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电子纳米映射器：利用本体论实现纳米材料风险评估的数据整合。

eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment.

作者信息

Hastings Janna, Jeliazkova Nina, Owen Gareth, Tsiliki Georgia, Munteanu Cristian R, Steinbeck Christoph, Willighagen Egon

机构信息

European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom.

IdeaConsult Ltd., 4.A.Kanchev str., Sofia, Bulgaria.

出版信息

J Biomed Semantics. 2015 Mar 21;6:10. doi: 10.1186/s13326-015-0005-5. eCollection 2015.

DOI:10.1186/s13326-015-0005-5
PMID:25815161
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4374589/
Abstract

Engineered nanomaterials (ENMs) are being developed to meet specific application needs in diverse domains across the engineering and biomedical sciences (e.g. drug delivery). However, accompanying the exciting proliferation of novel nanomaterials is a challenging race to understand and predict their possibly detrimental effects on human health and the environment. The eNanoMapper project (www.enanomapper.net) is creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. Here, we describe the development of the eNanoMapper ontology based on adopting and extending existing ontologies of relevance for the nanosafety domain. The resulting eNanoMapper ontology is available at http://purl.enanomapper.net/onto/enanomapper.owl. We aim to make the re-use of external ontology content seamless and thus we have developed a library to automate the extraction of subsets of ontology content and the assembly of the subsets into an integrated whole. The library is available (open source) at http://github.com/enanomapper/slimmer/. Finally, we give a comprehensive survey of the domain content and identify gap areas. ENM safety is at the boundary between engineering and the life sciences, and at the boundary between molecular granularity and bulk granularity. This creates challenges for the definition of key entities in the domain, which we also discuss.

摘要

工程纳米材料（ENMs）正在被开发，以满足工程和生物医学科学等不同领域的特定应用需求（例如药物递送）。然而，伴随着新型纳米材料令人兴奋的激增，一场理解和预测它们对人类健康和环境可能产生的有害影响的挑战性竞赛也随之而来。eNanoMapper项目（www.enanomapper.net）正在基于语义网标准和本体创建一个用于ENMs毒理学数据管理的泛欧计算基础设施。在此，我们描述了基于采用和扩展与纳米安全领域相关的现有本体而开发的eNanoMapper本体。生成的eNanoMapper本体可在http://purl.enanomapper.net/onto/enanomapper.owl获取。我们旨在使外部本体内容的重用无缝化，因此我们开发了一个库来自动提取本体内容的子集并将这些子集组装成一个完整的整体。该库（开源）可在http://github.com/enanomapper/slimmer/获取。最后，我们对该领域的内容进行了全面调查并确定了差距领域。ENM安全性处于工程与生命科学的边界，以及分子粒度与块状粒度的边界。这给该领域关键实体的定义带来了挑战，我们也对此进行了讨论。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/553e/4374589/cc4fab5c131f/13326_2015_5_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/553e/4374589/62926f121949/13326_2015_5_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/553e/4374589/9dd0b0dbe7c5/13326_2015_5_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/553e/4374589/d18c9c4e68dd/13326_2015_5_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/553e/4374589/cc4fab5c131f/13326_2015_5_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/553e/4374589/62926f121949/13326_2015_5_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/553e/4374589/9dd0b0dbe7c5/13326_2015_5_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/553e/4374589/d18c9c4e68dd/13326_2015_5_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/553e/4374589/cc4fab5c131f/13326_2015_5_Fig4_HTML.jpg

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