The Comparative Toxicogenomics Database: update 2011

By Allan Peter Davis, B. King, S. Mockus, Cynthia G. Murphy, Cynthia A. Saraceni-Richards, Michael C. Rosenstein, Thomas C. Wiegers, Carolyn J. Mattingly. Nucleic Acids Res., 2010

557 citations recorded by the source corpus.

The Comparative Toxicogenomics Database (CTD) is a public resource that promotes understanding about the interaction of environmental chemicals with gene products, and their effects on human health. Biocurators at CTD manually curate a triad of chemical–gene, chemical–disease and gene–disease relationships from the literature. These core data are then integrated to construct chemical–gene–disease networks and to predict many novel relationships using different types of associated data. Since 2009, we dramatically increased the content of CTD to 1.4 million chemical–gene–disease data points and added many features, statistical analyses and analytical tools, including GeneComps and ChemComps (to find comparable genes and chemicals that share toxicogenomic profiles), enriched Gene Ontology terms associated with chemicals, statistically ranked chemical–disease inferences, Venn diagram tools to discover overlapping and unique attributes of any set of chemicals, genes or disease, and enhanced gene pathway data content, among other features. Together, this wealth of expanded chemical–gene–disease data continues to help users generate testable hypotheses about the molecular mechanisms of environmental diseases. CTD is freely available at http://ctd.mdibl.org.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/8b683b12f9efc1d8bdf330182a0afd7c14369ce1

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Citations in the corpus

Open Targets: a platform for therapeutic target identification and validation (2016, methodology): “However, DisGeNET provides additional genedisease association via the Comparative Toxicogenomics Datatabase (CTD, (42)) to cover the effects of environmental chemicals on human health.”
PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species (2011, methodology): “…within other bacterial genomes), human genes associated with disease (Genetic Association Database [8, 57] and Comparative Toxicogenomics Database [14]), and disease-pathogen data (interactive graphics for relationships between pathogens, diseases, virulence genes, and disease-associated host…”
Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, unknown): “In this respect, the development of an international plant toxicogenomics database in the mould of the human Comparative Toxicogenomics Database (Davis et al., 2011) would be a great asset.”
The BioGRID interaction database: 2019 update (2018, methodology): “We examined the content of major chemical interaction databases, including DrugBank (60), BindingDB (61), CTD (62), PharmGKB (63), ChEMBL (64) and others to determine the fields common to each resource.”
Network Pharmacology: A New Approach for Chinese Herbal Medicine Research (2013, methodology): “In addition, the databases such as Comparative Toxicogenomics Database, National Toxicology Program, and Toxicology Data Network are widely used for network toxicology studies [68, 69].”