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Nucleic Acids Res. 2009 Jan;37(Database issue):D786-92. doi: 10.1093/nar/gkn580. Epub 2008 Sep 9.

Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks.

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  • 1Department of Bioinformatics, The Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA.

Abstract

The Comparative Toxicogenomics Database (CTD) is a curated database that promotes understanding about the effects of environmental chemicals on human health. Biocurators at CTD manually curate chemical-gene interactions, chemical-disease relationships and gene-disease relationships from the literature. This strategy allows data to be integrated to construct chemical-gene-disease networks. CTD is unique in numerous respects: curation focuses on environmental chemicals; interactions are manually curated; interactions are constructed using controlled vocabularies and hierarchies; additional gene attributes (such as Gene Ontology, taxonomy and KEGG pathways) are integrated; data can be viewed from the perspective of a chemical, gene or disease; results and batch queries can be downloaded and saved; and most importantly, CTD acts as both a knowledgebase (by reporting data) and a discovery tool (by generating novel inferences). Over 116,000 interactions between 3900 chemicals and 13,300 genes have been curated from 270 species, and 5900 gene-disease and 2500 chemical-disease direct relationships have been captured. By integrating these data, 350,000 gene-disease relationships and 77,000 chemical-disease relationships can be inferred. This wealth of chemical-gene-disease information yields testable hypotheses for understanding the effects of environmental chemicals on human health. CTD is freely available at http://ctd.mdibl.org.

PMID:
18782832
[PubMed - indexed for MEDLINE]
PMCID:
PMC2686584
Free PMC Article

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