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DDBJ Mail Magazine
No.40    Nov. 10, 2008
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  Fine weather in autumn
sky from DDBJ It's getting more and more cold and the sky clears nicely nowadays. We can see the Mt.Fuji with beautiful shape from here DDBJ which is located in Mishima-city Shizuoka. The visibility tends to be better during the cold season than in summer. Recently, we can see the top of it begins to be covered by snow. But it is surprising that the first snow cap date of this year was August 9th. It's 58 days earlier than last year's. The record has broken for the first time in 94 years. I wonder that it might be caused by the global warming.
By the way, enjoy a temporary nice weather and sceneries in autumn.
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.
  New function is added to ARSA
ARSA is a high-speed data retrieval system provided by DDBJ via WWW and Web API . As a functional enhancement of ARSA retrieval system, a new function is added.
It is the function "!" (AND NOT condition) as a logical operator which is used to connect keywords when you specify multiple keyword for a search in Quick search and etc.
The following is a retrieval that you can do by this function.
  • Search: Searching for the entry that contained "lung cancer" but not contained "Homo sapiens" in Quick search.
  • How to enter: Enter the keywords with "!" on the search box like the below.

    "lung cancer"!"Homo sapiens"

    ARSA

  • Result: Displayed the entries that contained "lung cancer", but not contained "Homo sapiens".
It enable us to use "!" (AND NOT conditions) when entering multiple search conditions in a single field. Please refer to the HELP for more details.
DDBJ will do all the more efforts for the development of ARSA. If you have any comments for ARSA, please send it from "Your comment" which is located in the upper blue zone of ARSA.
 Release of sequence data from DDBJ
Release of new Physcomitrella patens subsp. patens EST 56,525 entries
DDBJ released Physcomitrella patens subsp. patens EST 56,525 entries, which had been submitted by National Institute of Genetics .
The accession numbers are as follows;
  • DC901515-DC958039 (56,525 entries)
These entries were released as DDBJ daily updates on Oct. 1.
FTP site for DB download : Physcomitrella_patens_subsp._patens_EST_081001_1.seq.gz
Related site:
 Exhibit the DDBJ booth in BMB 2008
BMB 2008 (Joint Annual Meeting of the Molecular Biology Society of Japan and the Japanese Biochemical Society, 2008) is being held at Kobe Port Island from Dec. 9 (Tue) to 12 (Fri).
DDBJ has the booth in the exhibition that belongs to the event. The posters to introduce the activities and the services of DDBJ are displayed and some information paper is distributed there.
 Termination of providing SRS (Sequence Retrieval System) services  [Re-announcement]
DDBJ terminates providing SRS services (by WWW/WABI )as of the December 26, 2008. We appreciate very much using SRS since SRS was firstly launched by WWW in 1999. We apologize for your labor swiching your keyword searh system from SRS to ARSA, but, we hope ARSA is useful for all DDBJ users. Please refer the description of ARSA and SRS shown in below.
(1) ARSA and SRS Search functions
               A R S A S R S
Search
 Engine
High-speed XML database search engine "Interstage Shunsaku" was applied for the nucleotide sequence database retrieval Keyword search system developed by EBI(European Bioinformatics Institute) was applied and reconstructed for the DDBJ database retrieval
Key Features
  • Rapid response: Even in any complexed search keys, the results are returned within 5 seconds
  • In the DDBJ database retrieval, any combination of feature/qualifiers used in the DDBJ flat file format can be specified as search keys
  • Wide variety of WEB API programs such as SOAP/REST is applicable
  • From Quick Search (simple keyword search) to Advanced Search (specify a complexed search queries), multistage search condition can be selectable.
  • Wide variety of WEB API programs such as SOAP/REST is applicable
functions ARSA SRS
Cross search of multiple DB  Yes   Yes 
Specifying the search field  Yes   Yes 
Use of DDBJ flat file Feature/Qualifier  Yes   No 
Keyword search using the frequently  Yes   Yes 
Multiple keywords connection using and/or/not Yes*  Yes 
Relation to analysis tools  Yes   Yes 
Speed fast slow
*: Use of "not" in Quick Search is in being enhanced (as of Aug. 2008)
(2) ARSA Improvment History

    No. of
DBs
2004.12 Trial operation started at the DDBJ HP
"DDBJ" and "DDBJNEW" only
 2 
2005.12 Upgraded
Full-time operation started
 
2007.02 21DBs other than DDBJ was added  23 
2007.07 Extensive Enhancement and transfer to Official Operation
<Main New Functions>
  • The search results can be downloaded across databases
  • Change of the displayed items in the result view screen is possible
  • API(Application Program Interface) for Java/Perl was enhanced
 
2007.10 DDBJ HP design renewal
(ARSA is available at the search window of DDBJ HP)
 
2007.10 Sequence search program linked to TX Search was changed from SRS to ARSA  
2007.11 Further Upgrade subsequent to enhancement conductted in July"
<Main new functions>
  • Addition of KEGG Pathway Database
  • Specification of detailed search conditions in the all databases, as well as DDBJ
  • Cross search by the common search queris
 24 
2008.05 Removal of redundant DBs
4DBs related to PFAM were removed
 20 
(3) Growth of Number of ARSA and SRS Users In the following graph which shows the growth of ARSA and SRS users from January 2007 to June 200, the number of unique users of ARSA increases continuously, whereas that of SRS is on a downward or a flat tendency. In the pageview count, ARSA exceeded SRS in March, 2008.
      srstoarsa_static
Unique User: a number of an individual that has visited a Web site or received specific content,for a specified period of time such as a day or month. More than one time visits by the same user is counted as 1.
Page View: a request to load a single page of an Internet site. This number is widely used as an access index to the site
(4) Conclusion
DDBJ, since starting the ARSA services in December of 2004 as a trial operation, has built up continuous improvements for the more covenient keyword search system. Meanwhile, DDBJ has introduced ARSA at the scientific meeting and/or DDBJing tutorials. Increase of ARSA users reflects these efforts, and as a results, DDBJ decided to terminate providing SRS service.
DDBJ has do all the more efforts for the development of ARSA. If you have any comments for ARSA, please send it from "Your Comment" which is located in the upper blue zone.
 DDBJ Rel. 75.0 and DAD Rel. 45.0 released
The periodical release and the new data are available by FTP download from the "FTP/Web API" page.
 Update of databases related to the H-Invitational
The mirror H-Invitational Database (H-InvDB) was upgraded on October 23, 2008. The latest version 5.3 of H-InvDB is now available.
 Exhibit the DDBJ booth in BioJapan 2008
BioJapan 2008 was held at Pacifico Yokohama from Oct. 15 to 17.
DDBJ had the booth in the exhibition. The poster to introduce the activities and the services of DDBJ were exhibited and some information paper was distributed there.
  

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