In this article, the ontology based approach for modeling and management of profiles and competencies in virtual organization breeding environment (VBE) is presented. The main aim of creating the profile and competency ontology of VBE participants is utilizing them in the development of the intelligent agent for choosing the best partners in order to perform the research projects in the information technology (IT) domain. Large amount of information, diversity and dissimilarity of profiles and competencies justify the use of ontology for modeling and management. Thus, ontology with the unique characteristics can assist VBE cooperators to administer these breeding environments. The main contributions of this paper are: producing profile ontology by the capability of applying it in all research VBEs, and producing competency ontology with the aim of applying it in the VBEs whose goal is studying and probing in service oriented architecture and agents domain. Methontology and semi -automated methodology in competency ontology development proportional with the domain and goals of ontology are two methodologies used in creating profile and competency ontology. Eventually, for evaluating results, Gomez-Perez approach is used.