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BMC Bioinformatics

, 6:72

First Online: 24 March 2005Received: 02 November 2004Accepted: 24 March 2005


BackgroundThe 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.

ResultsGeneKeyDB 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.

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

List of abbreviationsRDBMSrelational database management system

SQLsimple query language

UIsuser interfaces

APIsapplication programming interfaces

GOTMGO Tree Machine

GRIFGene Reference Into Function

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-6-72 contains supplementary material, which is available to authorized users.

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Autor: SA Kirov - X Peng - E Baker - D Schmoyer - B Zhang - J Snoddy


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