Toxin and Toxin-Target Database: Difference between revisions

Revision as of 22:37, 11 August 2014

Revision as of 18:08, 9 June 2015

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{{Infobox biodatabase

|title =

|logo =[[File:T3DB logoT3db-banner.pngjpg|300px|T3DB logo]]

|description = Toxin and toxin target database

|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 Dr. David Wishart]

|author =

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

|pmid = T3DB: a comprehensively annotated database of common toxins and their targets. <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|page=D781-6|doi=10.1093/nar/gkp934|pmid=19897546|pmc=2808899}}</ref>

|released = 2009

|format =

|url = http://www.t3db.orgca

|download = http://www.t3db.orgca/downloads

|frequency = Every 3-4 years with periodic corrections and updates

|curation = Manually curated

}}

The '''Toxin and Toxin-Target Database (T3DB)'''<ref name=pmid25378312></ref><ref name=pmid19897546></ref>, isalso aknown comprehensive,as high-qualitythe '''Toxic [[Exposome]] Database''', is a freely accessible, online database of common [[substances that are toxic substance]]sto andhumans, along with their [[protein]]/, [[DNA]] or organ [[Biological_target|targets]]. The database currently houses nearly 3,053700 toxic compounds or [[poisons]] described by 32nearly 42,276000 synonyms. This list includes various groups of [[toxins]], including common [[pollutants]], [[pesticides]], [[drugs]], food toxins, household and foodindustrial/workplace toxins, cigarette toxins, and [[Uremic_toxin|uremic toxins]]. These [[toxic substance|toxic substances]] are linked to 12,670086 corresponding protein/DNA target records. In total there are 3742,084433 toxic substance-toxin target associations. Each toxic compound record (ToxCard) in T3DB contains nearly 60100 data fields and holds information such as chemical properties and descriptors, [[mechanisms of action]], [[toxicity]] or [[lethal dose]] values, molecular and cellular interactions, and medical (symptom and treatment) information (Fig. 1-3), [[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 518,454000 [http://classicwww.t3db.orgca/sources sources], which include [http://classicwww.t3db.orgca/w/databases other databases], government documents, books, and scientific literature.

[[File:T3DB toxin.png|thumb|left|150px|Fig. 1. T3DB Arsenic (T3D0001)]]

[[File:T3DB toxicity.png|thumb|left|150px|Fig. 2. T3DB Arsenic toxicity]]

[[File:T3DB targets.png|thumb|left|150px|Fig. 3. T3DB Arsenic targets]]

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]], and [[relational query]] and spectral searches. It is both modelled after and closely linked to the [[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 toxin-arsenic-toxicity.png|thumb|leftright|150px275px|Fig. 1. T3DB Arsenic (T3D0001)toxicity]]

==Scope and Access==

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== References ==

{{reflist}}|refs=

*

<ref name=pmid25378312>{{cite journal |title=T3DB: the toxic exposome database.|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|page=D928-34|doi=10.1093/nar/gku1004|pmid=25378312|pmc=4383875}}</ref>

*

*

|pmid = T3DB: a comprehensively annotated database of common toxins and their targets. <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|page=D781-6|doi=10.1093/nar/gkp934|pmid=19897546|pmc=2808899}}</ref>

*

}}

[[Category:Metabolomic databases]]