GEOmetadb: Powerful alternative search engine for the Gene Expression Omnibus

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

Research output: Contribution to journalArticlepeer-review

76 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)2798-2800
Number of pages3
JournalBioinformatics
Volume24
Issue number23
DOIs
StatePublished - Dec 2008
Externally publishedYes

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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