A Cell-Cycle Knowledge Integration Framework

The goal of the EU FP6 project DIAMONDS is to build a computational platform for studying the cell-cycle regulation process in several different (model) organisms (S. cerevisiae, S. pombe, A. thaliana and human). This platform will enable wet-lab biologists to use a systems biology approach encompassing data integration, modeling and simulation, thereby supporting analysis and interpretation of biochemical pathways involved in the cell cycle. To facilitate the computational handling of cell-cycle specific knowledge a detailed cell-cycle ontology is essential. The currently existing cell-cycle branch of the Gene Ontology (GO) provides only a static view and it is not rich enough to support in-depth cell-cycle studies. In this work, an enhanced Cell-Cycle Ontology (CCO) is proposed as an extension to existing GO. Besides the classical add-ons given by an ontology (data repository, knowledge sharing, validation, annotation, and so on), CCO is intended to further evolve into a knowledge-based system that provides reasoning services oriented to hypotheses evaluation in the context of cell-cycle studies. A data integration pipeline prototype, covering the entire life cycle of the knowledge base, is presented. Concrete problems and initial results related to the implementation of automatic format mappings between ontologies and inconsistency checking issues are discussed in detail.