Efficient retrieval of ontology fragments using an interval labeling scheme

Nowadays very large domain ontologies are being developed in life-science areas like Biomedicine, Agronomy, Astronomy, etc. Users and applications can benefit enormously from these ontologies in very different tasks, such as visualization, vocabulary homogenizing and data classification. However, due to their large size, they are often unmanageable for these applications. Instead, it is necessary to provide small and useful fragments of these ontologies so that the same tasks can be performed as if the whole ontology is being used. In this work we present a novel method for efficiently indexing and generating ontology fragments according to the user requirements. Moreover, the generated fragments preserve relevant inferences that can be made with the selected symbols in the original ontology. Such a method relies on an interval labeling scheme that efficiently manages the transitive relationships present in the ontologies. Additionally, we provide an interval’s algebra to compute some logical operations over the ontology concepts. We have evaluated the proposed method over several well-known biomedical ontologies. Results show very good performance and scalability, demonstrating the applicability of the proposed method in real scenarios.