OpenTox预测毒理学框架：基于毒理学本体论和语义媒体维基的OpenToxipedia

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

作者信息

Tcheremenskaia Olga, Benigni Romualdo, Nikolova Ivelina, Jeliazkova Nina, Escher Sylvia E, Batke Monika, Baier Thomas, Poroikov Vladimir, Lagunin Alexey, Rautenberg Micha, Hardy Barry

机构信息

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

出版信息

J Biomed Semantics. 2012 Apr 24;3 Suppl 1(Suppl 1):S7. doi: 10.1186/2041-1480-3-S1-S7.

DOI:10.1186/2041-1480-3-S1-S7

PMID:22541598

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3337268/

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).

AVAILABILITY

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/

摘要

背景

由OpenTox项目（http://www.opentox.org）的合作伙伴开发的OpenTox框架旨在提供对毒性数据、预测模型及验证程序的统一访问。资源的互操作性通过基于OpenTox本体的通用信息模型来实现，该模型描述了预测算法、模型及毒性数据。由于毒理学数据可能来自不同的异构源，因此部署一个统一术语和资源的本体对于数据的合理且可靠的组织及其自动处理至关重要。

结果

已为OpenTox开发了以下相关本体：a）毒理学本体——列出毒理学终点；b）器官系统与效应本体——涉及体内研究中观察到的器官、靶点/检查及效应；c）ToxML本体——表示ToxML模式的半自动转换；d）OpenTox本体——OpenTox框架组件的表示：化合物、数据集、算法类型、模型及验证网络服务；e）ToxLink - ToxCast测定本体；f）关于毒理学术语的OpenToxipedia社区知识资源。OpenTox组件通过标准化的REST网络服务提供，其中每个化合物、数据集和预测方法都有一个唯一的可解析地址（URI），用于检索其资源描述框架（RDF）表示，或启动相关计算并生成新的基于RDF的资源。这些服务支持整合来自各种来源的毒性和化学数据、生成和验证毒性效应的计算机模型、无缝集成新算法和科学合理的验证程序，并提供一个灵活的框架，允许构建任意数量的应用程序，以满足最终用户（如毒理学家）解决不同问题的需求。