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Bioinformatics Advance Access originally published online on October 7, 2008
Bioinformatics 2008 24(23):2798-2800; doi:10.1093/bioinformatics/btn520
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

Yuelin Zhu 1,2, Sean Davis 1, Robert Stephens 2, Paul S. Meltzer 1 and Yidong Chen 1,*

1Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 and 2Advanced Biomedical Computing Center, National Cancer Institute-Frederick/SAIC-Frederick Inc., Frederick, MD 21702, USA

*To whom correspondence should be addressed.


  Abstract

The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data in GEO can be challenging. We have developed GEOmetadb in an attempt to make querying the GEO metadata both easier and more powerful. All GEO metadata records as well as the relationships between them are parsed and stored in a local MySQL database. A powerful, flexible web search interface with several convenient utilities provides query capabilities not available via NCBI tools. In addition, a Bioconductor package, GEOmetadb that utilizes a SQLite export of the entire GEOmetadb database is also available, rendering the entire GEO database accessible with full power of SQL-based queries from within R.

Availability: The web interface and SQLite databases available at http://gbnci.abcc.ncifcrf.gov/geo/. The Bioconductor package is available via the Bioconductor project. The corresponding MATLAB implementation is also available at the same website.

Contact: yidong{at}mail.nih.gov

Associate Editor: Joaquin Dopazo

Received on April 22, 2008; revised on August 7, 2008; accepted on November 3, 2008

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