A Tractable Logic for Molecular Biology

We introduce a logic for knowledge representation and reasoning on protein-protein interactions. Modulo a theory, formulas describe protein structures and dynamic changes. They can be composed in order to add or remove static and dynamic observations. A second-order circumscription operator then enables nonmonotonic reasoning on the changes implied by a formula. We introduce deduction rules that produce formulas which are, up to equivalence, in a first-order fragment with decidable satisfiability and validity. Importantly, the rules can produce circumscribed formulas.