A collaborative semantic-based provenance management platform for reproducibility

Sheeba Samuel; Birgitta König-Ries

doi:10.7717/peerj-cs.921

A collaborative semantic-based provenance management platform for reproducibility

PeerJ Comput Sci. 2022 Mar 10:8:e921. doi: 10.7717/peerj-cs.921. eCollection 2022.

Authors

Sheeba Samuel^{1

2}, Birgitta König-Ries^{1

2}

Affiliations

¹ Michael Stifel Center Jena, Jena, Germany.
² Heinz Nixdorf Chair for Distributed Information Systems, Friedrich-Schiller Universität Jena, Jena, Thuringia, Germany.

Abstract

Scientific data management plays a key role in the reproducibility of scientific results. To reproduce results, not only the results but also the data and steps of scientific experiments must be made findable, accessible, interoperable, and reusable. Tracking, managing, describing, and visualizing provenance helps in the understandability, reproducibility, and reuse of experiments for the scientific community. Current systems lack a link between the data, steps, and results from the computational and non-computational processes of an experiment. Such a link, however, is vital for the reproducibility of results. We present a novel solution for the end-to-end provenance management of scientific experiments. We provide a framework, CAESAR (CollAborative Environment for Scientific Analysis with Reproducibility), which allows scientists to capture, manage, query and visualize the complete path of a scientific experiment consisting of computational and non-computational data and steps in an interoperable way. CAESAR integrates the REPRODUCE-ME provenance model, extended from existing semantic web standards, to represent the whole picture of an experiment describing the path it took from its design to its result. ProvBook, an extension for Jupyter Notebooks, is developed and integrated into CAESAR to support computational reproducibility. We have applied and evaluated our contributions to a set of scientific experiments in microscopy research projects.

Keywords: Jupyter Notebooks; Ontology; Provenance; Reproducibility; Research data management platform; Scientific experiments; Semantic Web; Visualization.

Grants and funding

This research is supported by the Deutsche Forschungsgemeinschaft (DFG) in Project Z2 of the CRC/TRR 166 High-end light microscopy elucidates membrane receptor function - ReceptorLight. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.