Anthony Kosky

Theoretical Aspects of Schema Merging

A general technique for merging database schemas is developed that has a number of advantages over existing techniques, the most important of which is that schemas are placed in a partial order that has bounded joins. This means that the merging operation, when it succeeds, is both associative and commutative, i.e., that the merge of schemas is independent of the order in which they are considered — a property not possessed by existing methods. The operation is appropriate for the design of interactive programs as it allows user assertions about relationships between nodes in the schemas to be considered as elementary schemas. These can be combined with existing schemas using precisely the same merging operation.

Semantics of Database Transformations

Database transformations arise in many different settings including database integration, evolution of database systems, and implementing user views and data-entry tools. This paper surveys approaches that have been taken to problems in these settings, assesses their strengths and weaknesses, and develops requirements on a formal model for specifying and implementing database transformations.

Exploring Heterogeneous Biological Databases: Tools and Applications

We present a tool-based strategy for exploring heterogeneous biological databases in the context of the Object-Protocol Model (OPM). Our strategy involves tools for examining the semantics of biological databases; constructing and maintaining OPM views for biological databases; assembling biological databases into an OPM-based multidatabase system, while documenting database schemas and known links between databases; supporting multidatabase queries via uniform OPM interfaces; and assisting scientists in specifying and interpreting multidatabase queries. We describe these tools and discuss some of their scientific applications.

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

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.

Facilitating transformations in a human genome project database

Human Genome Project databases present a confluence of interesting database challenges: rapid schema and data evolution, complex data entry and constraint management, and the need to integrate multiple data sources and software systems which range over a wide variety of models and formats. While these challenges are not necessarily unique to biological databases, their combination, intensity and complexity are unusual and make automated solutions imperative. We illustrate these problems in the context of the Philadelphia Genome Center for Human Chromosome 22, and describe a new approach to a solution for these problems, by means of a deductive language for expressing database transformations and constraints.

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

Solutions currently promoted for exploring heterogeneous molecular biology databases (MBDs) include providing Web links between MBDs or constructing MBDs consisting of links, physically integrating MBDs into data warehouses, and accessing MBDs using multidatabase query systems. Arguably the most difficult tasks in exploring heterogeneous MBDs are understanding the semantics of component MBDs and their connections, and specifying and interpreting queries expressed over MBDs. However, most existing solutions address only superficially these problems.

Developing and accessing scientific databases with the OPM data management tools

Summary form only given. The Object-Protocol Model (OPM) data management tools provide facilities for rapid development, documentation, and flexible exploration of scientific databases. The tools are based on OPM, an object-oriented data model which is similar to the ODMG standard, but also supports extensions for modeling scientific data. Databases designed using OPM can be implemented using a variety of commercial relational DBMSs, using schema translation tools that generate complete DBMS database definitions from OPM schemas. Further, OPM schemas can be retrofitted on top of existing databases defined using a variety of notations, such as the relational data model or the ASN.1 data exchange format, using OPM retrofitting tools. Several archival molecular biology databases have been designed and implemented using the OPM tools, including the Genome Database (GDB) and the Protein Data Bank (PDB), while other scientific databases, such as the Genome Sequence Database (GSDB), have been retrofitted with semantically enhanced views using the OPM tools.

A Formal Model for Databases with Applications to Schema Merging

In this paper we present a simple and general model for database schemas and their instances. The model is sufficiently expressive to represent complex, higher order data structures and incorporates representations for specialisation relations and object identity. It is general enough to encode data structures arising from many other semantic data models in a natural way, though we do not attempt to model some of the more sophisticated constraints that occur in other models.

Developing and accessing scientific databases with the Object-Protocol Model (OPM) data management tools

The Object-Protocol Model (OPM) data management tools provide facilities for rapid development, documentation, and flexible exploration of scientific databases. The tools are based on OPM, an object oriented data model which is similar to the ODMG standard, but also supports extensions for modeling scientific data (L.A. Chen and V.M. Markowitz, 1995). Databases designed using OPM can be implemented using a variety of commercial relational DBMSs, using schema translation tools that generate complete DBMS database definitions from OPM schemas (L.A. Chen and V.M. Markowitz, 1996). Further OPM schemas can be retrofitted on top of existing databases defined using a variety of notations, such as the relational data model or the ASN.1 data exchange format, using OPM retrofitting tools (L.A. Chen et al., 1997).