A CASE STUDY: DEVELOPMENT OF AN ORGANISM–SPECIFIC PROTEIN INTERACTION DATABASE AND ITS ASSOCIATED TOOLS

Abstract

In this paper, we describe the architecture of a protein interaction database and tools for manipulating Drosophila protein interaction data. The proposed system not only maintains interaction data collected by an experiment, but also associates the interaction data with valuable data from various genomic databases. The system inherits a layered-modular architecture by introducing a wrapper-mediator approach in order to solve the syntactic and semantic heterogeneity among multiple data sources. The component modules for wrapping and integrating the relevant data, querying the database, and visualizing the interaction data among proteins are discussed. The system wrapped the relevant data for 14,000 Drosophila proteins from 5 publicly accessible sources. A web-based query interface is developed to browse the database and a query result can be viewed as in a protein interaction map depicting functional pathways, complexes or networks. Protein interaction maps aid in understanding or predicting potential functions for uncharacterized proteins and in describing their functional networks in a biological context. We show that the proposed approach supports data association and data interoperability in a protein interaction database.