T3DB Abstract

arrogantpreviousInternet and Web Development

Feb 2, 2013 (5 years and 6 months ago)

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T3DB: The Toxin and Toxin Target Database


Allison Pon, Emilia Lim, Yannick Djoumbou, Craig Knox, Savita Shrivastava
,
An Chi Guo,
and
David Wishart


Toxicogenomics is a field of study that uses the combined fields of toxicology and genomics in
order to dec
ipher the mechanisms of action by which toxic substances exert their effects.
I
n
order to facilitate
this

study,
we have created the Toxin and
Toxin Target Database (T3DB
),

a
unique bioinformatics resource

that combine
s detailed toxin

data with
comprehensi
ve toxin
target

information.
The database currently houses over 2 500 toxins, including pollutants,
pesticides, drugs, and food toxi
ns
,
with

over 8
00 corresponding toxin target records
.
Each

toxin
record (ToxCard)

contains over 3
0 data fields
and

holds

inf
ormation such as
chemical properties
and descriptors, toxicity values, molecular and cellular interactions, and medical information.
This information has been extracted from numerous sources, including other databases,
government documents, books, and scie
ntific
literature
.
The focus of the T3DB is
on providing
mechanism
s

of toxicity
and target proteins
for e
ach toxin. This

dual nature of the
T3DB
, in
which
toxin and toxin target records are interactively linked in both directions, makes it unique
from exis
ting databases.
It is also

fully searchable

and support
s

extensive

text, sequence,
chemical structure
,

and relational query searches.
The
T3DB is housed on an Apple XServe in
the Wishart

Lab on the University of Alberta campus
,

and consists of a LIMS
built

using the Ruby
On Rails framework

along with

a Perl
-
based HTML public interface.
It is both modelled after and
closely linked to the Human Metabolome Database (HMDB) and DrugBank.
Potential
applications of T3DB include toxin

metabolism prediction, toxin/d
rug interaction prediction,
and general toxin hazard

awareness by the public
, making it

applicable to

various fields. Overall,
the variety and accessibility of the T3DB make it a valuable resource for both the casual user
and the advanced researcher. The T
3DB is available online at: http://
www.t3db.org
.