Introduction

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.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.

Publications

  1. GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus.
    Cite this
    Zhu Y, Davis S, Stephens R, Meltzer PS, Chen Y, 2008-12-01 - Bioinformatics (Oxford, England)

Credits

  1. Yuelin Zhu
    Developer

    Genetics Branch, National Cancer Institute, United States of America

  2. Sean Davis
    Developer

  3. Robert Stephens
    Developer

  4. Paul S Meltzer
    Developer

  5. Yidong Chen
    Investigator

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT006629
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByYidong Chen