOURCE Block, [C] REFERENCE Block, [D] COMMENT Block, [E] Feature Block, [F] Sequence Block


3. Patent application contents on FF
I showed correspondence relationship between patent application contents and description parts on JPO FF (Table. 1).

Table. 1 Application contents and description parts on JPO FF
Contents of patent application Describing line on JPO FF
Publication number DEFINITION line [A], KEYWORDS line [A], JOURNAL line [C], PN line [D]
Publication date JOURNAL line [C] , PD line [D]
Application number PF line [D]
Application date PF line [D]
Applicants JOURNAL line [C]
Inventors AUTHORS line [C], PI line [D]
Invention title DEFINITION line [A], TITLE line [C]
Priority application number PR line [D]
Priority date PR line [D]
Feature information FT line [D]
Organism name (JPO submission file) OS line [D]
Organism name (converted name in DDBJ) SOURCE line [B], ORGANISM line [B], /organism qualifier [E]
* Alphabet symbol after line name is corresponding to FF Block part in Fig. 2.

Patent application information is described mainly at [C] REFERENCE Block and [D] COMMENT Block. Amino acid sequence data is also described on same Blocks. Invention title is set on both DEFINITION line of [A] LOCUS Bloc and TITLE line of [C] REFERENCE Block.
In specially, applicants name is only set JOURNAL line on [C] REFERENCE Block (Fig. 3).

Fig. 3 [C] REFERENCE Block

Author comments
At second part, I will explain each line description of six Blocks in detail. Moreover, I would like to introduce the conversion process of organism name from JPO submission file in DDBJ.
Published by:DNA Data Bank of Japan (DDBJ)
Center for DNA Data Bank of Japan
National Institute of Genetics (NIG)
Research Organization of Information and Systems
1111 Yata, Mishima, Shizuoka 411-8540, JAPAN

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