Toxtree

Toxtree 1.51 (Java, GPL)
Toxtree is a full-featured and flexible user-friendly open source application, which is able to estimate toxic hazard by applying a decision tree approach. Currently it includes five plugins:

Plugins for:

1. Cramer rules (Cramer G. M., R. A. Ford, R. L. H* all, Estimation of Toxic Hazard - A Decision Tree Approach, J. Cosmet. Toxicol., Vol.16, pp. 255 -276, Pergamon Press, 1978);
2. Verhaar scheme for predicting toxicity mode of actions (Verhaar HJM, van Leeuwen CJ and Hermens JLM (1992) Classifying environmental pollutants. 1.Structure-activity relationships for prediction of aquatic toxicity. Chemosphere 25, 471-491);
3. A decision tree for estimating skin irritation and corrosion potential, based on rules published in “The Skin Irritation Corrosion Rules Estimation Tool (SICRET), John D. Walker, Ingrid Gerner, Etje Hulzebos, Kerstin Schlegel, QSAR Comb. Sci. 2005, 24, pp378-384”;
4. A decision tree for estimating eye irritation and corrosion potential, based on rules published in “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, Ingrid Gerner, Manfred Liebsch & Horst Spielmann, Alternatives to Laboratory Animals, 2005, 33, pp. 215-237”;
5. A decision tree for estimating carcinogenicity and mutagenicity, based on the rules published in the accompanying document: “The Benigni / Bossa rulebase for mutagenicity and carcinogenicity – a module of Toxtree”, by R. Benigni, C. Bossa, N. Jeliazkova, T. Netzeva, and A. Worth.

Descriptors calculation includes:

1. The CDK implementation of descriptors
2. Own implementation (crossectional diameter, partial molar refractivity, etc.)
3. Integration of OpenMopac for semiempirical quantum calculations

Recent publication
G. Patlewicz, N. Jeliazkova, R.J. Safford, A.P. Worth and B. Aleksiev, An evaluation of the implementation of the Cramer classification scheme in the Toxtree software, SAR and QSAR in Environmental Research, Vol. 19, Nos. 3–4, April–June 2008, 1–30

• Homepage: http://toxtree.sourceforge.net
• Subproject of: OpenTox
• Data: No
• Software: Yes
• Programming language: Java
• Operating system: Any
• Dependencies: The Chemistry Development Kit and ultiple open source libraries
• Interface: Java Swing
• Inter-process communication: can be embedded in other sofwtare by calling corresponding java classes
• Input format: Multiple text based formats
• Output format: Multiple text based formats
• Version control: SVN
• License: GPL