The Toxin and Toxin-Target Database (T3DB), also known as the Toxic

Exposome The exposome is a concept used to describe environmental exposures that an individual encounters throughout life, and how these exposures impact biology and health. It encompasses both external and internal factors, including chemical, physical ...

Database, is a freely accessible online database of common substances that are toxic to humans, along with their

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...

or organ

targets ''Targets'' is a 1968 American crime thriller film directed by Peter Bogdanovich in his theatrical directorial debut, and starring Tim O'Kelly, Boris Karloff, Nancy Hsueh, Bogdanovich, James Brown, Arthur Peterson and Sandy Baron. The film ...

. The database currently houses nearly 3,700 toxic compounds or

poisons A poison is any chemical substance that is harmful or lethal to living organisms. The term is used in a wide range of scientific fields and industries, where it is often specifically defined. It may also be applied colloquially or figurati ...

described by nearly 42,000 synonyms. This list includes various groups of

toxins A toxin is a naturally occurring poison produced by metabolic activities of living cells or organisms. They occur especially as proteins, often conjugated. The term was first used by organic chemist Ludwig Brieger (1849–1919), derived ...

, including common

pollutants A pollutant or novel entity is a substance or energy introduced into the environment that has undesired effect, or adversely affects the usefulness of a resource. These can be both naturally forming (i.e. minerals or extracted compounds like oi ...

pesticides Pesticides are substances that are used to pest control, control pest (organism), pests. They include herbicides, insecticides, nematicides, fungicides, and many others (see table). The most common of these are herbicides, which account for a ...

drugs A drug is any chemical substance other than a nutrient or an essential dietary ingredient, which, when administered to a living organism, produces a biological effect. Consumption of drugs can be via inhalation, injection, smoking, ingestio ...

, food toxins, household and industrial/workplace toxins, cigarette toxins, and uremic toxins. These

toxic substance A toxicant is any toxic substance, whether artificial or naturally occurring. By contrast, a toxin is a poison produced naturally by an organism (e.g. plant, animal, insect, bacterium). The different types of toxicants can be found in the air, so ...

s are linked to 2,086 corresponding protein/DNA target records. In total there are 42,433 toxic substance-toxin target associations. Each toxic compound record (ToxCard) in T3DB contains nearly 100 data fields and holds information such as chemical properties and descriptors,

mechanisms of action In pharmacology, the term mechanism of action (MOA) refers to the specific biochemical interaction through which a drug substance produces its pharmacological effect. A mechanism of action usually includes mention of the specific molecular targ ...

toxicity Toxicity is the degree to which a chemical substance or a particular mixture of substances can damage an organism. Toxicity can refer to the effect on a whole organism, such as an animal, bacteria, bacterium, or plant, as well as the effect o ...

lethal dose In toxicology, the lethal dose (LD) is an indication of the lethal toxicity of a given substance or type of radiation. Because resistance varies from one individual to another, the "lethal dose" represents a dose (usually recorded as dose per kilog ...

values, molecular and cellular interactions, medical (symptom and treatment) information (Fig. 1–3),

NMR Nuclear magnetic resonance (NMR) is a physical phenomenon in which atomic nucleus, nuclei in a strong constant magnetic field are disturbed by a weak oscillating magnetic field (in the near and far field, near field) and respond by producing ...

an MS spectra, and up- and down-regulated genes. This information has been extracted from over 18,00
sources
which includ
other databases
government documents, books, and scientific literature. The primary focus of the T3DB is on providing mechanisms of

and identifying target proteins for common toxic substances. While a number of other toxic compound databases do exist, their emphasis is on covering large numbers of chemical compounds that are almost never seen outside a chemical laboratory. T3DB attempts to capture data on only those toxic substances that are abundant or in widespread use and have been detected or measured in humans. T3DB is fully searchable and supports extensive text, sequence,

chemical structure A chemical structure of a molecule is a spatial arrangement of its atoms and their chemical bonds. Its determination includes a chemist's specifying the molecular geometry and, when feasible and necessary, the electronic structure of the target m ...

relational query A relational database (RDB) is a database based on the relational model of data, as proposed by E. F. Codd in 1970. A Relational Database Management System (RDBMS) is a type of database management system that stores data in a structured form ...

and spectral searches. It is both modelled after and closely linked to the

Human Metabolome Database The Human Metabolome Database (HMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in the human body. It has been created by the Human Metabolome Project funded by Genome Canada and is ...

( HMDB) and

DrugBank The DrugBank database is a comprehensive, freely accessible, online database containing information on drugs and drug targets created and maintained by the University of Alberta and The Metabolomics Innovation Centre located in Alberta, Canada. A ...

. Potential applications of T3DB include

metabolomics Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates, and products of cell metabolism. Specifically, metabolomics is the "systematic study of the unique chemical fingerpri ...

and environmental exposure studies, toxic compound

metabolism Metabolism (, from ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cellular processes; the co ...

prediction, toxin/drug interaction prediction, and general toxic substance awareness. T3DB-arsenic-toxicity

Scope and access

All data in T3DB is non-proprietary or is derived from a non-proprietary source. It is freely accessible and available to anyone. In addition, nearly every data item is fully traceable and explicitly referenced to the original source. T3DB data is available through a public web interface and downloads.

References

{{reflist, refs= {{cite journal , title=T3DB: the toxic exposome database., author1-link=David S. Wishart, last=Wishart, first=D, author2=Arndt D, author3=Pon A, author4=Sajed T, author5=Guo AC, author6=Djoumbou Y, author7=Knox C, author8=Wilson M, author9=Liang Y, author10=Grant J, author11=Liu Y, author12=Goldansaz SA, author13=Rappaport SM. , journal=Nucleic Acids Research, date=Jan 2015, volume=43, issue=Database issue, pages=D928-34, doi=10.1093/nar/gku1004, pmid=25378312, pmc=4383875 {{cite journal , title=T3DB: a comprehensively annotated database of common toxins and their targets., last=Lim, first=E, author2=Pon A , author3=Djoumbou Y , author4=Knox C , author5=Shrivastava S , author6=Guo AC , author7=Neveu V , author8=Wishart DS. , journal=Nucleic Acids Research, date=Jan 2010, volume=38, issue=Database issue, pages=D781-6, doi=10.1093/nar/gkp934, pmid=19897546, pmc=2808899 Biochemistry databases Metabolomic databases

Scope and access

See also

References