Knowledge management in a Systems Biology approach to translational medicine

Dieter Maier- Biomax Informatics AG

The integrative approach of Systems Biology promises a better understanding of complex phenotypes, such as chronic obstructive pulmonary disease (COPD), interconnecting current knowledge with experimental data, in-silico analysis and simulation. Layers of global and targeted datasets and knowledge need to be integrated and local sub-networks with associated experimental data need to be extracted. The EU BioBridge project coordinates clinical, experimental and computational groups generating a Systems Biology workflow for the analysis and therapeutic intervention of COPD.
The BioXM knowledge management environment is deployed as its central infrastructure. BioXM allows the dynamic, graphic generation of domain specific knowledge representations based on specific objects and their relations supporting annotations and ontologies. Wizards, automatically adapted to the created knowledge model, map data from external sources or for import. The Java based client-server application implements visual browse and query interfaces to traverse, query and retrieve the knowledge network providing a flexible, customisable framework.
A publicly available instance of BioXM has been set-up at http://www.biobridge.eu/bio, providing COPD specific molecular networks, clinical and experimental data. Pre-structured queries and reports support the retrieval of sub-networks spanning protein-protein interaction, pathway, SMBL model, gene - disease and gene - compound data for subsequent data analysis, model building and simulation. This knowledge infrastructure is integrated with modelling and simulation tools such as MathModelica, IsoDyn and ByoDyn to generate and simulate deterministic models. Network inference based on Banjo and ARACNE connects and expands existing networks with expression, metabolomic and proteomic data.