Collaborative networked organizations are composed of heterogeneous and autonomous entities. Thus it is natural that each member has its own set of values and preferences, as a result, conflicts among partners might emerge due to some values misalignment. Therefore, tools to support the analysis of Value Systems in a collaborative context are relevant to improve the network management. Since a Value System reflects the set of values and preferences of an actor, which are cognitive issues, a cognitive approach based on qualitative causal maps is suggested. Qualitative inference methods are presented in order to assess the potential for conflicts among network members and the positive impact between members' Value Systems. The software tool developed, in order to support the proposed framework and the qualitative inference methods, is briefly presented.