Toxin and Toxin-Target Database: Difference between revisions

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{{one source|date=August 2014}}

{{Infobox biodatabase

|title = T3DB

|logo =[[File:T3db-banner.jpg|300px|T3DB logo]]

|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 = <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=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. 1–3), [[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 '''Toxin and Toxin-Target Database (T3DB)'''<ref name=pmid19897546></ref> is a comprehensive online database of over 2900 toxins and over 1300 corresponding toxin targets. These toxins include pollutants, food toxins, drugs, and pesticides.<ref>{{cite web|title=Toxin and Toxin Target Database (T3DB)|url=http://t3db.org/|accessdate=11 January 2012}}</ref> T3DB was created by researchers at the University of Alberta, under the leadership of Dr. David Wishart.

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.

Each toxin is displayed as a "ToxCard" with over 50 data fields including toxicity values, medical information, molecular and cellular interactions, and chemical properties and descriptors. The Wishart Research Group<ref>{{cite web|title=Wishart Research Group|url=http://wishartlab.com/|accessdate=17 January 2012}}</ref> extracted information from over 5600 sources to build this database. The various sources include the scientific literature, books, government documents, and numerous external databases (such as [[PubChem]], [[UniProt]], [[PubMed]], [[DrugBank]], [[Human Metabolome Database]] (HMDB), NIST Chemistry WebBook, [[KEGG]], NCI Database Browser, PharmGKB, [[Food and Drug Administration]], [[ChEBI]], and ChemExper). T3DB enables users to discover mechanisms of toxicity for various toxins as well as the target proteins with which each toxin interacts. Researchers can use T3DB to predict toxin-drug interactions, predict toxin metabolism, and to increase their general awareness of toxins. Much of T3DB's content is downloadable<ref>{{cite web|title=T3DB: Downloads|url=http://t3db.org/downloads|accessdate=11 January 2012}}</ref> including its descriptive fields, tables, and images.<ref>{{cite web|title=Toxin and Toxin Target Database (T3DB)|url=http://t3db.org/|accessdate=11 January 2012}}</ref>

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

T3DB is part of a suite of metabolomics databases that also includes [[HMDB]], [[DrugBank]], and [[The Small Molecule Pathway Database]] (SMPDB). While [[DrugBank]] includes information on 6707 drugs and 4228 non-redundant drug targets, enzymes, transporters, and carriers, HMDB houses over 7900 small molecule metabolites found in the human body. The suite is complemented by SMPDB with its pathway diagrams for more than 350 human metabolic and disease pathways.

==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.

==See also==

*[[Poison]]

*[[Toxin]]

*[[List of extremely hazardous substances]]

*[[Category:ChemicalList 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 = <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:BiologicalBiochemistry databases]]

[[Category:Metabolomic databases]]

[[Category:Chemical databases]]

[[Category:Biological databases]]