Multiple Representations of Biological Processes
Carolyn Talcott and David L. Dill,
Transactions on Computational Systems Biology, 2006
This paper describes representations of biological processes based on
Rewriting Logic and Petri net formalisms and mappings between these
representations used in the Pathway Logic Assistant. The mappings are
shown to preserve properties of interest. In addition a relevant
subnet transformation is defined, that specializes a Petri net model
to a specific query to reduce the number of transitions that must be
considered when answering the query. The transformation is shown to
preserve the query in the sense that no answers are lost.
Keywords: Signal transduction, biological process, Pathway Logic, Rewriting Logic, Petri Net.