Building Integrated Systems for Data Representation and Analysis in Molecular Biology

of eukaryotic genomes centered on the relations between genomic sequences and their chromosomal localization [8]. In their early stages of development, ColiGene and MultiMap integrated a few sequence analysis methods. But, little by little, we found useful to provide access to the methods associated with a peculiar knowledge base to the other. Moreover, it was obvious that the methods integrated in ColiGene and MultiMap lacked of standardization and that their integration in the knowledge bases was a bit artificial (i.e. they were more associated pieces of software than really integrated tools). This is why we have decided to separate methods from the biological objects, while maintaining communication possibilities between these two kind of knowledge. To this purpose, we have developed two complementary packages: Digit and Misa. The first one was primarily designed as a graphical layer for a knowledge base devoted to the methodology in multivariate analysis: Slot [9]. The genericity of the tools available in Digit allows their use with any knowledge base developed with the Shirka system. After Digit, we have developed Misa, a more specific system which is able to virtually integrate any available sequence analysis method, this due to its modular conception. The modules that are part of the Misa system are now our basis in the building of a more advanced system in which methods — defined as “tasks” — are managed under an “intelligent” system guiding the user in the choices and the chainings to do in a way to perform complex analyses. Biochemical techniques have given to biology experimental tools for sequencing genome fragments. These fragments were of a short length — often corresponding to a single gene — this until the development of extremely fast sequencing methods. By now, large sequencing projects have been started, leading to the availability of huge continuous fragments (300 kb for yeast chromosome III). Besides the problem of storing and representing such an amount of data, there is also the fact that the internal organization of these large fragments is often completely unknown. Consecutively, in the near future, the data and knowledge bases dedicated to molecular biology will be most certainly associated to sequence analysis systems in a way to help study the unannotated fragments. We present here an example of such association between two “biological” objectoriented knowledge bases — ColiGene and MultiMap — and two sets of methods that are able to communicate with them. Then, we show how it is possible to formalize the methods under an object-oriented knowledge representation model for tasks.