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Toxtree

Toxtree is a flexible and user-friendly open-source application that places chemicals into categories and predicts various kinds of toxic effect by applying decision tree approaches. The following decision trees are currently implemented: 

Toxtree was developed by Ideaconsult Ltd (Sofia, Bulgaria) under the terms of a JRC contract. The software is made freely available as a service to scientific researchers and anyone with an interest in the application of computer-based estimation methods in the assessment of chemical toxicity.

    

Toxtree (Version 2.5.0) (August 2011)

 

Toxtree 2.5.0 is a standalone software application that can be run on the Microsoft Windows operating system as well as other platforms with the Java 2 Runtime Environment (Standard Edition 1.5 or newer) installed.

Toxtree 2.5.0 can be downloaded from the Sourceforge website:

Toxtree (Version 1.60) - Download area (July 2009)


The Toxtree software can be downloaded (free of charge) from this website. Toxtree 1.60 is a standalone software application that can be run on the Microsoft Windows operating system as well as other platforms with the Java Runtime Environment (Standard Edition 1.5 or newer) installed.

The setup ("exe") file contains all the required packages for Windows, including the Java(TM) Runtime Environment (JRE 5.0). The archive ("zip") file is an archive of the program without the Windows installer; this can be used to run the program also on a Unix/Linux platform.

In addition to the rulebases already implemented in Toxtree 1.60, the following plug-in was developed by the Istituto Superiore di Sanita' (Rome, Italy) to provide a means of identifying organic functional groups. The ISSFUNC rulebase is a functional groups profiler that implements a set of 204 organic functional groups recognised by the "Checkmol" program, developed by Norbert Haider (University of Vienna, Austria). The jar file should be placed in the "Toxtree\ext\" directory of the Toxtree installation.

 

Feedback


Please report any comments, enquiries or bug reports via the dedicated Sourceforge webpage.

 

Key features


    • Easy to install.
    • Easy to follow manual provided.
    • End-user modifications of the tree possible (by adding new structural rules).
    • Classification of chemical structures by an interactive 2D graphical editor.
    • Batch mode classification possible; CSV, TXT or SDF file formats supported.
    • Results (with classification path explained) viewable in a graphical user interface or saved (file formats supported: CSV, SDF or TXT).
    • Implementation of Cramer decision tree approach to estimate toxic hazard.
    • Implementation of Verhaar scheme for modes of toxic action.
    • Implementation of BfR and SICRET rules to predict skin irritation and corrosion.
    • Implementation of BfR rules to predict eye irritation and corrosion.
    • Implementation of Benigni-Bossa rules to predict mutagenicity and carcinogenicity.

 

Copyright and Disclaimer Notice


Toxtree is open source software; you are authorised to redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 (June 1991) of the License, or any later version. For more details, see the GNU General Public License at http://www.gnu.org/licenses/gpl.txt.

We request that proper credit is given to the copyright and authorship for Toxtree. This includes adding the following copyright notice to the beginning of your source code files, and to any copyright notice that you may distribute with programs based on this work:
    Developed by Dr Nina Jeliazkova (Ideaconsult Ltd; contact nina@acad.bg) on behalf of the Joint Research Centre (JRC). Copyright European Union (2005, 2007 & 2008).

The Toxtree software is made available by the JRC as a service to the worldwide scientific and regulatory communities. The JRC and European Communities provide no technical support, warranties or remedies for this software. It does not imply any endorsement or acceptance by the JRC or by the European Commission of the algorithms encoded in the software. The European Commission shall not be liable to the User or any third party for any direct or indirect, special, incidental, punitive, cover or consequential damages, arising out of the use of, or inability to use, Toxtree.

 

References


  1. Benigni R, Bossa C, Jeliazkova N, Netzeva T & Worth A (2008). The Benigni / Bossa rulebase for mutagenicity and carcinogenicity - a module of Toxtree. European Commission report EUR 23241 EN.
    Download paper
  2. Patlewicz G, Jeliazkova N, Safford RJ, Worth AP & Aleksiev B (2008). An evaluation of the implementation of the Cramer classification scheme in the Toxtree software. SAR and QSAR in Environmental Research 19, 495-524
  3. Cramer GM, Ford RA & Hall RL (1978) Estimation of Toxic Hazard - A Decision Tree Approach. Food and Cosmetics Toxicology 16, 255-276.
  4. Gerner I, Liebsch M & Spielmann H (2005). Assessment of the eye irritating properties of chemicals by applying alternatives to the Draize rabbit eye test: the use of QSARs and in vitro tests for the classification of eye irritation. ATLA 33, 215-237.
  5. Verhaar HJM, van Leeuwen CJ & Hermens JLM (1992). Classifying environmental pollutants. 1. Structure-activity relationships for prediction of aquatic toxicity. Chemosphere 25, 471-491.
  6. Verhaar HJM, Mulder W & Hermens JLM (1995). QSARs for ecotoxicity. In: Overview of structure-activity relationships for environmental endpoints, Part 1: General outline and procedure. Hermens JLM (Ed), Report prepared within the framework of the project "QSAR for Prediction of Fate and Effects of Chemicals in the Environment", an international project of the Environment; Technologies RTD Programme (DGXII/D-1) of the European Commission under contract number EV5V-CT92-0211.
  7. Verhaar HJM, Solbe J, Speksnijder J, van Leeuwen CJ & Hermens JLM (2000). Classifying environmental pollutants: Part 3. External validation of the classification system. Chemosphere 40, 875-883.
  8. Walker JD, Gerner I, Hulzebos E & Schlegel K (2005). The Skin Irritation Corrosion Rules Estimation Tool (SICRET). QSAR Comb. Sci. 24, 378-384.
  9. Lapenna S & Worth A (2011). Analysis of the Cramer classification scheme for oral systemic toxicity - implications for its implementation in Toxtree. EUR 24898 EN. Publications Office of the European Union, Luxembourg. Download paper

 

 

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