Exploring Heterogeneous Molecular Biology Databases in the Context of the Object-Protocol Model

Victor M. Markowitz
I-Min A. Chen
Anthony S. Kosky

Information and Computing Sciences Division
Lawrence Berkeley National Laboratory, Berkeley, CA 94720

Abstract:

We propose a tool-based strategy for exploring heterogeneous MBDs in the context of the Object-Protocol Model (OPM). Our strategy involves developing tools that provide facilities for examining the semantics of MBDs; constructing and maintaining OPM views for MBDs; assembling MBDs into an OPM-based multidatabase system, while documenting MBD schemas and known schema links between MBDs; supporting multidatabase queries via uniform OPM interfaces; and assisting scientists in specifying and interpreting multidatabase queries. Each of these tools can be used independently and therefore represents a valuable resource in its own right. We discuss the status of implementing our strategy and our plans in pursuing further this strategy.

• Introduction
• Semantic Problems of Exploring Molecular Biology Databases
  • Semantics of Global Schemas and Views
  • Semantics of Data Exploration
• Exploring Heterogeneous Molecular Biology Databases in the Context of the Object-Protocol Model
  • The Object-Protocol Model and Tools
  • The OPM Tool-Based Strategy
    • Constructing OPM Views for MBDs
    • The Multidatabase Directory
    • Supporting Multidatabase Queries
    • Formulating and Interpreting Multidatabase Queries
• An Example
  • The GDB-GSDB Multidatabase System
  • Examples of Queries Expressed over GDB and GSDB
• Pursuing the OPM Tool Based Strategy
  • Constructing OPM Views
  • The Multidatabase Directory
  • Supporting Multidatabase Queries
  • Technological Alternatives
• References
• About this document ...