eLabFTW: An open source laboratory notebook for research labs

Carpi, Nicolas; Minges, Alexander; Piel, Matthieu

doi:10.21105/joss.00146

Cited by 41 publications

(48 citation statements)

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“…For the purpose of this study, we asked the researchers to use an ELN for the documentation of their wet-lab activities, resulting in eight ELN protocols, one for the first experiment and seven for the latter, representing different permutations of the sequential execution of Ca-imaging for different electrical stimulation parameters. In particular, elabFTW (Deltablot, https://www.elabftw.net/ , v3.6.7) [ 10 ] a domain-independent ELN was used. Figure 2 shows an excerpt of a protocol from the use case.…”

Section: Use Casementioning

confidence: 99%

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

et al. 2022

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Background 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. Methods 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. Results 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. Conclusions 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.

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Section: Use Casementioning

confidence: 99%

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

et al. 2022

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“…It should be noted that the concept of LIMS is a wellestablished one (Gibbon, 1996), and numerous mature commercial and open source projects exist to support both highly specific and general laboratory data workflows (Cheung et al, 2009;Blaiszik et al, 2016;Carey et al, 2016;Jacobsen et al, 2016;Arkilic et al, 2017;CARPi et al, 2017;Nguyen et al, 2017;Zakutayev et al, 2018;Abbott Laboratories, 2020;Bika Lab Systems, 2020;Dataworks Development, Inc, 2020), 1 many of which were marshaled as part of the materials data infrastructure efforts of the Materials Genome Initiative (MGI; Warren & Ward, 2018). As such, the implementation of a LIMS in general is not a novel effort.…”

Section: Introductionmentioning

confidence: 99%

NexusLIMS: A Laboratory Information Management System for Shared-Use Electron Microscopy Facilities

et al. 2021

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“…Finally, eLabFTW provides an extensive search tool. 7 Disadvantages and advantages of ELN on experimental and lab management level Overall acceptance for the usage of ELNs in the academic field is rather low. This seems to be due to perceived disadvantages, when using ELNs.…”

Section: Introductionmentioning

confidence: 99%

eLabFTW as an Open Science tool to improve the quality and translation of preclinical research

Hewera

Hänggi

Gerlach³

et al. 2021

F1000Res

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Reports of non-replicable research demand new methods of research data management. Electronic laboratory notebooks (ELNs) are suggested as tools to improve the documentation of research data and make them universally accessible. In a self-guided approach, we introduced the open-source ELN eLabFTW into our life-science lab group and, after using it for a while, think it is a useful tool to overcome hurdles in ELN introduction by providing a combination of properties making it suitable for small life-sceience labs, like ours. We set up our instance of eLabFTW, without any further programming needed. Our efforts to embrace open data approach by introducing an ELN fits well with other institutional organized ELN initiatives in academic research and our goals towards data quality management.

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eLabFTW: An open source laboratory notebook for research labs

Cited by 41 publications

References 0 publications

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

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

NexusLIMS: A Laboratory Information Management System for Shared-Use Electron Microscopy Facilities

eLabFTW as an Open Science tool to improve the quality and translation of preclinical research

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