Toxin and Toxin-Target Database: Difference between revisions

Revision as of 06:25, 28 April 2016

Latest revision as of 14:58, 19 January 2024

(6 intermediate revisions by 4 users not shown)

Line 6:

|scope = Small molecule poisons, toxic compounds and toxins, chemical structures, toxic compound descriptions, chemical taxonomy, toxin targets and transporters, target protein sequences, mechanisms of action, lethal doses, chemical properties, nomenclature, synonyms, NMR spectra, MS spectra, gene regulation, concentrations

|center = University of Alberta and [http://www.metabolomicscentre.ca The Metabolomics Innovation Centre]

|laboratory = [http://www.wishartlab.com[David DrS. David Wishart]]

|author =

|citation = T3DB: the toxic exposome database.<ref name=pmid25378312 />

Line 16:

|curation = Manually curated

}}

The '''Toxin and Toxin-Target Database (T3DB)''',<ref name=pmid25378312 /><ref name=pmid19897546 /> also known as the '''Toxic [[Exposome]] Database''', is a freely accessible online database of common substances that are toxic to humans, along with their [[protein]], [[DNA]] or organ [[Biological target|targets]]. The database currently houses nearly 3,700 toxic compounds or [[poisons]] described by nearly 42,000 synonyms. This list includes various groups of [[toxins]], including common [[pollutants]], [[pesticides]], [[drugs]], food toxins, household and industrial/workplace toxins, cigarette toxins, and [[uremic toxin]]s. These [[toxic substance]]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]], [[toxicity]] or [[lethal dose]] values, molecular and cellular interactions, medical (symptom and treatment) information (Fig. 1-31–3), [[Nuclear magnetic resonance spectroscopy|NMR]] an [[Mass spectrum|MS spectra]], and [[Regulation of gene expression#Up-regulation and down-regulation|up- and down-regulated genes]]. This information has been extracted from over 18,000 [http://www.t3db.ca/sources sources], which include [http://www.t3db.ca/w/databases other databases], government documents, books, and scientific literature.

The primary focus of the T3DB is on providing mechanisms of [[toxicity]] 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]], [[relational query]] and spectral searches. It is both modelled after and closely linked to the [[Human Metabolome Database]] ([[Human Metabolome Database|HMDB]]) and [[DrugBank]]. Potential applications of T3DB include [[metabolomics]] and environmental exposure studies, toxic compound [[metabolism]] prediction, toxin/drug interaction prediction, and general toxic substance awareness.

[[File:T3DB-arsenic-toxicity.png|thumb|right|275px|Fig. 1. T3DB Arsenic toxicity]]

==Scope and Accessaccess==

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.

Line 31:

*[[List of biological databases]]

*[[KEGG]]

*[[Human Metabolome Database|HMDB]]

*[[SMPDB]]

Line 37:

{{reflist|refs=

<ref name=pmid25378312>{{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|pagepages=D928-34|doi=10.1093/nar/gku1004|pmid=25378312|pmc=4383875}}</ref>

<ref name=pmid19897546>{{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|pagepages=D781-6|doi=10.1093/nar/gkp934|pmid=19897546|pmc=2808899}}</ref>

}}

[[Category:ChemicalBiochemistry databases]]

[[Category:Metabolomic databases]]

[[Category:Chemical databases]]

[[Category:Biological databases]]