Systems Biology


Semantic web technologies play an increasingly important role in describing and managing biological knowledge.

Whereas Systems Biology aims to provide an understanding of biological systems through the (mathematical) modelling of biological knowledge, Semantic Systems Biology (SSB) is designed to provide help in knowledge integration and network building, computational reasoning, and automated hypothesis generation and assessment. The Kuiper group collaborates with several wet-lab science groups to demonstrate the potential of SSB for the understanding of biological processes, mainly through the use of network- and pathway based analysis approaches.

The group has developed the (BioGateway semantic knowledge base), which uses ontologies and semantic web technologies for the integration and exploration of biological knowledge. Several application ontologies for studying cell cycle control and regulation of gene expression have been constructed, and tools for orthology prediction (orthagogue),and the visualisation of ontologies (OLSVis,) have been published. More recently, the group extended its focus on the development of procedures and approaches to build high quality knowledge sources (the ‘Knowledge Commons’) for understanding gene regulation processes (Transcription Factor Checkpoint), (Gene Regulation Consortium), and the production of regulatory, or ‘causal’, statements from which logical models can be constructed that can be instrumental to predict effects of system perturbations.