Institute of Communications Engineering, University of Rostock, Rostock, Germany.
University Library, University of Rostock, Rostock, Germany.
J Biomed Semantics. 2022 Jan 31;13(1):4. doi: 10.1186/s13326-021-00257-x.
Electronic Laboratory Notebooks (ELNs) are used to document experiments and investigations in the wet-lab. Protocols in ELNs contain a detailed description of the conducted steps including the necessary information to understand the procedure and the raised research data as well as to reproduce the research investigation. The purpose of this study is to investigate whether such ELN protocols can be used to create semantic documentation of the provenance of research data by the use of ontologies and linked data methodologies.
Based on an ELN protocol of a biomedical wet-lab experiment, a retrospective provenance model of the raised research data describing the details of the experiment in a machine-interpretable way is manually engineered. Furthermore, an automated approach for knowledge acquisition from ELN protocols is derived from these results. This structure-based approach exploits the structure in the experiment's description such as headings, tables, and links, to translate the ELN protocol into a semantic knowledge representation. To satisfy the Findable, Accessible, Interoperable, and Reuseable (FAIR) guiding principles, a ready-to-publish bundle is created that contains the research data together with their semantic documentation.
While the manual modelling efforts serve as proof of concept by employing one protocol, the automated structure-based approach demonstrates the potential generalisation with seven ELN protocols. For each of those protocols, a ready-to-publish bundle is created and, by employing the SPARQL query language, it is illustrated that questions about the processes and the obtained research data can be answered.
The semantic documentation of research data obtained from the ELN protocols allows for the representation of the retrospective provenance of research data in a machine-interpretable way. Research Object Crate (RO-Crate) bundles including these models enable researchers to easily share the research data including the corresponding documentation, but also to search and relate the experiment to each other.
电子实验室笔记本 (ELN) 用于记录湿实验室中的实验和研究。ELN 中的方案包含对所进行步骤的详细描述，包括理解过程和提出的研究数据以及重现研究调查所需的必要信息。本研究的目的是调查这种 ELN 方案是否可以通过使用本体论和链接数据方法来创建研究数据起源的语义文档。
基于生物医学湿实验室实验的 ELN 方案，手动设计了一个研究数据起源的回溯模型，以机器可解释的方式描述实验的细节。此外，还从这些结果中得出了一种从 ELN 方案中自动获取知识的方法。这种基于结构的方法利用实验描述中的结构，如标题、表格和链接，将 ELN 方案转换为语义知识表示。为了满足可查找、可访问、可互操作和可重用 (FAIR) 的指导原则，创建了一个准备发布的捆绑包，其中包含研究数据及其语义文档。
虽然手动建模工作通过使用一个方案作为概念验证，但基于结构的自动化方法通过七个 ELN 方案展示了潜在的泛化能力。对于每个协议，都创建了一个准备发布的捆绑包，并通过使用 SPARQL 查询语言，说明了可以回答关于流程和获得的研究数据的问题。
从 ELN 方案中获得的研究数据的语义文档允许以机器可解释的方式表示研究数据的回溯起源。包括这些模型的研究对象罐 (RO-Crate) 捆绑包使研究人员能够轻松共享包括相应文档的研究数据，还可以搜索和相互关联实验。
