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Bioinformatics Advance Access originally published online on January 21, 2009
Bioinformatics 2009 25(5):692-694; 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: 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, US EPA and 2Lockheed Martin, Research Triangle Park, NC 27711, USA

*To whom correspondence should be addressed.


  Abstract

Summary: The Distributed Structure-Searchable Toxicity (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 September 20, 2008). 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 resource, 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: Supplementary data are available at Bioinformatics online.

Associate Editor: Alex Bateman

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

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Home page
 Toxicol SciHome page
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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