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Biosphere: the interoperation of web services in microarray cluster analysis
Kei-Hoi Cheung1, Remko de Knikker, Youjun Guo
1Center for Medical Informatics, Yale University, 300 George Street, New Haven, CT 06511, USA. kei.cheung@yale.edu
Applied Bioinformatics
|February 11, 2005
Summary
Biosphere integrates diverse DNA microarray analysis tools using web services, enabling unified data clustering, visualization, and retrieval of gene information. This approach overcomes software heterogeneity for comprehensive biomedical research.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- DNA microarrays are widely used in biomedical research, leading to numerous analysis tools.
- Software heterogeneity hinders interoperability between different analysis programs and methods.
Purpose of the Study:
- To address the challenge of software heterogeneity in DNA microarray data analysis.
- To develop a unified platform for accessing and utilizing diverse microarray analysis tools.
Main Methods:
- Employed the Simple Object Access Protocol (SOAP)-based web service approach for uniform programmatic interfaces.
- Developed Biosphere, a web server application interoperating geographically distributed web services.
- Integrated clustering, sequence retrieval (XEMBL), and gene annotation (GetGO, GetHAPI, GetUMLS) web services.
Main Results:
- Biosphere enables users to cluster gene expression data using seven algorithms.
- Provides statistical visualization of clustering results.
- Facilitates retrieval of sequence, annotation, and citation data for genes of interest.
Conclusions:
- The SOAP-based web service approach effectively overcomes software heterogeneity in microarray analysis.
- Biosphere offers a unified platform for comprehensive analysis of DNA microarray data.
- Enhances accessibility and utility of diverse bioinformatics tools for researchers.