Toxin and Toxin Target Database (T3DB) is a unique bioinformatics resource that combines detailed toxin data with comprehensive toxin target information. The database currently houses over 2900 toxins described by over 34 200 synonyms, including pollutants, pesticides, drugs, and food toxins, which are linked to over 1300 corresponding toxin target records. Altogether there are over 33 800 toxin, toxin target associations. Each toxin record (ToxCard) contains over 50 data fields and holds information such as chemical properties and descriptors, toxicity values, molecular and cellular interactions, and medical information. This information has been extracted from over 5600 sources, which include other databases, government documents, books, and scientific literature. The focus of the T3DB is on providing mechanisms of toxicity and target proteins for each toxin. This dual nature of the T3DB, in which toxin and toxin target records are interactively linked in both directions, makes it unique from existing databases. It is also fully searchable and supports 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/drug 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. All of T3DB's images, descriptive fields and tables may be downloaded here.
T3DB is supported by David Wishart, Departments of Computing Science & Biological Sciences, University of Alberta.
Users may query T3DB in any number of ways. The simple text query (above) supports general text queries of the entire textual component of the database. Clicking on the Browse button (on the T3DB navigation panel above) generates a tabular synopsis of T3DB's content. This browse view allows users to casually scroll through the database or re-sort its contents. Clicking on a given ToxinCard button brings up the full data content for the corresponding toxin. A complete explanation of all the ToxinCard fields and sources is given here. The ChemQuery button allows users to draw (using MarvinSketch applet) or write (SMILES string) a chemical compound and to search T3DB for chemicals similar or identical to the query compound. The TextQuery button supports a more sophisticated text search (partial word matches, case sensitive, misspellings, etc.) of the text portion of T3DB. The SeqSearch button allows users to conduct BLASTP (protein) sequence searches of the sequences contained in T3DB. Both single and multiple sequence (i.e. whole proteome) BLAST queries are supported. The Data Extractor button opens an easy-to-use relational query search tool that allows users to select or search over various combinations of subfields. The Data Extractor is the most sophisticated search tool for T3DB. Users may download selected text components and sequence data from T3DB and track the latest T3DB statistics by clicking on the Download button.