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Computational toxicology using the OpenTox application programming interface and Bioclipse

Egon L Willighagen12*, Nina Jeliazkova3, Barry Hardy4, Roland C Grafström25 and Ola Spjuth1

Author Affiliations

1 Department of Pharmaceutical Bioinformatics, Uppsala University, Uppsala, Sweden

2 Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden

3 Ideaconsult Ltd, A. Kanchev 4, Sofia 1000, Bulgaria

4 Douglas Connect, Baermeggenweg 14, 4314 Zeiningen, Switzerland

5 VTT Technical Research Center of Finland, Medical Biotechnology, FI-20521 Turku, Finland

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BMC Research Notes 2011, 4:487  doi:10.1186/1756-0500-4-487

Published: 10 November 2011

Abstract

Background

Toxicity is a complex phenomenon involving the potential adverse effect on a range of biological functions. Predicting toxicity involves using a combination of experimental data (endpoints) and computational methods to generate a set of predictive models. Such models rely strongly on being able to integrate information from many sources. The required integration of biological and chemical information sources requires, however, a common language to express our knowledge ontologically, and interoperating services to build reliable predictive toxicology applications.

Findings

This article describes progress in extending the integrative bio- and cheminformatics platform Bioclipse to interoperate with OpenTox, a semantic web framework which supports open data exchange and toxicology model building. The Bioclipse workbench environment enables functionality from OpenTox web services and easy access to OpenTox resources for evaluating toxicity properties of query molecules. Relevant cases and interfaces based on ten neurotoxins are described to demonstrate the capabilities provided to the user. The integration takes advantage of semantic web technologies, thereby providing an open and simplifying communication standard. Additionally, the use of ontologies ensures proper interoperation and reliable integration of toxicity information from both experimental and computational sources.

Conclusions

A novel computational toxicity assessment platform was generated from integration of two open science platforms related to toxicology: Bioclipse, that combines a rich scriptable and graphical workbench environment for integration of diverse sets of information sources, and OpenTox, a platform for interoperable toxicology data and computational services. The combination provides improved reliability and operability for handling large data sets by the use of the Open Standards from the OpenTox Application Programming Interface. This enables simultaneous access to a variety of distributed predictive toxicology databases, and algorithm and model resources, taking advantage of the Bioclipse workbench handling the technical layers.