Comparative Toxicogenomics Database
| Developer(s) | Department of Bioinformatics, The Mount Desert Island Biological Laboratory |
|---|---|
| Available in | English |
| Type | Bioinformatics, data analysis |
| Website | http://ctdbase.org/ |
The Comparative Toxicogenomics Database (CTD) is a public website and research tool that curates scientific data describing relationships between chemicals, genes, and human diseases.[1][2][3][4]
The database is maintained by the Department of Bioinformatics at the Mount Desert Island Biological Laboratory in Salisbury Cove, Maine.
CTD was launched on the web on November 12, 2004.
Goals and objectives
One of the primary goals of CTD is to advance the understanding of the effects of environmental chemicals on human health.
The etiology of many chronic diseases involves interactions between environmental factors and genes that modulate important physiological processes. Chemicals are an important component of the environment. Conditions such as asthma, cancer, diabetes, hypertension, immunodeficiency, and Parkinson's disease are known to be influenced by the environment; however, the molecular mechanisms underlying these correlations are not well understood. CTD may help resolve these mechanisms.
Core data
CTD is a unique resource where biocurators[5][6] read the scientific literature and manually curate three types of core data:
- Chemical-gene interactions
- Chemical-disease associations
- Gene-disease associations
Data integration
By integrating the above three data sets, CTD automatically constructs putative chemical-gene-disease networks to illuminate molecular mechanisms underlying environmentally-influenced diseases.
Users can search CTD to explore scientific data for chemicals, genes, diseases, or interactions between any of these three concepts. Currently, CTD integrates toxicogenomic data for vertebrates and invertebrates, including 59,000 chemicals, 1.2 million gene and protein sequences (and their associated Gene Ontology, KEGG, and Reactome annotations), 83,000 taxonomic terms, and 6,000 human diseases to produce a unique resource for the cross-species analysis of chemical, gene, and disease interactions.
CTD integrates data from or hyperlinks to these databases:
- ChemIDplus
- DrugBank
- GOAnnotations@EBI
- Gene Ontology Consortium
- KEGG
- NCBI Entrez-Gene
- NCBI PubMed
- NCBI Taxonomy
- NLM Medical Subject Headings
- OMIM
- Reactome
References
- ^ Mattingly CJ, Rosenstein MC, Colby GT, Forrest JN, Boyer JL (2006). "The Comparative Toxicogenomics Database (CTD): A Resource for Comparative Toxicological Studies". J Exp Zoolog. Part a Comp Exp Biol. 305 (9): 689–92. doi:10.1002/jez.a.307. PMC 1586110. PMID 16902965.
{{cite journal}}: Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link) - ^ Mattingly CJ, Rosenstein MC, Davis AP, Colby GT, Forrest JN, Boyer JL (2006). "The Comparative Toxicogenomics Database (CTD): A Cross-Species Resource for Building Chemical-Gene Interaction Networks". Toxicol. Sci. 92 (2): 587–95. doi:10.1093/toxsci/kfl008. PMC 1586111. PMID 16675512.
{{cite journal}}: Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link) - ^ Mattingly CJ, Colby GT, Rosenstein MC, Forrest JN, Boyer JL (2004). "Promoting comparative molecular studies in environmental health research: an overview of the comparative toxicogenomics database (CTD)". Pharmacogenomics J. 4 (1): 5–8. doi:10.1038/sj.tpj.6500225. PMID 14735110.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Mattingly CJ, Colby GT, Forrest JN, Boyer JL (2003). "The Comparative Toxicogenomics Database (CTD)". Environ Health Perspect. 111 (6): 793–5. doi:10.1289/ehp.6028. PMC 1241500. PMID 12760826.
{{cite journal}}: Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link) - ^ Bourne PE, McEntyre J (2006). "Biocurators: Contributors to the World of Science". PLoS Comput Biol. 2 (10): e142. doi:10.1371/journal.pcbi.0020142. PMC 1626157. PMID 17411327.
{{cite journal}}: Unknown parameter|month=ignored (help)CS1 maint: unflagged free DOI (link) - ^ Salimi N, Vita R (2006). "The Biocurator: Connecting and Enhancing Scientific Data". PLoS Comput Biol. 2 (10): e125. doi:10.1371/journal.pcbi.0020125. PMC 1626147. PMID 17069454.
{{cite journal}}: Unknown parameter|month=ignored (help)CS1 maint: unflagged free DOI (link)