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

Max Schröder,Frank Krüger,Susanne Staehlke,Paul Groth,Sascha Spors,J Barbara Nebe

doi:10.1186/s13326-021-00257-x

Max Schröder, Frank Krüger + Show 4 more

Open Access

https://doi.org/10.1186/s13326-021-00257-x

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Abstract

BackgroundElectronic 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.MethodsBased 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.ResultsWhile 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.ConclusionsThe 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.

Highlights

Electronic Laboratory Notebooks (ELNs) are used to document experiments and investigations in the wet-lab
We introduce the use case and derive questions regarding the provenance of the corresponding research data
First, we present the details of the manually engineered semantic representation of the Ca-imaging procedure which served as (i) a proof of concept for the effectiveness of retrospective provenance documentation from ELN protocols, (ii) a basis for analysis of the ELN protocol structure, and (iii) the development of the protocol template for research guidance

Summary

Introduction

Electronic Laboratory Notebooks (ELNs) are used to document experiments and investigations in the wet-lab. Knowledge about the generating process helps to understand research data and allows for the reproduction of research investigations This includes sources of input data such as parameters and assumptions and information about instrumentation, devices and materials. The focus of these tools is the documentation of laboratory activities that produce research data in so-called ELN protocols In addition to this textual description, the FAIR principles [1] provide general guidance on research data documentation in terms of metadata. They do not prescribe technical details about the implementation of such documentation [2]

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