OpenTox - the creation of a Semantic Web for Toxicology

author: Barry Hardy, Douglas Connect
published: Sept. 6, 2011,   recorded: August 2011,   views: 529
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A new paradigm of 21st century human-oriented safety testing approaches is now emerging based on a combination of in silico and in vitro approaches. The new predictive test systems developed from this growing “grand challenge” effort will need to combine evidences from a great variety of data, protocols, and concepts. The combination of these sources of knowledge within an ontology-based mechanistic knowledge-oriented framework to produce reliable test systems demands the development of a semantic web for toxicology. The OpenTox Framework (1,2) has been developed to support the communication between toxicology resources, based on standard representations of data and metadata, the ability for distributed resources to exchange data and metadata, build and validate models, and generate reporting information relevant for research analysis or risk assessment. I will describe the design and semantic architecture of OpenTox and example applications it can currently enable including a) creation and validation of models addressing the regulatory requirements of the REACH legislation for chemical safety evaluation (3), b) application in drug discovery infrastructure development and weight-of-evidence library profiling of drug candidate molecules (4), c) infrastructure development for the interdisciplinary research activities of a large cluster of over 70 partners collaborating on the replacement of animal testing in the area of systemic toxicology (5,6), and d) relevance for ecosystem protection and biodiversity preservation, including sustainable development contexts in both Europe and Africa (7).

(1) OpenTox - An Open Source Predictive Toxicology Framework, is funded under the EU Seventh Framework Program: HEALTH-2007-1.3-3 Promotion, development, validation, acceptance and implementation of QSARs (Quantitative Structure-Activity Relationships) for toxicology, Project Reference Number Health-F5-2008-200787 (2008-2011). More information at http://www.opentox.org

(2) Collaborative Development of Predictive Toxicology Applications Barry Hardy, Nicki Douglas, Christoph Helma, Micha Rautenberg, Nina Jeliazkova, Vedrin Jeliazkov, Ivelina Nikolova, Romualdo Benigni, Olga Tcheremenskaia, Stefan Kramer, Tobias Girschick, Fabian Buchwald, Joerg Wicker, Andreas Karwath, Martin Gutlein, Andreas Maunz, Haralambos Sarimveis, Georgia Melagraki, Antreas Afantitis, Pantelis Sopasakis, David Gallagher, Vladimir Poroikov, Dmitry Filimonov, Alexey Zakharov, Alexey Lagunin, Tatyana Gloriozova, Sergey Novikov, Natalia Skvortsova, Dmitry Druzhilovsky, Sunil Chawla, Indira Ghosh, Surajit Ray, Hitesh Patel and Sylvia Escher Journal of Cheminformatics 2010, 2:7 (31 August 2010) Full text and supplementary information available in Open Access at: http://www.jcheminf.com/content/2/1/7

(3) REACH, http://ec.europa.eu/environment/chemicals/reach/reach_intro.htm

(4) Scientists Against Malaria, http://scientistsagainstmalaria.net/

(5) SEURAT-1, http://www.seurat-1.eu/

(6) ToxBank, http://www.toxbank.net/

(7) SETAC Africa Conference, 2011, http://cameroon.setac.eu/

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