Just as mereology partially orders physical structures based upon parthood causality partially orders physical processes based upon precedence. Both mereology and causality should play a fundamental role in any ontology dealing with physical objects. The Standard Upper Merged Ontology (SUMO) seems well suited enough to deal with both sorts of reasoning as it explicitly distinguishes between physical objects and physical processes in its ontology.
Causal reasoning plays a fundamental role in AI as any intelligent agent should be able to perform causal recognition by taking an effect and then determining what its causes may be and prediction by taking a cause and then determining what its effects may be. In either case probabilistic methods may play a role in the reasoning process as a system may use the frequencies of certain effects produced by a cause in order to help predict what the effect will be.
One interesting theory is that of causal sets which unifies quantum gravity and relativity by positing that the physical universe is fundamentally structured by causality. Time dilation indicates that we cannot place an absolute total ordering on events so the only way to effectively understand time is with a causal partial order like the one provided by causal set theory.
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