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 Human Genome Database for Chromosome 22 (Chr22DB), and describe a new approach to a solution for these problems, by means of a deductive language for expressing database transformations and constraints

Recommendations for Evolving Relational Databases

International audienceRelational databases play a central role in many information systems. Their schemas contain structural and behavioral entity descriptions. Databases must continuously be adapted to new requirements of a world in constant change while: (1) relational database management systems (RDBMS) do not allow inconsistencies in the schema; (2) stored procedure bodies are not meta-described in RDBMS such as PostgreSQL that consider their bodies as plain text. As a consequence , evaluating the impact of an evolution of the database schema is cumbersome , being essentially manual. We present a semi-automatic approach based on recommendations that can be compiled into a SQL patch fulfilling RDBMS constraints. To support recommendations, we designed a meta-model for relational databases easing computation of change impact. We performed an experiment to validate the approach by reproducing a real evolution on a database. The results of our experiment show that our approach can set the database in the same state as the one produced by the manual evolution in 75% less time

A Call to Arms: Revisiting Database Design

Good database design is crucial to obtain a sound, consistent database, and - in turn - good database design methodologies are the best way to achieve the right design. These methodologies are taught to most Computer Science undergraduates, as part of any Introduction to Database class. They can be considered part of the "canon", and indeed, the overall approach to database design has been unchanged for years. Moreover, none of the major database research assessments identify database design as a strategic research direction. Should we conclude that database design is a solved problem? Our thesis is that database design remains a critical unsolved problem. Hence, it should be the subject of more research. Our starting point is the observation that traditional database design is not used in practice - and if it were used it would result in designs that are not well adapted to current environments. In short, database design has failed to keep up with the times. In this paper, we put forth arguments to support our viewpoint, analyze the root causes of this situation and suggest some avenues of research.Comment: Removed spurious column break. Nothing else was change

Information Integration - the process of integration, evolution and versioning

At present, many information sources are available wherever you are. Most of the time, the information needed is spread across several of those information sources. Gathering this information is a tedious and time consuming job. Automating this process would assist the user in its task. Integration of the information sources provides a global information source with all information needed present. All of these information sources also change over time. With each change of the information source, the schema of this source can be changed as well. The data contained in the information source, however, cannot be changed every time, due to the huge amount of data that would have to be converted in order to conform to the most recent schema.\ud In this report we describe the current methods to information integration, evolution and versioning. We distinguish between integration of schemas and integration of the actual data. We also show some key issues when integrating XML data sources

ADEPT2 - Next Generation Process Management Technology

If current process management systems shall be applied to a broad spectrum of applications, they will have to be significantly improved with respect to their technological capabilities. In particular, in dynamic environments it must be possible to quickly implement and deploy new processes, to enable ad-hoc modifications of single process instances at runtime (e.g., to add, delete or shift process steps), and to support process schema evolution with instance migration, i.e., to propagate process schema changes to already running instances. These requirements must be met without affecting process consistency and by preserving the robustness of the process management system. In this paper we describe how these challenges have been addressed and solved in the ADEPT2 Process Management System. Our overall vision is to provide a next generation process management technology which can be used in a variety of application domains