Toxmatch

ToxmatchToxmatch is a flexible and user-friendly open-source software application that encodes several chemical similarity indices to facilitate the grouping of chemicals into categories and read-across. The core functionalities include the ability to compare datasets based on various structural and descriptor-based similarity indices as well as the means to calculate pair wise similarity between compounds or aggregated similarity of a compound to a set.

Toxmatch 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. The results viewable in a graphical user interface like scatter plots, pair wise or composite similarity histograms and similarity matrices can be exported as .jpg and .png formats.

ToxMatch 1.x (January 2009)

The authors’ interest in exploring the similarity concept emerged while preparing a review on the approaches to measure similarity and, later, with the development and maintenance of the open source ToxMatch 1.x software [doi:10.1016/j.yrtph.2008.05.012], which encodes a variety of chemical similarity indices and facilitates visual exploration of structure and activity similarities in datasets.

The similarity paradox

Fundamental in both the review and the software is the understanding that similarity is not an absolute concept and that the “similarity paradoxes” should not be ignored, but rather should be studied in greatest detail. ToxMatch 1.x is an implementation of a tailored similarity space – in essence, requiring a training set and supervised machine learning algorithms in order to apply similarity measures for property prediction.

In the years following ToxMatch 1.x development, it became widely recognized that the “neighbourhood behaviour“, although a useful hypothesis, is not valid everywhere in the chemical space. The multitude of approaches to characterize activity landscapes, exemplify that this is now a mainstream knowledge, but unambiguous characterization of activity landscapes is an yet unsolved scientific problem.

Toxmatch 1.07 can be downloaded (free of charge) from the Ideaconsult website. It is a standalone software application that can be run on the Microsoft Windows operating system as well as other platforms with 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.
Source code URL

Download Toxmatch Installation Manual
Download Toxmatch User Manual
Download Toxmatch 1.07 exe file (for Windows; JRE 5.0 embedded)
Download Toxmatch 1.07 zip archive (for other platforms; no JRE 5.0, no installer)

Contact persons

Please send any comments, enquiries or bug reports

Key features

  • Easy to install.
  • Detailed user manual provided with case study.
  • Preloaded datasets for four endpoints (skin irritation, skin sensitisation, bioconcentration factor and aquatic toxicity).
  • Results viewable in a graphical user interface; scatter plots, pairwise/composite similarity histograms and similarity matrices can be exported as .jpg and .png formats.
  • Implementation of a range of similarity indices, including distance-Like similarity indices and correlation-like similarity indices:.
  • Implementation of Verhaar scheme for modes of toxic action.
  • Implementation of BfR and SICRET rules to predict skin irritation and corrosion.

Copyright and Disclaimer Notice

Toxmatch Version 1.07 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 Toxmatch. 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 (2007, 2008 & 2009).

The Toxmatch software is being 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, Toxmatch.

References

 

  1. Gallegos Saliner A, Poater A, Jeliazkova N, Patlewicz G & Worth AP (2008). Toxmatch - A Chemical Classification and Activity Prediction Tool based on Similarity Measures. Regulatory Toxicology and Pharmacology 52, 77-84.
  2. Patlewicz G, Jeliazkova N, Gallegos Saliner A & Worth AP (2008). Toxmatch - A new software tool to aid in the development and evaluation of chemically similar groups. SAR and QSAR in Environmental Research 19, 397-412.
  3. Pavan M & Worth AP (2008). Thirteenth International Workshop on QSARs in the Environmental Sciences: Publicly-accessible QSAR software tools developed by the Joint Research Centre. SAR and QSAR in Environmental Research 19 (7-8), 785-799.