Mediator Infrastructure for Information Integration and Semantic Data Integration Environment for Biomedical Research

  • Jeffrey S. Grethe
  • Edward Ross
  • David Little
  • Brian Sanders
  • Amarnath Gupta
  • Vadim Astakhov
Part of the Methods in Molecular Biology™ book series (MIMB, volume 569)


This paper presents current progress in the development of semantic data integration environment which is a part of the Biomedical Informatics Research Network (BIRN; project. BIRN is sponsored by the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH). A goal is the development of a cyberinfrastructure for biomedical research that supports advance data acquisition, data storage, data management, data integration, data mining, data visualization, and other computing and information processing services over the Internet. Each participating institution maintains storage of their experimental or computationally derived data. Mediator-based data integration system performs semantic integration over the databases to enable researchers to perform analyses based on larger and broader datasets than would be available from any single institution’s data. This paper describes recent revision of the system architecture, implementation, and capabilities of the semantically based data integration environment for BIRN.

Key words

Cyber infrastructure Neuroinformatics Biomedical informatics Distributed information management Database Data federation Semantics Information integration Ontology 



This work is supported by NIH BIRN-CC Award No. U24 RR019701-01 (NCRR BIRN Coordinating Center Project BIRN005). The authors thank their colleagues and students involved in the BIRN project for their contributions, in particular, Willy WaiHo Wong, Joshua Tran, Asif Memon, and Ilya Zaslavsky.


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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Jeffrey S. Grethe
    • 1
  • Edward Ross
    • 2
  • David Little
    • 3
  • Brian Sanders
    • 3
  • Amarnath Gupta
    • 4
  • Vadim Astakhov
    • 5
  1. 1.Biomedical Informatics Research NetworkLa JollaUSA
  2. 2.Biomedical Informatics Research NetworkSan DiegoUSA
  3. 3.The Center for Research in Biological Systems (CRBS)La JollaUSA
  4. 4.San Diego Supercomputer Center, University of California – San DiegoLa JollaUSA
  5. 5.Biomedical Informatics Research Network Coordination Center, The Center for Research in Biological Systems (CRBS), UCSDLa JollaUSA

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