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This article is part of the supplement: Proceedings of the Bio-Ontologies Special Interest Group 2011

Open Access Proceedings

OpenTox predictive toxicology framework: toxicological ontology and semantic media wiki-based OpenToxipedia

Olga Tcheremenskaia1*, Romualdo Benigni1, Ivelina Nikolova2, Nina Jeliazkova2, Sylvia E Escher3, Monika Batke3, Thomas Baier3, Vladimir Poroikov4, Alexey Lagunin4, Micha Rautenberg5 and Barry Hardy6*

Author Affiliations

1 Istituto Superiore di Sanità, Environment and Health Department, Viale Regina Elena 299, Rome 00161, Italy

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

3 Fraunhofer Institute for Toxicology & Experimental Medicine, Nikolai-Fuchs-Str. 1, 30625 Hannover, Germany

4 Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Pogodinskaya Street 10, 119121 Moscow, Russia

5 In silico Toxicology, Altkircher Str. 4, CH-4052 Basel, Switzerland

6 Douglas Connect, Baermeggenweg 14, CH-4314 Zeiningen, Switzerland

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Journal of Biomedical Semantics 2012, 3(Suppl 1):S7  doi:10.1186/2041-1480-3-S1-S7

Published: 24 April 2012

Abstract

Background

The OpenTox Framework, developed by the partners in the OpenTox project (http://www.opentox.org webcite), aims at providing a unified access to toxicity data, predictive models and validation procedures. Interoperability of resources is achieved using a common information model, based on the OpenTox ontologies, describing predictive algorithms, models and toxicity data. As toxicological data may come from different, heterogeneous sources, a deployed ontology, unifying the terminology and the resources, is critical for the rational and reliable organization of the data, and its automatic processing.

Results

The following related ontologies have been developed for OpenTox: a) Toxicological ontology – listing the toxicological endpoints; b) Organs system and Effects ontology – addressing organs, targets/examinations and effects observed in in vivo studies; c) ToxML ontology – representing semi-automatic conversion of the ToxML schema; d) OpenTox ontology– representation of OpenTox framework components: chemical compounds, datasets, types of algorithms, models and validation web services; e) ToxLink–ToxCast assays ontology and f) OpenToxipedia community knowledge resource on toxicology terminology.

OpenTox components are made available through standardized REST web services, where every compound, data set, and predictive method has a unique resolvable address (URI), used to retrieve its Resource Description Framework (RDF) representation, or to initiate the associated calculations and generate new RDF-based resources.

The services support the integration of toxicity and chemical data from various sources, the generation and validation of computer models for toxic effects, seamless integration of new algorithms and scientifically sound validation routines and provide a flexible framework, which allows building arbitrary number of applications, tailored to solving different problems by end users (e.g. toxicologists).

Availability

The OpenTox toxicological ontology projects may be accessed via the OpenTox ontology development page http://www.opentox.org/dev/ontology webcite; the OpenTox ontology is available as OWL at http://opentox.org/api/1 1/opentox.owl webcite, the ToxML - OWL conversion utility is an open source resource available at http://ambit.svn.sourceforge.net/viewvc/ambit/branches/toxml-utils/ webcite