SBML 2 SMW : bridging System Biology with semantic web technologies for biomedical knowledge acquisition and h ypothesis elicitation

Motivation: Generation of biomedical hypothesis is a very important task in the pharmaceutical industry since it serves the whole drug development pipeline: which are the physiopathological mechanisms underlying a disease, which biomarkers shall be measured in a clinical trial in order then to be able to do proper data mining and then deliver best service to the patients, which unexpected events could occur if one inhibits a certain molecular pathway, which could be new indications for a given compound. These are only few of the many questions which require discovery of hidden links. In this work we describe our experiences and a small tool we developed and make freely available which bridges in bidirectional way semantic wiki and system biology technologies. This CellDesigner plugin therefore enable easy share and reuse of knowledge. Source code available at http://code.google.com/p/sbml2smw/