Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2008 Dec 1;24(23):2798-800.
doi: 10.1093/bioinformatics/btn520. Epub 2008 Oct 7.

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

Yuelin Zhu  1 , Sean Davis, Robert Stephens, Paul S Meltzer, Yidong Chen
Affiliations

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

Yuelin Zhu et al. Bioinformatics. .

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.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
Diagram of GEO entity relationships in GEOmetadb.
Fig. 2.
Fig. 2.
Screen-capture of GEOmetadb online search: combined GSE-GPL-GSM search.
See this image and copyright information in PMC

References

    1. Edgar R, et al. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002;30:207–210. - PMC - PubMed
    1. Barrett T, et al. NCBI GEO: mining tens of millions of expression profiles—database and tools update. Nucleic Acids Res. 2007;35:D760–D765. - PMC - PubMed
    1. Brazma A, et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet. 2001;29:365–371. - PubMed
    1. Gentleman RC, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5:R80.1–R80.16. - PMC - PubMed
    1. Davis S, Meltzer PS. GEOquery: a bridge between the Gene Expression Omnibus (GEO) and Bioconductor. Bioinformatics. 2007;23:1846–1847. - PubMed

Publication types