The Comparative Toxicogenomics Database (CTD) is a public website and research tool launched in November 2004 that curates scientific data describing relationships between chemicals/drugs, genes/proteins, diseases, taxa, phenotypes, GO annotations, pathways, and interaction modules. The database is maintained by the Department of Biological Sciences at North Carolina State University.
| Developer(s) | Department of Biological Sciences at North Carolina State University and the Department of Bioinformatics, MDI Biological Laboratory |
|---|---|
| Initial release | 12 November 2004 |
| Available in | English |
| Type | Bioinformatics, data analysis |
| Website | ctdbase |
Background
editThe Comparative Toxicogenomics Database (CTD) is a public website and research tool that curates scientific data describing relationships between chemicals, genes/proteins, diseases, taxa, phenotypes, GO annotations, pathways, and interaction modules, launched on November 12, 2004.[1][2][3][4] The database is maintained by the Department of Biological Sciences at North Carolina State University.[citation needed]
Goals and objectives
editOne of the primary goals of CTD is to advance the understanding of the effects of environmental chemicals on human health on the genetic level, a field called toxicogenomics.
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. The most up-to-date extensive list of peer-reviewed scientific articles about CTD is available at their publications page[5]
Core data
editCTD is a unique resource where biocurators[6][7] read the scientific literature and manually curate four types of core data:
- Chemical-gene interactions
- Chemical-disease associations
- Gene-disease associations
- Chemical-phenotype associations
Data integration
editBy integrating the above four data sets, CTD automatically constructs putative chemical-gene-phenotype-disease networks to illuminate molecular mechanisms underlying environmentally-influenced diseases.
These inferred relationships are statistically scored and ranked and can be used by scientists and computational biologists to generate and verify testable hypotheses about toxicogenomic mechanisms and how they relate to human health.
Users can search CTD to explore scientific data for chemicals, genes, diseases, or interactions between any of these three concepts. Currently,[when?] CTD integrates toxicogenomic data for vertebrates and invertebrates.
CTD integrates data from or hyperlinks to these databases:
- ChemIDplus, a dictionary of more than 400,000 chemicals housed in the US National Library of Medicine[8]
- DrugBank
- Data Infrastructure for Chemical Safety project (diXa) Data Warehouse by the European Bioinformatics Institute[9][10] which as of November 2015 contained 469 compounds, 188 disease datasets in three sub-categories liver, kidney and cardiovascular disease.[11]
- Gene Ontology Consortium
- KEGG
- NCBI Entrez-Gene
- NCBI PubMed
- NCBI Taxonomy[12]
- NLM Medical Subject Headings
- OMIM
- Reactome
References
edit- ^ Mattingly CJ, Rosenstein MC, Colby GT, Forrest JN, Boyer JL (Sep 2006). "The Comparative Toxicogenomics Database (CTD): A Resource for Comparative Toxicological Studies". Journal of Experimental Zoology Part A: Comparative Experimental Biology. 305 (9): 689–92. doi:10.1002/jez.a.307. PMC 1586110. PMID 16902965.
- ^ Mattingly CJ, Rosenstein MC, Davis AP, Colby GT, Forrest JN, Boyer JL (Aug 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.
- ^ 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.
- ^ Mattingly CJ, Colby GT, Forrest JN, Boyer JL (May 2003). "The Comparative Toxicogenomics Database (CTD)". Environ. Health Perspect. 111 (6): 793–5. doi:10.1289/ehp.6028. PMC 1241500. PMID 12760826. Archived from the original on 2010-06-06.
- ^ CTD Publications page ctdbase.org
- ^ Bourne PE, McEntyre J (Oct 2006). "Biocurators: Contributors to the World of Science". PLOS Comput. Biol. 2 (10): e142. Bibcode:2006PLSCB...2..142B. doi:10.1371/journal.pcbi.0020142. PMC 1626157. PMID 17411327.
- ^ Salimi N, Vita R (Oct 2006). "The Biocurator: Connecting and Enhancing Scientific Data". PLOS Comput. Biol. 2 (10): e125. Bibcode:2006PLSCB...2..125S. doi:10.1371/journal.pcbi.0020125. PMC 1626147. PMID 17069454.
- ^ ChemIDplus US National Library of Medicine, n.d., retrieved 7 November 2015
- ^ diXa Data Warehouse n.d., retrieved 7 November 2015
- ^ Hendrickx, D. M.; Aerts, H. J. W. L.; Caiment, F.; Clark, D.; Ebbels, T. M. D.; Evelo, C. T.; Gmuender, H.; Hebels, D. G. A. J.; Herwig, R.; Hescheler, J.; Jennen, D. G. J.; Jetten, M. J. A.; Kanterakis, S.; Keun, H. C.; Matser, V.; Overington, J. P.; Pilicheva, E.; Sarkans, U.; Segura-Lepe, M. P.; Sotiriadou, I.; Wittenberger, T.; Wittwehr, C.; Zanzi, A.; Kleinjans, J. C. S. (12 December 2014). "diXa: a data infrastructure for chemical safety assessment". Bioinformatics. 31 (9): 1505–1507. doi:10.1093/bioinformatics/btu827. PMC 4410652. PMID 25505093.
- ^ Train online, Disease data European Molecular Biology Laboratory, n.d., retrieved 7 November 2015
- ^ NCBI Taxonomy