Comparative Toxicogenomics Database
Encyclopedia
The Comparative Toxicogenomics Database (CTD) is a public website and research tool that curates scientific data describing relationships between chemicals, genes, and human diseases.
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.
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.
s read the scientific literature and manually curate three types of core data:
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:
The database is maintained by the Department of Bioinformatics at the Mount Desert Island Biological Laboratory
Mount Desert Island Biological Laboratory
Mount Desert Island Biological Laboratory is a private, nonprofit biological research and education institution located in Salisbury Cove, Maine on Mount Desert Island, founded in 1989...
in Salisbury Cove, Maine
Maine
Maine is a state in the New England region of the northeastern United States, bordered by the Atlantic Ocean to the east and south, New Hampshire to the west, and the Canadian provinces of Quebec to the northwest and New Brunswick to the northeast. Maine is both the northernmost and easternmost...
.
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
Etiology
Etiology is the study of causation, or origination. The word is derived from the Greek , aitiologia, "giving a reason for" ....
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
Asthma is the common chronic inflammatory disease of the airways characterized by variable and recurring symptoms, reversible airflow obstruction, and bronchospasm. Symptoms include wheezing, coughing, chest tightness, and shortness of breath...
, cancer
Cancer
Cancer , known medically as a malignant neoplasm, is a large group of different diseases, all involving unregulated cell growth. In cancer, cells divide and grow uncontrollably, forming malignant tumors, and invade nearby parts of the body. The cancer may also spread to more distant parts of the...
, diabetes
Diabetes mellitus
Diabetes mellitus, often simply referred to as diabetes, is a group of metabolic diseases in which a person has high blood sugar, either because the body does not produce enough insulin, or because cells do not respond to the insulin that is produced...
, hypertension
Hypertension
Hypertension or high blood pressure is a cardiac chronic medical condition in which the systemic arterial blood pressure is elevated. What that means is that the heart is having to work harder than it should to pump the blood around the body. Blood pressure involves two measurements, systolic and...
, immunodeficiency
Immunodeficiency
Immunodeficiency is a state in which the immune system's ability to fight infectious disease is compromised or entirely absent. Immunodeficiency may also decrease cancer immunosurveillance. Most cases of immunodeficiency are acquired but some people are born with defects in their immune system,...
, and Parkinson's disease
Parkinson's disease
Parkinson's disease is a degenerative disorder of the central nervous system...
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 biocuratorBiocurator
A biocurator is a professional scientist who collects, annotates, and validates information that is disseminated by biological and model organism databases...
s 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
Gene Ontology
The Gene Ontology, or GO, is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species...
, KEGG, and Reactome
Reactome
Reactome is a database of biological pathways. There are several Reactomes that concentrate on a specific organism, the largest of these is focused on human biology, but includes pathway steps inferred to exist in humans based on experimental data from model organisms and pathways computationally...
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
- DrugBankDrugBankThe DrugBank database available at the University of Alberta is a bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information...
- GOAnnotations@EBI
- Gene Ontology ConsortiumGene OntologyThe Gene Ontology, or GO, is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species...
- KEGG
- NCBI Entrez-GeneEntrezThe Entrez Global Query Cross-Database Search System is a powerful federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information website...
- NCBI PubMedPubMedPubMed is a free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez information retrieval system...
- NCBI Taxonomy
- NLM Medical Subject HeadingsMedical Subject HeadingsMedical Subject Headings is a comprehensive controlled vocabulary for the purpose of indexing journal articles and books in the life sciences; it can also serve as a thesaurus that facilitates searching...
- OMIMMendelian Inheritance in ManOnline Mendelian Inheritance in Man is a database that catalogues all the known diseases with a genetic component, and—when possible—links them to the relevant genes in the human genome and provides references for further research and tools for genomic analysis of a catalogued gene. OMIM is one...
- ReactomeReactomeReactome is a database of biological pathways. There are several Reactomes that concentrate on a specific organism, the largest of these is focused on human biology, but includes pathway steps inferred to exist in humans based on experimental data from model organisms and pathways computationally...