Reasoning about Triggered Actions in AnsProlog and its Application to
Molecular Interactions in Cells
N. Tran and C. Baral
Abstract
Reasoning about molecular interactions and signal 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 or binding with 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 side effects reasoning, explaining
observations, and drug and therapy design in our language through
implementations using AnsProlog.