Title: Database and software tool interoperation for microarray data analysis

The DNA microarray technology has created a new frontier in biomedical research
by allowing parallel study of the expression patterns of large numbers of genes.
The rapid growth of this technology has led to the generation of massive amounts
of genomic data whose interpretation is key to addressing a wide variety of complex
biomedical research problems. The large-scale analysis of gene expression data often
requires the researchers to use a set of heterogeneous bioinformatics tools and databases.
It is a challenge to interoperate these databases and tools due to the syntactic and
semantic heterogeneities involved. To address this informatics challenge, we first
identify the issues involved in interoperating data and tools in the context of large-scale
gene expression analysis. Next we propose the use of standard XML-based approaches in
tackling the problem of interoperation of microarray-related data and tools. Finally,
we will discuss the current and future effort of the Yale Microarray Database (YMD)
project as a demonstration of how to address this interoperation problem.