GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

Bioinformatics. 2008 Dec 1;24(23):2798-800. doi: 10.1093/bioinformatics/btn520. Epub 2008 Oct 7.


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 The Bioconductor package is available via the Bioconductor project. The corresponding MATLAB implementation is also available at the same website.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Databases, Genetic*
  • Gene Expression Profiling*
  • Gene Expression*
  • Information Storage and Retrieval
  • Oligonucleotide Array Sequence Analysis
  • Software*
  • User-Computer Interface