There has been a large focus in recent years on making assets in scientific research findable, accessible, interoperable and reusable, collectively known as the FAIR principles. A particular area of focus lies in applying these principles to scientific computational workflows. Jupyter notebooks are a very popular medium by which to program and communicate computational scientific analyses. However, they present unique challenges when it comes to reuse of only particular steps of an analysis without disrupting the usual flow and benefits of the notebook approach, making it difficult to fully comply with the FAIR principles. Here we present an approach and toolset for adding the power of semantic technologies to Python-encoded scientific workflows in a simple, automated and minimally intrusive manner. The semantic descriptions are published as a series of nanopublications that can be searched and used in other notebooks by means of a Jupyter Lab plugin. We describe the implementation of the proposed approach and toolset, and provide the results of a user study with 15 participants, designed around image processing workflows, to evaluate the usability of the system and its perceived effect on FAIRness. Our results show that our approach is feasible and perceived as user-friendly. Our system received an overall score of 78.75 on the System Usability Scale, which is above the average score reported in the literature.
|Title of host publication
|Subtitle of host publication
|Proceedings of the 11th Knowledge Capture Conference
|Association for Computing Machinery, Inc
|Number of pages
|Published - Dec 2021
|11th ACM International Conference on Knowledge Capture, K-CAP 2021 - Virtual, Online, United States
Duration: 2 Dec 2021 → 3 Dec 2021
|11th ACM International Conference on Knowledge Capture, K-CAP 2021
|2/12/21 → 3/12/21
Bibliographical noteFunding Information:
This work was supported by the Dutch Research Council (NWO) (No. 628.011.011) and the Netherlands eScience Center (No. NLeSC P 17.0201). We would like to thank Vincent Emonet for his invaluable help in setting up and hosting the evaluation notebook containers.
© 2021 Owner/Author.
- notebook environments