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 North Carolina State University (NC State) is a public land-grant research university in Raleigh, North Carolina. Founded in 1887 and part of the University of North Carolina system, it is the largest university in the Carolinas. The univers ...

Background

The 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. The database is maintained by the Department of Biological Sciences at North Carolina State University.

Goals and objectives

One 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 Toxicogenomics is a subdiscipline of pharmacology that deals with the collection, interpretation, and storage of information about gene and protein activity within a particular cell or tissue of an organism in response to exposure to toxic subs ...

. The

etiology Etiology (pronounced ; alternatively: aetiology or ætiology) is the study of causation or origination. The word is derived from the Greek (''aitiología'') "giving a reason for" (, ''aitía'', "cause"); and ('' -logía''). More completely, ...

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 Asthma is a long-term inflammatory disease of the airways of the lungs. It is characterized by variable and recurring symptoms, reversible airflow obstruction, and easily triggered bronchospasms. Symptoms include episodes of wheezing, co ...

, cancer,

diabetes Diabetes, also known as diabetes mellitus, is a group of metabolic disorders characterized by a high blood sugar level ( hyperglycemia) over a prolonged period of time. Symptoms often include frequent urination, increased thirst and increased ...

hypertension Hypertension (HTN or HT), also known as high blood pressure (HBP), is a long-term medical condition in which the blood pressure in the arteries is persistently elevated. High blood pressure usually does not cause symptoms. Long-term high b ...

immunodeficiency Immunodeficiency, also known as immunocompromisation, is a state in which the immune system's ability to fight infectious diseases and cancer is compromised or entirely absent. Most cases are acquired ("secondary") due to extrinsic factors that a ...

, and

Parkinson's disease Parkinson's disease (PD), or simply Parkinson's, is a long-term degenerative disorder of the central nervous system that mainly affects the motor system. The symptoms usually emerge slowly, and as the disease worsens, non-motor symptoms beco ...

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

Core data

CTD is a unique resource where

biocurator Biocuration is the field of life sciences dedicated to organizing biomedical data, information and knowledge into structured formats, such as spreadsheets, tables and knowledge graphs. The biocuration of biomedical knowledge is made possible by th ...

s 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

By 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, 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 * DrugBank *Data Infrastructure for Chemical Safety project (diXa) Data Warehouse by the European Bioinformatics Institute which as of November 2015 contained 469 compounds, 188 disease datasets in three sub-categories liver, kidney and cardiovascular disease. * Gene Ontology Consortium *

KEGG KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis i ...

* NCBI Entrez-Gene * NCBI PubMed *NCBI TaxonomyNCBI Taxonomy
/ref> * NLM Medical Subject Headings *

OMIM Online Mendelian Inheritance in Man (OMIM) is a continuously updated catalog of human genes and genetic disorders and traits, with a particular focus on the gene-phenotype relationship. , approximately 9,000 of the over 25,000 entries in OMIM ...

Reactome Reactome is a free online database of biological pathways. There are several Reactomes that concentrate on specific organisms, the largest of these is focused on human biology, the following description concentrates on the human Reactome. It is aut ...

References

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External links

Comparative Toxicogenomics Database

MDI Biologicjfxal Laboratory
Genetics databases Ontology (information science) Toxicology Chemical databases Molecular genetics Environmental science Comparisons