FORMAL DESIGN AND IMPLEMENTATION OF AN IMPROVED DDBJ DNA DATABASE WITH A NEW SCHEMA AND OBJECT-ORIENTED LIBRARY

Motivation: The DNA Data Bank of Japan (DDBJ) has developed a new DNA database system with a new schema design to accommodate rapid change a nd growth of requirements on the system. Results: The new schema and s ystems were created using an object-oriented design approach. The desi gn was accomplished in accordance with ANSI/SPARC three-level schema a rchitecture. First, the conceptual schema was designed using a functio nal model named AIS (associative information structure) and was visual ized in extended diagram format. The model is a natural extension of a n ER (entity relationship) model and describes real-world objects of b inary associations between entities with the concept of order. Second, the schema was mapped on a relational database as a physical schema. All details are concentrated in this schema and the layer lying above enjoys physical independence. Finally, as another layer, external mode ling was introduced for the database applications interface. It provid es set-at-a-time basis operations and was implemented as a C++ object- oriented library. On this common framework of a new schema, a new anno tator's workbench named Yamato II and a World Wide Web (WWW) submissio n system named Sakura have been successfully developed to improve dras tically daily transactions in the DDBJ.