Title: bcnQL: A query language for biochemical networks

Authors: H. Yang, R. Sunderraman, H. Tian

Addresses: Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA. ' Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA. ' Chronic Viral Diseases Branch Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30333, USA

Abstract: This paper proposes a graph data model that can represent information present in Biochemical Networks. The study presented in this paper also proposes a query language, called bcnQL, which empowers users to query entities, interactions, processes and pathways with arbitrary conditions. We then discuss the query-processing techniques, more specifically, the translation of bcnQL queries into G-algebra and a set of algebraic operators on graph objects. Some query examples are presented to demonstrate the applicability of the language for this specific domain. Finally, we provide details of a prototype implementation for the query language.

Keywords: graph data modelling; query languages; G-algebra; biochemical networks; bioinformatics; query processing.

DOI: 10.1504/IJDMB.2010.035901

International Journal of Data Mining and Bioinformatics, 2010 Vol.4 No.5, pp.571 - 587

Published online: 08 Oct 2010 *

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