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BioGraphDB: A New graphDB Collecting Heterogeneous Data for Bioinformatics Analysis

Authors:
Antonino Fiannaca
Massimo La Rosa
Laura La Paglia
Antonio Messina
Alfonso Urso

Keywords: Integrated database; Graph database; GraphDB; OrientDB; Bioinformatics database

Abstract:
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 comprehensive system. Our integrated database is structured as a NoSQL graph database, based on the OrientDB platform. This way we exploits 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.

Pages: 28 to 34

Copyright: Copyright (c) IARIA, 2016

Publication date: June 26, 2016

Published in: conference

ISSN: 2308-4383

ISBN: 978-1-61208-488-6

Location: Lisbon, Portugal

Dates: from June 26, 2016 to June 30, 2016