Towards knowledge-based semantic integration of models

12 Oct 2007

Carolyn Talcott
Computer Science Lab
SRI International


In spite of standards efforts such as SMBL and BioPax it remains difficult to share models of biological processes (for example signal transduction or metabilism). It is even more difficult to combine models of similar processes developed by different researchers not to mention models of different processes/aspects, to obtain a bigger picture.

I will present some preliminary thoughts on a possible approach to improving the situation based on an attempt to represent the biological knowledge underlying the models in a framework that is (hopefully) independent of specific analysis tools (MatLab, PRISM ...) but that supports reasoning about the knowledge.

I will also discuss some of the specific issues that arose in a modest case study of models of signaling due to EGF stimulation. I will also mention similar issues that arise when importing models from publicly avaialable data bases.

Hopefully this will elicit discussion of additional issues that must be faced and lead to some productive brainstorming about how to make progress in practice.

current theory lunch schedule