Abstract: The diagrammatic language for pathways is widely used for representing systems knowledge as a network of causal relations. Biologists infer and hypothesize with pathways to design experiments and verify models, and to identify potential drug targets. Although there have been many approaches to formalize pathways to simulate a system, reasoning with incomplete and high level knowledge has not been possible. We present a qualitative formalization of a pathway language with incomplete causal descriptions and its translation into propositional temporal logic to automate the reasoning process. Such automation accelerates the identifcation of drug targets in pathways.