Human body systems are interconnected and dependent and they can’t function separately. Diseases which affect any of these systems will affect other systems as well. In existing disease diagnosis systems, diseases were classified based on different dimensions such as cause, treatment, types of diseases, etc. On the other hand the existing disease information systems are for pest control management and they cannot be extended to human diseases. In existing systems traditional database approach was used. A database provides queried information and the retrieval method is not efficient in the case of biomedical systems. The proposed system will classify the diseases into the ‘system-wise diseases’ instead of many dimensions. The system needs careful handling of disease information. A disease information system would be appreciable instead of databases since the information systems may provide more precise and descriptive information. Therefore it is required to develop a disease information system by providing more relevant information as per the user query. The ontology based disease information system is being build and semantic based rules are designed to respond to the corresponding user query. The proposed information system is mainly focusing on improving the query results and also supports ease of use to the user.