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Bioinformatics Vol. 19 no. 14 2003
Pages 1844-1845
© 2003 Oxford University Press

Applications Note

An XML message broker framework for exchange and integration of microarray data

Donny Tjandra 1,*, Stephen Wong 2,3, Weimin Shen 1, Brian Pulliam 4, Elaine Yu 5 and Laura Esserman 1,5,6

1 UCSF Department of Radiology, 505 Parnassus Avenue, Box 0628, San Francisco, CA 94143-0628, USA, 2 Harvard Center for Neurodegeneration and Repair (HCNR), Harvard Medical School, Boston, MA 02115, USA, 3 Department of Radiology, Brigham & Women Hospital, Harvard Medical School, Boston, MA 02115, USA, 4 Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA, 5 Carol Franc Buck Breast Care Center, University of California, San Francisco, CA 94115, USA and 6 Department of Surgery, School of Medicine, University of California, San Francisco, CA 94143, USA

Received on January 6, 2003 ; revised on March 18, 2003 ; accepted on April 17, 2003

Motivation: Microarrays are an important research tool for the advancement of basic biological sciences. However this technology has yet to be integrated with clinical decision making. We have implemented an information framework based on the Microarray Gene Expression Markup Language (MAGE-ML) specification. We are using this framework to develop a test-bed integrated database application to identify genomic and imaging markers for diagnosis of breast cancer.

Results: We developed extensible software architecture for retrieving data from different microarray databases using MAGE-ML and for combining microarray data with breast cancer image analysis and clinical data for correlation studies. The framework we developed will provide the necessary data integration to move microarray research from basic biological sciences to clinical applications.

Availability: Open source software will be available from SourceForge (http://sourceforge.net/projects/microsoap/).

Contact: donny.tjandra{at}radiology.ucsf.edu

* To whom correspondence should be addressed.


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