A key step in the design of autonomous, robust and cooperative distributed systems which utilize knowledge-intensive algorithms is choosing the appropriate algorithm(s). Thanks to advances in technology the application possibilities of such systems are covering more and more areas. With the increasing variety of potential tasks and environments emerged the need of a general methodology and toolkit for the support of design, testing and validation of these systems. Such a toolkit has to contain a decision support system that provides advice to choose the algorithm that is the most suitable for the requirements of the particular task. This system needs an underlying knowledge base which can describe the effectiveness of knowledge-intensive algorithms considering different tasks and environments. This thesis begins with a short overview of this topic, being connected to the European R3‑COP project, which specifically aims to work out the details of the mentioned methodology and toolkit. This work presents a detailed proposal about how to design the ontology behind the decision support system.