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"Structure-based knowledge acquisition from electronic lab notebooks for research data provenance documentation"

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 ... (Full article...)

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