Abstract. The article presents models and methods of ontological data analysis aimed at identifying conceptual structure, or formal ontology, of the studied knowledge domain (KD). The realities of the accumulation of empirical data are reflected in model of generalized "object-properties" table and the incompleteness of this information implies the need for models of multi-valued logic. For the first time detailed models and method of accounting for "existence constraints", which can be known priori by the researcher of KD in the context of measured attributes of the objects' learning sample.Keywords: formal ontology, ontological data analysis, formal concept analysis, multi-valued logic, properties existence constraints Citation:Semenova VA, Smirnov SV. Intelligent analysis of incomplete data to building formal ontologies.