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Probabilistic Risk Assessment is a technique to assess the probability of failure or success of a mission. Results provided by the risk assessment methodology are used to make decisions concerning choice of upgrades, scheduling of maintenance, decision to launch, etc. However, current PRA neglects the contribution of software to the risk of failure of the mission. This paper presents a framework for "Integrating Software into PRA", a methodology for systematic integration of the software contribution to risk in system failure analysis. In particular, we established a software-related failure mode taxonomy and a three-level PRA sub-model to account for the impact of software to the classical PRA structure. Application and validation of the taxonomy are discussed in this paper. Future research is also summarized.