ToxTree

Contact: Nina Jeliazkova

Categories: Prediction, Descriptor calculation

Exposed methods:

Description:

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 the following modules:
1. Cramer rules [CRA78]
2. Verhaar scheme for predicting toxicity mode of actions [VER92]
3. A decision tree for estimating skin irritation and corrosion potential, based on rules published in [WAL05]
4. A decision tree for estimating eye irritation and corrosion potential, based on rules published in [GER05]
5. A decision tree for estimating carcinogenicity and mutagenicity [BEN07], [BEN08]
Toxtree could be applied to datasets from various compatible file types. User-defined molecular structures are
also supported - they could be entered by SMILES, or by using the built-in 2D structure diagram editor.
The Toxtree has been designed with flexible capabilities for future extensions in mind (e.g. other classification
schemes that could be developed at a future date). New decision trees with arbitrary rules can be built with the
help of graphical user interface or by developing new plug-ins.

Bias (instance-selection bias, feature-selection bias, combined instance-selection/feature-selection bias, independence assumptions?, ...)
Predefined rules, based on publications. No learning phase, no feature selection.

Lazy learning/eager learning
Predefined rules; does not involve a learning phase

Interpretability of models (black box model?, ...)
Highly interpretable, structural alerts and properties

Type of Descriptor:

Interfaces: Standalone application, Library

Priority: Medium

Development status: Production

Homepage: http://toxtree.sourceforge.net

Dependencies:
OpenTox components: MOPAC
External components: Chemistry Development Kit (CDK)

Technical details

Data: No

Software: Yes

Programming language(s): Java

Operating system(s): Any

Input format: Multiple text based formats

Output format: Multiple text based formats

License: GPL

References

References:
[BEN07] R. Benigni, C. Bossa, T. Netzeva, A. Rodomonte, and I. Tsakovska (2007) Mechanistic QSAR of aromatic amines: new models for discriminating between mutagens and nonmutagens, and validation of models for carcinogens. Environ mol mutag 48:754-771
[BEN08] R. Benigni, C. Bossa, N. Jeliazkova, T. Netzeva, and A. Worth (2008) The Benigni / Bossa rulebase for mutagenicity and carcinogenicity – a module of Toxtree, JRC Scientific and Technical Reports, http://ecb.jrc.it/documents/QSAR/EUR_23241_EN.pdf
[GER05] Ingrid Gerner, Manfred Liebsch & Horst Spielmann (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, Alternatives to Laboratory Animals, 33, pp. 215-237
[CRA78] Cramer G. M., R. A. Ford, R. L. Hall (1978), Estimation of Toxic Hazard - Decision Tree Approach, J. Cosmet. Toxicol., Vol.16, pp. 255 -276, Pergamon Press
[PAT 08] 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 QSAR Environ Res.19(5-6):495-524.
[VER92] Verhaar HJM, van Leeuwen CJ and Hermens JLM (1992) Classifying environmental pollutants. Structure-activity relationships for prediction of aquatic toxicity . Chemosphere 25, 471- 491
[WAL05] John D. Walker, Ingrid Gerner, Etje Hulzebos, Kerstin Schlegel, The Skin Irritation Corrosion Rules Estimation Tool (SICRET), QSAR Comb. Sci. 2005, 24, pp378-384