In EDS ansehen

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

Gespeichert in:
Bibliographische Detailangaben
Titel: JBioWH: an open-source Java framework for bioinformatics data integration.
Autoren: Vera R; Department of Physics, Polytechnic University Jose E. Echeverria, Havana, Cuba. Roberto.Vera@icgeb.org, Perez-Riverol Y, Perez S, Ligeti B, Kertész-Farkas A, Pongor S
Quelle: Database : the journal of biological databases and curation [Database (Oxford)] 2013 Jul 11; Vol. 2013, pp. bat051. Date of Electronic Publication: 2013 Jul 11 (Print Publication: 2013).
Publikationsart: Journal Article; Research Support, Non-U.S. Gov't
Sprache: English
Info zur Zeitschrift: Publisher: Oxford Journals Country of Publication: England NLM ID: 101517697 Publication Model: Electronic-Print Cited Medium: Internet ISSN: 1758-0463 (Electronic) Linking ISSN: 17580463 NLM ISO Abbreviation: Database (Oxford) Subsets: MEDLINE
Imprint Name(s): Original Publication: Oxford : Oxford Journals, 2009-
MeSH-Schlagworte: Computational Biology* , Database Management Systems* , Databases as Topic* , Programming Languages* , User-Computer Interface*, Pharmaceutical Preparations
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: Database (Oxford). 2011 Nov 13;2011:bar049. (PMID: 22083790)
AMIA Annu Symp Proc. 2005;:779-83. (PMID: 16779146)
Bioinformatics. 2009 Jun 1;25(11):1422-3. (PMID: 19304878)
Nucleic Acids Res. 2007 Jan;35(Database issue):D572-4. (PMID: 17135203)
Nucleic Acids Res. 2011 Jan;39(Database issue):D32-7. (PMID: 21071399)
Nat Genet. 2000 May;25(1):25-9. (PMID: 10802651)
Nucleic Acids Res. 2008 Jan;36(Database issue):D13-21. (PMID: 18045790)
Nucleic Acids Res. 2005 Oct 24;33(19):6083-9. (PMID: 16246909)
Nucleic Acids Res. 2012 Jan;40(Database issue):D71-5. (PMID: 22102590)
Nucleic Acids Res. 2012 Jan;40(Database issue):D841-6. (PMID: 22121220)
Genome Res. 2004 Jan;14(1):160-9. (PMID: 14707178)
Nucleic Acids Res. 2012 Jan;40(Database issue):D84-90. (PMID: 22086963)
Nucleic Acids Res. 2012 Jan;40(Database issue):D284-9. (PMID: 22096231)
BMC Bioinformatics. 2006 Mar 28;7:176. (PMID: 16569235)
Bioinformatics. 2012 Oct 15;28(20):2693-5. (PMID: 22877863)
Comput Appl Biosci. 1993 Feb;9(1):49-57. (PMID: 8435768)
Nat Genet. 2012 Jan 27;44(2):121-6. (PMID: 22281772)
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D449-51. (PMID: 14681454)
Nat Rev Genet. 2003 May;4(5):337-45. (PMID: 12728276)
BMC Bioinformatics. 2003 Sep 11;4:41. (PMID: 12969510)
BMC Bioinformatics. 2006 Mar 23;7:170. (PMID: 16556315)
BMC Bioinformatics. 2005 Feb 21;6:34. (PMID: 15723693)
Nat Biotechnol. 2010 Sep;28(9):935-42. (PMID: 20829833)
Database (Oxford). 2012 Mar 20;2012:bar059. (PMID: 22434828)
Nucleic Acids Res. 2012 Jan;40(Database issue):D109-14. (PMID: 22080510)
Nucleic Acids Res. 2009 Jan;37(Database issue):D767-72. (PMID: 18988627)
Nucleic Acids Res. 2001 Jan 1;29(1):137-40. (PMID: 11125071)
Nucleic Acids Res. 2003 Jan 1;31(1):248-50. (PMID: 12519993)
Nucleic Acids Res. 2000 Jan 1;28(1):304-5. (PMID: 10592255)
Nucleic Acids Res. 2012 Jan;40(Database issue):D130-5. (PMID: 22121212)
Genome Res. 2002 Oct;12(10):1611-8. (PMID: 12368254)
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D514-7. (PMID: 15608251)
Nucleic Acids Res. 2010 Jan;38(Database issue):D340-5. (PMID: 19892825)
Nucleic Acids Res. 2011 Jan;39(Database issue):D1035-41. (PMID: 21059682)
Brief Bioinform. 2002 Dec;3(4):331-41. (PMID: 12511062)
Bioinformatics. 2005 Aug 15;21(16):3439-40. (PMID: 16082012)
BMC Bioinformatics. 2006 Feb 15;7:70. (PMID: 16480510)
Substance Nomenclature: 0 (Pharmaceutical Preparations)
Entry Date(s): Date Created: 20130713 Date Completed: 20131021 Latest Revision: 20240324
Update Code: 20260130
PubMed Central ID: PMC3708619
DOI: 10.1093/database/bat051
PMID: 23846595
Datenbank: MEDLINE
Beschreibung
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.
ISSN:1758-0463
DOI:10.1093/database/bat051