Formal design and implementation of an improved DDBJ DNA database with a new schema and object-oriented library

Area of Science:

• Bioinformatics
• Database Systems
• Genomic Data Management

Background:

• The DNA Data Bank of Japan (DDBJ) required a scalable database system to manage evolving genomic data.
• Existing systems faced challenges in accommodating rapid changes and growth in data requirements.

Purpose of the Study:

• To design and implement a new DNA database system at DDBJ.
• To improve the efficiency and capacity of genomic data handling and submission processes.

Main Methods:

• Employed an object-oriented design approach adhering to the ANSI/SPARC three-level schema architecture.
• Developed a conceptual schema using the Associative Information Structure (AIS) functional model, extending the Entity-Relationship (ER) model.
• Implemented a physical schema mapped to a relational database and an external schema for application interfaces using a C++ object-oriented library.

Main Results:

• Successfully developed a new DNA database system with enhanced schema design.
• Created the annotator's workbench Yamato II and the World Wide Web (WWW) submission system Sakura.
• Drastically improved daily transaction efficiency within the DDBJ.

Conclusions:

• The new object-oriented database system and its associated tools provide a robust framework for DDBJ.
• The implemented schema architecture ensures physical independence and facilitates application development.
• The enhanced system significantly boosts the DDBJ's capacity for managing and processing genomic data.