Object-Oriented Knowledge Bases for the Analysis of Prokaryotic and Eukaryotic Genomes

The amount of biological sequences introduced in the general collections, and the growing complexity of the biological knowledge require the construction of models to formalize this knowledge and particularly the relationships between several data types. Two examples of such situations are presented here, they result from the biological research lead in our team in the field of molecular evolution. ColiGene is a modelling of E. coli genetics devoted to the analysis of relationships between genomic sequences and gene expressivity. MultiMap implements a new formalization of genome maps allowing manipulation of "maps of maps" in two species. Application of ColiGene and MultiMap are not restricted to molecular evolution and, for instance, MultiMap offers new capabilities for infering data on a genome from knowledge on another species. This could be essential for many mapping projects (human, mouse but also other mammals like pig). Development and implementation of those models have been done using an object-oriented knowledge base management system (SHIRKA) interfaced with a dedicated genomic data base management system (ACNUC). Graphical interfaces have been designed to give an environment similar to the biological representations used by biologists.