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This paper describes a knowledgebase of sharable and reusable medical ontological theories, organized according to a proposed classification of ontologies. Accurate representation of physiological models using a set of mathematical equation are useful for studying and understanding the dynamic behavior of physiological states of infected patient. The research work attempts to develop an ontology consisting of well structured knowledge base on anatomical parts and physiological states of infected patient and also to maximize the use of inference engine inbuilt in prolog. One way of capturing knowledge within bioinformatics applications and database is the use of Ontologies. An ontology is the concrete form of a conceptualization of knowledge within a specific domain. It describes the process of building an ontology, introducing to the readers the techniques and methods currently used in ontology development. Domain ontological analysis method was used for building the ontology andit deals with categorization of common concepts or objects and operations with a clear and unambiguous definition of concepts and the relationship between them.