Hepatobiliary system is one of the most important systems in the human body. It is responsible for many processes, which are necessary to keep body regulated and healthy. In our previous research, we exploited the existing Medical Ontologies for building a new Hepatobiliary System Diseases (HSD) Ontology in pathology domain. This Ontology is represented in the Web Ontology Language (OWL) that has recently become the standard language for the semantic web. In its current format, the HSD Ontology can be accessed only by the computer science specialists. In this paper, we present a system for Hepatobiliary system diseases prognosis and treatment. The system shares the Ontology knowledge by replying the inquiries of both physicians and medical students. The presented system is a web service-based, thus it can be integrated with intelligent systems. The proposed system utilizes the causal relations among diseases to predict the incoming diseases. During the patient visits, the system supports the physician by diagnosing the case, suggesting a treatment plan, and expecting the patient status progress. The system has been evaluated using a real dataset of 40 anonymous patients, and the diagnosis accuracy of the system is 92.5%.