Skip Navigation



Bioinformatics Advance Access published online on October 7, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn520
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrowOA All Versions of this Article:
24/23/2798    most recent
btn520v2
btn520v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Zhu, Y.
Right arrow Articles by Chen, Y.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Zhu, Y.
Right arrow Articles by Chen, Y.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus (GEO)

Yuelin Zhu 1,2, Sean Davis 1, Robert Stephens 2, Paul S. Meltzer 1 and Yidong Chen 1,*

1Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, US.
2Advanced Biomedical Computing Center, National Cancer Institute-Frederick/SAIC-Frederick Inc., Frederick, MD 21702, US.

*To whom correspondence should be addressed. Yidong Chen, E-mail: yidong{at}mail.nih.gov


  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://meltzerlab.nci.nih.gov/apps/geo. The Bioconductor package is available via the Bioconductor project. The corresponding MATLAB implementation is also available at the same website.

Contact: yidong{at}mail.nih.gov

Associate Editor: Dr. Joaquin Dopazo

Received on April 22, 2008; revised on August 7, 2008; accepted on October 3, 2008

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
J. Caldas, N. Gehlenborg, A. Faisal, A. Brazma, and S. Kaski
Probabilistic retrieval and visualization of biologically relevant microarray experiments
Bioinformatics, June 15, 2009; 25(12): i145 - i153.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.