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

T. Okayama*, T. Tamura, Takashi Gojobori, Y. Tateno, K. Ikeo, S. Miyazaki, K. Fukami-Kobayashi, H. Sugawara

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

16 Scopus citations

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 ANS1/SPARC three-level schema archirecture. 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 in 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. Availability: Sakura is available at the following address: http://sakura.ddbj.nig.ac.jp. Contact: hsugawar@@@genes.nig.ac.jp.

Original languageEnglish (US)
Pages (from-to)472-478
Number of pages7
JournalBioinformatics
Volume14
Issue number6
DOIs
StatePublished - Sep 19 1998

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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