Constructing and maintaining scientific database views in the framework of the object-protocol model

Abstract

Scientific databases (ScDBs) are used to archive and retrieve data describing objects of scientific inquiry. Since these ScDBs must provide continuous and efficient access to large communities of scientists, they are often developed with reliable commercial relational database management systems (DBMSs) or file systems. However, relational DBMSs and flat files do not provide constructs for representing directly ScDB-specific objects and experimental procedures, and therefore they are often hard to develop, maintain, and explore. The authors present a retrofitting tool for constructing and maintaining ScDB views using an object-oriented data model, and describe their experience with retrofitting ScDBs that have been originally developed using relational DBMSs and file systems. The retrofitting tool is part of a data management toolkit based on the object-protocol model (OPM). The OPM toolkit provides facilities for developing databases defined using OPM and for querying and browsing such ScDBs in terms of OPM constructs. The OPM retrofitting tool allows constructing (one or several) OPM views for ScDBs that have not been originally developed with the OPM tools. ScDBs with native OPM schemas or retrofitted OPM views can be browsed and queried via OPM interfaces, reorganized, or incorporated into an OPM-based database federation.