title: JBioWH: an open-source Java framework for bioinformatics data integration.
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.
authors.affiliation: Department of Physics, Polytechnic University Jose E. Echeverria, Havana, Cuba. Roberto.Vera@icgeb.org
authors.forename: Roberto
authors.initials: R
authors.lastname: Vera
authors.forename: Yasset
authors.initials: Y
authors.lastname: Perez-Riverol
authors.forename: Sonia
authors.initials: S
authors.lastname: Perez
authors.forename: Balázs
authors.initials: B
authors.lastname: Ligeti
authors.forename: Attila
authors.initials: A
authors.lastname: Kertész-Farkas
authors.forename: Sándor
authors.initials: S
authors.lastname: Pongor
mesh_terms: D019295:Computational Biology; D003628:Database Management Systems; D019992:Databases as Topic; D004364:Pharmaceutical Preparations; D011381:Programming Languages; D014584:User-Computer Interface
chemical_list: D004364:Pharmaceutical Preparations