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. 2005 Mar 24:6:72.
doi: 10.1186/1471-2105-6-72.

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

S A Kirov  1 , X Peng, E Baker, D Schmoyer, B Zhang, J Snoddy
Affiliations

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

S A Kirov et al. BMC Bioinformatics. .

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.

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Figures

Figure 1
Figure 1
GeneKeyDB sub-modules, external database identifiers and connecting tables. The connecting tables may convert between the central key and another unique key used throughout the sub-module and are shown next to the connector lines.
Figure 2
Figure 2
A workflow schema of GeneKeyDB creation and export to other RDBMS. *LocusLink is parsed first as other sub-modules depend on it with respect to the central key of the database. PROD refers to the current production stage database.
See this image and copyright information in PMC

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