Adverse Outcome Pathways (AOPs) have been proposed to facilitate mechanistic understanding of interactions of chemicals/materials with biological systems. Each AOP starts with a molecular initiating event (MIE) and possibly ends with adverse outcome(s) (AOs) via a series of key events (KEs). So far, the interaction of engineered nanomaterials (ENMs) with biomolecules, biomembranes, cells, and biological structures, in general, is not yet fully elucidated. There is also a huge lack of information on which AOPs are ENMs-relevant or -specific, despite numerous published data on toxicological endpoints they trigger, such as oxidative stress and inflammation. We propose to integrate related data and knowledge recently collected. Our approach combines the annotation of nanomaterials and their MIEs with ontology annotation to demonstrate how we can then query AOPs and biological pathway information for these materials. We conclude that a FAIR (Findable, Accessible, Interoperable, Reusable) representation of the ENM-MIE knowledge simplifies integration with other knowledge. This study introduces a new database linking nanomaterial stressors to the first known MIE or KE. Second, it presents a reproducible workflow to analyze and summarize this knowledge. Third, this work extends the use of semantic web technologies to the field of nanoinformatics and nanosafety.

中文翻译：

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从论文到基于 RDF 的物理化学数据整合和纳米材料的不良结果途径

不良结果途径（AOP）已被提出，以促进对化学品/材料与生物系统相互作用的机械理解。每个 AOP 都以分子起始事件 (MIE) 开始，并可能通过一系列关键事件 (KE) 以不良结果 (AO) 结束。到目前为止，工程纳米材料（ENM）与生物分子、生物膜、细胞和生物结构的相互作用尚未完全阐明。尽管有大量关于 AOP 引发的毒理学终点（例如氧化应激和炎症）的数据已发表，但关于哪些 AOP 与 ENM 相关或特定的信息也非常缺乏。我们建议整合最近收集的相关数据和知识。我们的方法将纳米材料及其 MIE 的注释与本体注释相结合，以演示如何查询这些材料的 AOP 和生物途径信息。我们得出的结论是，ENM-MIE 知识的公平（可查找、可访问、可互操作、可重用）表示简化了与其他知识的集成。这项研究引入了一个新的数据库，将纳米材料应激源与第一个已知的 MIE 或 KE 联系起来。其次，它提供了一个可重复的工作流程来分析和总结这些知识。第三，这项工作将语义网络技术的使用扩展到纳米信息学和纳米安全领域。