Bioinformatics Advance Access originally published online on November 5, 2004
Bioinformatics 2005 21(7):1246-1256; doi:10.1093/bioinformatics/bti137
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ISYMOD: a knowledge warehouse for the identification, assembly and analysis of bacterial integrated systems
1Laboratoire d'Informatique Fondamentale de Marseille 39 rue Joliot Curie 13453 Marseille cedex 13, France
2Laboratoire de Chimie Bactérienne, CNRS 31 Chemin Joseph Aiguier, 13402 Marseille cedex 20, France
3Laboratoire de Microbiologie et Génétique Moléculaires, UMR 5100 CNRS-Université Paul Sabatier Toulouse Cedex, France
*To whom correspondence should be addressed.
Motivation: Complex biological functions emerge from interactions between proteins in stable supra-molecular assemblies and/or through transitory contacts. Most of the time protein partners of the assemblies are composed of one or several domains which exhibit different biochemical functions. Thus the study of cellular process requires the identification of different functional units and their integration in an interaction network; such complexes are referred to as integrated systems. In order to exploit with optimum efficiency the increased release of data, automated bioinformatics strategies are needed to identify, reconstruct and model such systems. For that purpose, we have developed a knowledge warehouse dedicated to the representation and acquisition of bacterial integrated systems involved in the exchange of the bacterial cell with its environment.
Results: ISYMOD is a knowledge warehouse that consistently integrates in the same environment the data and the methods used for their acquisition. This is achieved through the construction of (1) a domain knowledge base (DKB) devoted to the storage of the knowledge about the systems, their functional specificities, their partners and how they are related and (2) a methodological knowledge base (MKB) which depicts the task layout used to identify and reconstruct functional integrated systems. Instantiation of the DKB is obtained by solving the tasks of the MKB, whereas some tasks need instances of the DKB to be solved. AROM, an object-based knowledge representation system, has been used to design the DKB, and its task manager, AROMTASKS, for developing the MKB. In this study two integrated systems, ABC transporters and two component systems, both involved in adaptation processes of a bacterial cell to its biotope, have been used to evaluate the feasibility of the approach.
Contact: julie.chabalier{at}ibsm.cnrs-mrs.fr