BioGraphDB: a New GraphDB Collecting Heterogeneous Data for Bioinformatics Analysis

Antonino Fiannaca, La Rosa, Laura Paglia, Antonio Messina, Alfonso Urso
unpublished
Current bioinformatics databases provide huge amounts of different biological entities such as genes, proteins, diseases, microRNA, annotations, literature references. In many case studies, a bioinformatician often needs more than one type of resource in order to fully analyse his data. In this paper, we introduce BioGraphDB, a bioinformatics database that allows the integration of different types of data sources, so that it is possible to perform bioinformatics analysis using only a
more » ... ve system. Our integrated database is structured as a NoSQL graph database, based on the OrientDB platform. This way we exploit the advantages of that technology in terms of scalability and efficiency with regards to traditional SQL database. At the moment, we integrated ten different resources, storing and linking data about genes, proteins, microRNAs, molecular pathways, functional annotations, literature references and associations between microRNA and cancer diseases. Moreover, we illustrate some typical bioinformatics scenarios for which the user just needs to query the BioGraphDB to solve them.
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