Toxin and Toxin-Target Database: Difference between revisions

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{{one source|date=August 2014}}

{{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 = Dr. [[David S. Wishart]]

|author =

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

|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|coauthors=Pon A, Djoumbou Y, Knox C, Shrivastava S, Guo AC, Neveu V, 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=pmid19897546pmid25378312 /></ref name=pmid19897546 /> 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 [[toxinsuremic toxin]]s. These [[toxic substancessubstance]]s 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. 1-31–3), [[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 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]] ([[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==

==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.

==See Alsoalso==

*[[Poison]]

*[[Toxin]]

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*[[List of biological databases]]

*[[KEGG]]

*[[Human Metabolome Database|HMDB]]

*[[SMPDB]]

== References ==

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

==External links==

* [http://t3db.org/ T3DB website]

|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|coauthorsauthor2=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>

* [http://www.panamp.ca/ The Metabolomics Innovation Centre (TMIC)]

* [http://wishartlab.com/ Wishart Research Group website]

}}

* [http://hmdb.ca HMDB website]

* [http://drugbank.ca DrugBank website]

* [http://smpdb.ca SMPDB website]

[[Category:ChemicalBiochemistry databases]]

[[Category:Metabolomic databases]]

[[Category:Chemical databases]]

[[Category:Biological databases]]