Paper Info
Title
Formal design and implementation of an improved DDBJ DNA database with a new schema and object-oriented library.
Abstract
Motivation: The DNA Data Bank of Japan (DDBJ) has developed a new DNA database system with a new schema design to accommodate rapid change and growth of requirements on the system. Results: The new schema and systems were created using an object-oriented design approach. The design was accomplished in accordance with ANSI/SPARC three-level schema architecture. First, the conceptual schema was designed using a functional model named AIS (associative information structure) and was visualized in extended diagram format. The model is a natural extension of an ER (entity relationship) model and describes real-world objects of binary 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 modeling was introduced for the database applications interface. It provides 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 annotator's workbench named Yamato II and a World Wide Web (WWW) submission system named Sakura have been successfully developed to improve drastically daily transactions in the DDBJ.
Year
DOI
Venue
1998
10.1093/bioinformatics/14.6.472
BIOINFORMATICS
Keywords
Field
DocType
object oriented
Data mining,Conceptual schema,Schema migration,Semi-structured model,Computer science,Document Structure Description,Database schema,Information schema,Physical schema,XML Schema Editor
Journal
Volume
Issue
ISSN
14
6
1367-4803
Citations 
PageRank 
References 
8
0.75
0
Authors
8
Name
Order
Citations
PageRank
T Okayama192.45
Takuro Tamura2416.45
Takashi Gojobori3439241.79
Y Tateno4278209.00
K Ikeo59533.32
Shuichi Miyazaki647041.34
K Fukami-Kobayashi74362.47
Hideaki Sugawara8591264.11