GEOmetadb: GEO Microarray Search Tool

What is GEOmetadb?

The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data of interest can be challenging using current tools. GEOmetadb is an attempt to make access to the metadata associated with GEO samples, platforms, and datasets much more feasible. This is accomplished by parsing all the NCBI GEO metadata into a MySQL database. A SQLite database version of it can be stored and queried locally. GEOmetadb Bioconductor package is simply a thin wrapper around the SQLite database along with associated documentation. Finally, the SQLite database is updated regularly as new data is added to GEO and can be downloaded at will for the most up-to-date metadata.

What's new about GEOmetadb?

GEOmetadb has been updated to version 2.0. New feature includes:

• Database tables and search interfaces have been modified significantly
• Search performance has been improved
• Several user-friendly functions have been added, e.g. drill-down search, download search results, ...
• Read more

GEOmetadb Web Interface:

GEOmetadb Distributions:

Get Started: Joint Search | GSE Search

• Main features:
  • Search by individual data types
  • Search by GSE-GPL-GSM cross data types
  • GEO entities are linked by relationships between them
  • Multiple field query
  • Query within results
  • List creation
  • Flexible display options
  • Export or view details
• Read More

If you want to find GEO microarray data of interest directly within R by using power of SQL? And then reanalyze it with many new and rigorous methods/algorithms in BioConductor? Please try combination use of GEOmetadb and GEOquery.

• BioConductor package:
  • Released in BioC 2.2 with R2.7
  • Document and Download:
    GEOmetadb
    
• SQLite3 database:
  • Last updated:
    July 19 2008 10:30:30.
  • Download:
    GEOmetadb.sqlite.gz ( 40 MB)

- Matlab GEOtools:

• Download: MATLAB_GEOtools.zip (Mac OS X, Intel)
• Document: GEOmetadb_matlab.pdf (pdf)