There are so many increasing amount of information in the today's world-wide web. For these increasing amounts of information, we need efficient and effective index structure when we have to find needed information. Most indexing techniques directly matched terms from the document and terms from query. The role of usage of domain specific ontology is very wide for the specific application area. Ontology can be defined as a formal explicit specification of a shared conceptualization. It is a formal and declarative representation which includes vocabulary for referring to the terms in that subject area and logical statements that describe the relationships among the terms. This system proposes a semantic-based indexing structure that is built on the basic context document by using semantic suffix tree clustering, context ontology and semantic suffix tree clustering with context ontology. This paper shows the results of these three methods on the same application area.