OpenLB
Open Library of Bioscience
Advanced Search
Database : the journal of biological databases and curation
2013;2013 bat051.

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

Roberto Vera, Yasset Perez-Riverol, Sonia Perez, Balázs Ligeti, Attila Kertész-Farkas, Sándor Pongor
Author Information
  1. Roberto Vera: Department of Physics, Polytechnic University Jose E. Echeverria, Havana, Cuba. Roberto.Vera@icgeb.org
PMID: 23846595 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.

References

  1. Database (Oxford). 2011 Nov 13;2011:bar049 [PMID: 22083790]
  2. AMIA Annu Symp Proc. 2005;:779-83 [PMID: 16779146]
  3. Bioinformatics. 2009 Jun 1;25(11):1422-3 [PMID: 19304878]
  4. Nucleic Acids Res. 2007 Jan;35(Database issue):D572-4 [PMID: 17135203]
  5. Nucleic Acids Res. 2011 Jan;39(Database issue):D32-7 [PMID: 21071399]
  6. Nat Genet. 2000 May;25(1):25-9 [PMID: 10802651]
  7. Nucleic Acids Res. 2008 Jan;36(Database issue):D13-21 [PMID: 18045790]
  8. Nucleic Acids Res. 2005 Oct 24;33(19):6083-9 [PMID: 16246909]
  9. Nucleic Acids Res. 2012 Jan;40(Database issue):D71-5 [PMID: 22102590]
  10. Nucleic Acids Res. 2012 Jan;40(Database issue):D841-6 [PMID: 22121220]
  11. Genome Res. 2004 Jan;14(1):160-9 [PMID: 14707178]
  12. Nucleic Acids Res. 2012 Jan;40(Database issue):D84-90 [PMID: 22086963]
  13. Nucleic Acids Res. 2012 Jan;40(Database issue):D284-9 [PMID: 22096231]
  14. BMC Bioinformatics. 2006 Mar 28;7:176 [PMID: 16569235]
  15. Bioinformatics. 2012 Oct 15;28(20):2693-5 [PMID: 22877863]
  16. Comput Appl Biosci. 1993 Feb;9(1):49-57 [PMID: 8435768]
  17. Nat Genet. 2012 Jan 27;44(2):121-6 [PMID: 22281772]
  18. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D449-51 [PMID: 14681454]
  19. Nat Rev Genet. 2003 May;4(5):337-45 [PMID: 12728276]
  20. BMC Bioinformatics. 2003 Sep 11;4:41 [PMID: 12969510]
  21. BMC Bioinformatics. 2006 Mar 23;7:170 [PMID: 16556315]
  22. BMC Bioinformatics. 2005 Feb 21;6:34 [PMID: 15723693]
  23. Nat Biotechnol. 2010 Sep;28(9):935-42 [PMID: 20829833]
  24. Database (Oxford). 2012 Mar 20;2012:bar059 [PMID: 22434828]
  25. Nucleic Acids Res. 2012 Jan;40(Database issue):D109-14 [PMID: 22080510]
  26. Nucleic Acids Res. 2009 Jan;37(Database issue):D767-72 [PMID: 18988627]
  27. Nucleic Acids Res. 2001 Jan 1;29(1):137-40 [PMID: 11125071]
  28. Nucleic Acids Res. 2003 Jan 1;31(1):248-50 [PMID: 12519993]
  29. Nucleic Acids Res. 2000 Jan 1;28(1):304-5 [PMID: 10592255]
  30. Nucleic Acids Res. 2012 Jan;40(Database issue):D130-5 [PMID: 22121212]
  31. Genome Res. 2002 Oct;12(10):1611-8 [PMID: 12368254]
  32. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D514-7 [PMID: 15608251]
  33. Nucleic Acids Res. 2010 Jan;38(Database issue):D340-5 [PMID: 19892825]
  34. Nucleic Acids Res. 2011 Jan;39(Database issue):D1035-41 [PMID: 21059682]
  35. Brief Bioinform. 2002 Dec;3(4):331-41 [PMID: 12511062]
  36. Bioinformatics. 2005 Aug 15;21(16):3439-40 [PMID: 16082012]
  37. BMC Bioinformatics. 2006 Feb 15;7:70 [PMID: 16480510]

MeSH Term

Computational Biology
Database Management Systems
Databases as Topic
Pharmaceutical Preparations
Programming Languages
User-Computer Interface

Chemicals

Pharmaceutical Preparations
Journal Article Research Support, Non-U.S. Gov't
Article has an altmetric score of 9

Word Cloud

Created with Highcharts 10.0.0dataJBioWHframeworkcanJavaopen-sourcedatabasesourcesintensiveMySQLincludesapplicationhttp://codegooglecom/p/jbiowhBioWareHouseprojectplatform-independentprogrammingallowsuserbuildhis/herintegratedpopularusedqueryingmultiplecreationstreamlinedtask-specificsetslocalPCsbasedrelationalschemeJAVAAPIparserfunctionsretrieving20publicdatabasesegNCBIKEGGetcalsoclientdesktopnon-programmerusersqueryadditiontailoredusespecificcircumstancesincludinghandlingmassivequerieshigh-throughputanalysesCPUcalculationsprovidedcompletedocumentationexamplesdownloadedProjectWebsiteserveravailabledemonstrationpurposeshydraxicgebtriesteit:3307DatabaseURL:JBioWH:bioinformaticsintegration

Similar Articles

Cited By