CCO pipeline. The CCO data integration pipeline scheme plots the principal phases: set-up, data integration and system's life cycle. In the 'set-up' phase, several existing ontologies are integrated and merged: the Gene Ontology, the Relations Ontology, the Molecular Interactions ontology, an upper level ontology (see 'An upper level ontology for application ontologies in the life sciences' section) and an ontology holding taxonomical terms for the four model organisms supported by CCO (A. thaliana, H. sapiens, S. cerevisiae and S. pombe). A core cell cycle ontology is generated as output from this set-up phase, which in turn serves as input for the 'data integration phase' where GOA annotations and protein data, such as protein-protein interactions, are integrated. Finally, 'life cycle' phase depicts the maintenance of the system by considering the stages of updating the integrated data (such as ontologies, protein data). This phase also shows the generation (export) in different formats for further exploitation.