The central entity in the ToxAlerts database is a structural alert (a substructure or, more universally, a SMARTS string), which is uniquely identified by the following:
In addition to these key components, the database is designed to store any other additional information, such as:
A simplified schema of the database is presented on the following figure:
As it was mentioned above, ToxAlerts uses SMARTS patterns to represent toxicological alerts. The major advantage of using SMARTS is that a compound can be matched against an alert in an automatic manner using one of the available chemical software libraries. For our purposes, we use the MolSearch utility from Chemaxon (www.chemaxon.com). Although SMARTS are not always easily interpretable by human, a visual depiction, the chemical name and the description provide a sound way to understand the alert.
In some cases, SMARTS patterns may not be sufficient to represent a desired alert. ToxAlerts provides and extended syntax, which supports logical operations (conjunction and inversion), restrictions on molecular weight and on count of molecular fragments. In brief, a user can write expression like
MW > 100 AND [NX3](=O)=O > 2 |
to match molecules with molecular weight of more than 100 and containing more than two nitro groups.