Nam Tran and Chitta Baral
Reasoning about molecular interactions and signaling pathways is important from various perspectives such as predicting side effects of drugs, explaining unusual cellular behavior and drug and therapy design. Because of the vast size of these interactions a typical biologist can only focus on a very small part of the network. Thus there is a great need to develop knowledge representation and reasoning formalisms and their implementations for modelling and reasoning about molecular interactions in cells of organisms. An important component of these interactions is the action} of one molecule interacting with or binding to another, or one molecule separating into multiple other molecules. Thus, action theories and action languages are good candidates to model these interactions. One major lacking of most existing action languages is the notion of triggered actions, which is a common phenomena in the cellular domain. In this paper, we introduce a language for representing and reasoning about triggered actions, and show how to model reasoning about side effects, explaining observations, and designing drugs in our language through implementations using AnsProlog.