Journal Article

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

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

in Bioinformatics

Volume 24, issue 23, pages 2798-2800
Published in print December 2008 | ISSN: 1367-4803
Published online November 2008 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btn520

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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@mail.nih.gov

Journal Article.  1052 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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