title: OpenTox predictive toxicology framework: toxicological ontology and semantic media wiki-based OpenToxipedia.
abstract: BACKGROUND
  The OpenTox Framework, developed by the partners in the OpenTox project (http://www.opentox.org), 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).
  
  
  BACKGROUND
  The OpenTox toxicological ontology projects may be accessed via the OpenTox ontology development page http://www.opentox.org/dev/ontology; the OpenTox ontology is available as OWL at http://opentox.org/api/1 1/opentox.owl, the ToxML - OWL conversion utility is an open source resource available at http://ambit.svn.sourceforge.net/viewvc/ambit/branches/toxml-utils/
authors.affiliation: Istituto Superiore di Sanità, Environment and Health Department, Viale Regina Elena 299, Rome 00161, Italy. olga.tcheremenskaia@iss.it.
authors.forename: Olga
authors.initials: O
authors.lastname: Tcheremenskaia
authors.forename: Romualdo
authors.initials: R
authors.lastname: Benigni
authors.forename: Ivelina
authors.initials: I
authors.lastname: Nikolova
authors.forename: Nina
authors.initials: N
authors.lastname: Jeliazkova
authors.forename: Sylvia E
authors.initials: SE
authors.lastname: Escher
authors.forename: Monika
authors.initials: M
authors.lastname: Batke
authors.forename: Thomas
authors.initials: T
authors.lastname: Baier
authors.forename: Vladimir
authors.initials: V
authors.lastname: Poroikov
authors.forename: Alexey
authors.initials: A
authors.lastname: Lagunin
authors.forename: Micha
authors.initials: M
authors.lastname: Rautenberg
authors.forename: Barry
authors.initials: B
authors.lastname: Hardy