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GIMS-a data warehouse for storage and analysis of genome sequence and functional data

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10 Author(s)
Cornell, M. ; Dept. of Comput. Sci., Manchester Univ., UK ; Paton, N.W. ; Shengli Wu ; Goble, C.A.
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Effective analysis of genome sequences and associated functional data requires access to many different kinds of biological information. For example, when analysing gene expression data, it may be useful to have access to the sequences upstream of the genes, or to the cellular location of their protein products. Such information is currently stored in different formats at different sites in a way that does not readily allow integrated analyses. The Genome Information Management System (GIMS) is an object database that integrates genome sequence data with functional data on the transcriptome and on protein-protein interactions in a single data warehouse. We have used GIMS to store the Saccharomyces cerevisiae (yeast) genome and to demonstrate how the integrated storage of diverse kinds of genomic data can be beneficial for analysing data using context-rich queries and analyses. GIMS allows data to be stored in a way that reflects the underlying mechanisms in the organism, and permits complex questions to be asked of the data. This paper provides an overview of the GIMS system and describes some analyses that illustrate its use for analysing functional data sets for S. cerevisiae

Published in:

Bioinformatics and Bioengineering Conference, 2001. Proceedings of the IEEE 2nd International Symposium on

Date of Conference:

4-6 Nov 2001