JBioWH: an open-source Java framework for bioinformatics data integration.

Sándor Pongor,Yasset Perez-Riverol,Roberto Vera,Attila Kertész-Farkas,Sonia Perez,Balázs Ligeti

doi:10.1093/database/bat051

Abstract

The Java BioWareHouse (JBioWH) project is an open-source platform-independent programming framework that allows a user to build his/her own integrated database from the most popular data sources. JBioWH can be used for intensive querying of multiple data sources and the creation of streamlined task-specific data sets on local PCs. JBioWH is based on a MySQL relational database scheme and includes JAVA API parser functions for retrieving data from 20 public databases (e.g. NCBI, KEGG, etc.). It also includes a client desktop application for (non-programmer) users to query data. In addition, JBioWH can be tailored for use in specific circumstances, including the handling of massive queries for high-throughput analyses or CPU intensive calculations. The framework is provided with complete documentation and application examples and it can be downloaded from the Project Web site at http://code.google.com/p/jbiowh. A MySQL server is available for demonstration purposes at hydrax.icgeb.trieste.it:3307.Database URL: http://code.google.com/p/jbiowh

Highlights

Integrating heterogeneous bioinformatics data is perhaps one of the most challenging tasks in biomedical research today
A complete overview of the subject would be beyond the scope of this article, as virtually all current bioinformatics efforts contain some kind of data integration [for in-depth reviews see [2,3,4,5]]
Java BioWareHouse (JBioWH) is based on the free and platform-independent Java language to create a MySQL-based data warehouse that is built around a modular relational database scheme

Summary

Introduction

Integrating heterogeneous bioinformatics data is perhaps one of the most challenging tasks in biomedical research today. Warehouse databases integrate data sources in one place: examples of this approach include BioWarehouse [13], Biozon [14], Atlas [15], EnsMart [16] and IGD [17]. Java BioWareHouse (JBioWH) is an open-source framework aiming to reach users who need to query multiple public data sets in a flexible way using their PC or a local workstation.

Results

Conclusion