GIB について

=ゲノムブラウザー問題= 生物別にいろいろブラウザーがある. それぞれゲノムを決めた研究者などがおまけで作るばかりで維持更新のコストが出ない. また継時的にあれもこれもと他のデータを取り込んで　更新運用に手間がかかる. 複雑怪奇でわかりにくくなる. GIBももともと大腸菌用のブラウザー(田村) を一般サーキュラゲノム　リネアゲノム汎用に変え　外部のアノテーション等のデータやORFの分類等いろいろデータを付け加えた様子. ただどこを見ても情報源のリスト　処理のリスト　等がない　内外のサービス特に改変中の内部サービスへのリンクが再利用を困難にしている. プライマリーサイトとしてはどうするべきか？　大きな情報処理が必要な部分だけ先に行って下流に配る方法(DDBJにはGUIはいらない）というふうにならないか？　とにかくユニークな部分や再利用可能なモジュールがあればクレジットして再利用できるが完成品のままの維持管理引き継ぎは予算上困難.

=GIB 解説= Fumoto, M., Miyazaki, S. and Sugawara, H. (2002)

GIB (http://gib.genes.nig.ac.jp/) is the comprehensive data repository of complete microbial genomes in the public domain. GIB will diffuse the genome sequence data and annotation in a day whenever the data is submitted to the International Nucleotide Sequence Databases (DDBJ, EMBL database and GenBank).

You can explore any microbial genome by clone name, ORF name/number, function, gene name, product name, location, sequence (namely, homology search), and other features/qualifiers defined by INSD. The result of query is displayed either in graphics or in a table format.

Comparative genomics can be carried out to some extent. Just click "Comparative Genomes" in the below to retrieve and compare data of multiple genomes.

It is to be noted that both fragments and genomes are download-able.

[Reference] Fumoto, M., Miyazaki, S. and Sugawara, H. (2002). Genome Information Broker (GIB): data retrieval and comparative analysis system for completed microbial genomes and more, Nucleic Acids Res. 30: 66-68

What is

 * The primary source of information for GIB is entries of the INSD. Whenever genome data are made pubic from the INSD, the data are immediately converted and implemented into GIB.
 * We assemble flat files of the INSD piece entries into a single large flat file of the whole genome by using contiguous information in the CON entry of INSD corresponding to the genome. The assembled whole genome flat file is then implemented into the GIB database.
 * The new version of GIB stores and processes information on any features described in the flat files in addition to CDS and RNA.
 * In addition, GIB has added functional category information other than in addition to the information in the flat files annotation. We use functional category information from TIGR (http://www.tigr.org/).

=Original Form= Takuro Tamura∗, E-mail The Corresponding Author, Hirotada Mori‡, E-mail The Corresponding Author, Hideaki Sugawara¶, E-mail The Corresponding Author
 * Genome information broker for large and small genomes

The core of GIB developed for E. coli occupies about 200MB disk in an NT4.0 machine with 130MB memory. The core of GIB for other microbial genomes utilizes also about 200MB disk in a UNIX workstation with 64MB memory. The blast search and the acquisition of sequence are done in a separate UNIX workstation. The GIB is composed of two components: - Java applet for the display of genome information - CGI program which constructs Web pages with commands embedded in HTML �les 
 * 2.1 Genome Information Broker (GIB)

=移行= 大久保先生　掲題バックアップの状況は以下のとおりです　菅原

-- 転送メッセージ -- From: Yasumasa Shigemoto  日付: 2012年2月6日18:39 件名: Re: Fw: MiGAPのデータ To: SUGAWARA Hideaki  Cc: Sei Miyamoto 

菅原先生 重元です. GTPS, GBIF, biobase については買い取りサーバで 稼働していますので、対象外です. GIB については 2/15 の停止後に一通りバックアップを取るとのことでした. WABI については私のほうでバックアップを取っておきます. 以上です.