The purpose of the paper is to propose a framework for the development of a decision support system in order to evaluate the knowledge boundaries in agricultural value chain. Knowledge boundaries exist due to differences in the way we work, share our knowledge, expertise, different organisational culture, etc. In this paper we identify the most common knowledge boundaries that are reported in the literature, and propose a general framework for a preparation of a decision support system to evaluate the existing knowledge boundaries. In particular, we are interested in identifying the knowledge boundaries in agricultural value chain, evaluating them and providing possible solutions of crossing them. It is a two-step method: firstly, a semi-automatic ontology is generated using the freely available tool OntoGen, which we use to define the most commonly reported concepts in crossing knowledge boundaries, and then, based on the obtained ontology, we propose a decision support system for evaluation of the level to which the boundaries exist.