title: Dynamic integration of biological data sources using the data concierge.
abstract: BACKGROUND
  The ever-changing landscape of large-scale network environments and innovative biology technologies require dynamic mechanisms to rapidly integrate previously unknown bioinformatics sources at runtime. However, existing integration technologies lack sufficient flexibility to adapt to these changes, because the techniques used for integration are static, and sensitive to new or changing bioinformatics source implementations and evolutionary biologist requirements.
  
  
  METHODS
  To address this challenge, in this paper we propose a new semantics-based adaptive middleware, the Data Concierge, which is able to dynamically integrate heterogeneous biological data sources without the need for wrappers. Along with the architecture necessary to facilitate dynamic integration, API description mechanism is proposed to dynamically classify, recognize, locate, and invoke newly added biological data source functionalities. Based on the unified semantic metadata, XML-based state machines are able to provide flexible configurations to execute biologist's abstract and complex operations.
  
  
  CONCLUSIONS
  Experimental results demonstrate that for obtaining dynamic features, the Data Concierge sacrifices reasonable performance on reasoning knowledge models and dynamically doing data source API invocations. The overall costs to integrate new biological data sources are significantly lower when using the Data Concierge.
  
  
  CONCLUSIONS
  The Data Concierge facilitates the rapid integration of new biological data sources in existing applications with no repetitive software development required, and hence, this mechanism would provide a cost-effective solution to the labor-intensive software engineering tasks.
authors.affiliation: Biomedical and Multimedia Information Technology (BMIT) Research Group, School of Information Technologies, the University of Sydney, Sydney, NSW 2006 Australia ; Department of PET and Nuclear Medicine, RPA Hospital, Camperdown, NSW 2050 Australia.
authors.forename: Peng
authors.initials: P
authors.lastname: Gong
keywords: Biology; Data integration; Middleware; Ontology; State machine
references.citation: J Biomed Inform. 2008 Oct;41(5):706-16
references.pmid: 18472304
references.citation: Brief Bioinform. 2000 Feb;1(1):9-21
references.pmid: 11466976
references.citation: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W719-23
references.pmid: 20501602
references.citation: J Biomed Inform. 2008 Oct;41(5):687-93
references.pmid: 18358788
references.citation: IEEE Trans Inf Technol Biomed. 2004 Jun;8(2):154-60
references.pmid: 15217260
references.citation: Stud Health Technol Inform. 2004;107(Pt 2):783-7
references.pmid: 15360919
references.citation: Bioinformatics. 2001 Feb;17(2):115-25
references.pmid: 11238067
references.citation: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W23-7
references.pmid: 19420058
references.citation: Bioinformatics. 2001 Feb;17(2):180-8
references.pmid: 11238075
references.citation: IEEE Trans Inf Technol Biomed. 2002 Jun;6(2):123-8
references.pmid: 12075666
references.citation: Chem Biodivers. 2010 May;7(5):1124-41
references.pmid: 20491070
references.citation: BMC Bioinformatics. 2006 Feb 15;7:70
references.pmid: 16480510
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D1160-7
references.pmid: 22121219
references.citation: Stud Health Technol Inform. 2004;107(Pt 2):768-72
references.pmid: 15360916
references.citation: IEEE Trans Inf Technol Biomed. 2002 Jun;6(2):116-22
references.pmid: 12075665
references.citation: Bioinformatics. 2004 Jan 1;20(1):51-7
references.pmid: 14693808
references.citation: IEEE Trans Inf Technol Biomed. 2006 Oct;10(4):714-21
references.pmid: 17044405
references.citation: Bioinformatics. 2003 Oct 12;19(15):1927-33
references.pmid: 14555625
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D9-12
references.pmid: 22144683
references.citation: BMC Bioinformatics. 2003 Dec 16;4:63
references.pmid: 14678565
references.citation: Bioinformatics. 2001 Jan;17(1):83-94
references.pmid: 11222265
references.citation: Nucleic Acids Res. 2003 Jan 1;31(1):1-12
references.pmid: 12519937
references.citation: Biochimie. 2008 Apr;90(4):584-94
references.pmid: 18294970