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Open Access Database

GeneKeyDB: A lightweight, gene-centric, relational database to support data mining environments

SA Kirov1, X Peng1, E Baker3, D Schmoyer2, B Zhang1 and J Snoddy12*

Author Affiliations

1 Graduate School for Genome Science and Technology, Oak Ridge National Laboratory-University of Tennessee, Oak Ridge, USA

2 Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, USA

3 Department of Engineering and Computer Science, Baylor University, Waco, USA

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BMC Bioinformatics 2005, 6:72  doi:10.1186/1471-2105-6-72

Published: 24 March 2005

Abstract

Background

The analysis of biological data is greatly enhanced by existing or emerging databases. Most existing databases, with few exceptions are not designed to easily support large scale computational analysis, but rather offer exclusively a web interface to the resource. We have recognized the growing need for a database which can be used successfully as a backend to computational analysis tools and pipelines. Such database should be sufficiently versatile to allow easy system integration.

Results

GeneKeyDB is a gene-centered relational database developed to enhance data mining in biological data sets. The system provides an underlying data layer for computational analysis tools and visualization tools. GeneKeyDB relies primarily on existing database identifiers derived from community databases (NCBI, GO, Ensembl, et al.) as well as the known relationships among those identifiers. It is a lightweight, portable, and extensible platform for integration with computational tools and analysis environments.

Conclusion

GeneKeyDB can enable analysis tools and users to manipulate the intersections, unions, and differences among different data sets.