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Bioinformatics Advance Access published online on January 21, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp042
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

DSSTox Chemical-index Files for Exposure-Related Experiments in ArrayExpress and Gene Expression Omnibus (GEO): Enabling Toxico-chemogenomics Data Linkages

ClarLynda R. Williams-DeVane 1,*, Maritja A. Wolf 2 and Ann M. Richard 1

1National Center for Computational Toxicology, Office of Research and Development, U.S. EPA, Research Tri-angle Park, NC 27711, USA.
2Lockheed Martin (Contractor to U.S. EPA), Research Triangle Park, NC 27711, USA.

*To whom correspondence should be addressed. Mrs. ClarLynda Williams-DeVane, E-mail: williams.clarlynda{at}epa.gov, richard.ann{at}epa.gov


  Abstract

Summary: The DSSTox ARYEXP and GEOGSE files are newly published, structure-annotated files of the chemical-associated and chemical exposure-related summary experimental content contained in the ArrayExpress Repository and Gene Expression Omnibus (GEO) Series (based on data extracted on 20Sept2008). ARYEXP and GEOGSE contain 887 and 1064 unique chemical substances mapped to 1835 and 2381 chemical exposure-related experiment accession IDs, respectively. The standardized files allow one to assess, compare, and search the chemical content in each re-source, in the context of the larger DSSTox toxicology data network, as well as across large public cheminformatics resources such as PubChem (http://pubchem.ncbi.nlm.nih.gov).

Availability: Data files and documentation may be accessed online at http://epa.gov/ncct/dsstox/.

Contact: williams.clarlynda{at}epa.gov

Supplementary Information: Supplemental Tables available online.

Disclaimer

This manuscript was approved by the U.S. EPA's National Center for Computational Toxicology for publication; the contents do not necessarily reflect the views and policies of the EPA and mention of trade names or commercial products does not constitute endorse-ment or recommendation for use.

Associate Editor: Dr. Alex Bateman

Received on October 31, 2008; revised on January 12, 2009; accepted on January 18, 2009

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C. R. Williams-Devane, M. A. Wolf, and A. M. Richard
Toward a Public Toxicogenomics Capability for Supporting Predictive Toxicology: Survey of Current Resources and Chemical Indexing of Experiments in GEO and ArrayExpress
Toxicol. Sci., June 1, 2009; 109(2): 358 - 371.
[Abstract] [Full Text] [PDF]


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