Ontology similarity calculation is important research topics in information retrieval and widely used in science and engineering. In this paper, we consider the ontology applications on biology and chemical sciences. The new ontology sparse vector learning algorithm is obtained via dual program computation, and the new algorithm is applied to ontology similarity measure and ontology mapping. Via the ontology sparse vector learning, the ontology graph is mapped into a line consists of real numbers. The similarity between two concepts then can be measured by comparing the difference between their corresponding real numbers. The experiment results show that the proposed new algorithm has high accuracy and efficiency on ontology similarity calculation and ontology mapping.