グライコナビの開発
トーゴーの⽇シンポジウム2011 〜ライフサイエンス分野のデータベース統合の“カタチ”を探る〜 (⽇本科学未来館

７ＦみらいCANホール)2011年10⽉5⽇（⽔）○⼭⽥⼀作、本庄秀之、弘瀬友理⼦、森昌⼦、⽔野真盛
公益財団法⼈野⼝研究所 糖鎖有機化学研究室
独⽴⾏政法⼈科学技術振興機構，バイオサイエンスデータベースセンター（NBDC）
e-mail: issaku@noguchi.or.jp
Carbohydrates are prime biological substances abundant in nature. They are deeply involved in many biological activities and have complicated chemical structure. Due to their complexity, synthetic carbohydrate chemistry is
considered as a challenging field for most organic chemists. As a results, the lack of organic chemists who have mastered the synthetic techniques has become a hindrance for the stable supply of authentic and homogeneous
samples of carbohydrates, which is the key element to advance the research in the field. To support the carbohydrate research, we have developed Glyco-Navigation (GlycoNAVI) system (http://glyconavi.org) utilizing informatics
technology. The back-end of this system consists of the database systems and Web services, while the front-end interface is composed of Web and desktop applications. GlycoNAVI database consists of a number of databases forglyco-organic chemistry: chemical synthesis method (chemical reaction) database, chemical abbreviation (synonyms) database, molecular database and so on. These database systems can be accessed through the Internet with abrowser and the desktop application (CSEditor). Web service of this system includes the conversion functions. One of the functions can convert the data format from chemical format such as molfile to glyco-sequence format suchas KCF (KEGG Chemical Function). It is also noteworthy that GlycoNAVI database has been cooperated with Japanese Consortium for Glycobiology and Glycotechnology DataBase (JCGGDB: http://jcggdb.jp).
CSEditor is a two-dimensional molecular editing tool which can be used as a gateway to GlycoNAVI. The functions of this software are as follows: 1) it can generate the search query for the database system; 2) it can identify
the monosaccharide symbols and the glycosidic bond types from the chemical structure; 3) it can distinguish the chair conformation (4C1 or 1C4) and the anomeric configuration (α or β); 4) it can display a monosaccharide in theform of graphic symbol defined in CFG (the Consortium for Functional Glycomics). These functions are useful for a researcher who is new to this field to understand the nature of carbohydrates.

GlycoNAVI Databases

Overview••Web application

Databasemajor web browsers•

Molecule Database

Molecule database contains chemical structures,chemical names and The IUPAC International
Chemical Identifier.

Chemical Reaction Database

Chemical Reaction database contains reaction
scheme, reagents, products, solvents, catalysts,
comment of reaction, and references.

Chemical Abbreviation Database

Chemical abbreviation database contains chemicalabbreviation, synonyms,abbreviationsynonyms chemical names
names.

Desktopapplication

Web service

Tool: CSEditor

CSEditor is a two-dimensional molecular editing tool which canbe used as a gateway to GlycoNAVI.

Databases
GlycoNAVI database consists of a number of databases for glyco-organic chemistry: chemical synthesis method (chemical reaction) database, chemical abbreviation (synonyms) database,molecular database and so on. These database systems can be accessed through the Internet with a browser and the desktop application (CSEditor).

Basic handling for CSEditor
CreateSelectChangeCreateChangelariatSelectDelete

Move

RotateMolecule Database

Chemical Abbreviation Database

Monosaccharide recognition
Detail

List

Search (keyword)

Structure

Detail & Search

List

Chemical Reaction Database

Monosaccharide numbering

Search (ID)

Search (DOI/PMID)

Detail

Search (keyword)

Search (structure key)

Structure search

Molecule

Monosaccharide conformation

Acknowledgements

Database

Storing system of chemical reactions

Chemical reaction
Query Structure

Function of the Storing System
Editing of chemical structure using CSEditor
Registration of reaction information to local system
Retrieval of reaction information
Editing of reaction information (temperature, reaction
time, etc…)
Entering of comments, usage, and/or yield for eachcompoundMicrosoft product screen shot(s) reprinted with permission from Microsoft Corporation.

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