End-to-End provenance representation for the understandability and reproducibility of scientific experiments using a semantic approach

Journal of Biomedical Semantics

Sheeba Samuel¹  Birgitta König-Ries¹ 

[1] Heinz-Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University, Jena, Germany;Michael Stifel Center Jena, Jena, Germany;

关键词: Provenance;    Reproducibility;    Semantic web;    Ontology;    Jupyter notebooks;    Experiments;   

DOI  :  10.1186/s13326-021-00253-1

来源: Springer

【 摘 要 】

BackgroundThe advancement of science and technologies play an immense role in the way scientific experiments are being conducted. Understanding how experiments are performed and how results are derived has become significantly more complex with the recent explosive growth of heterogeneous research data and methods. Therefore, it is important that the provenance of results is tracked, described, and managed throughout the research lifecycle starting from the beginning of an experiment to its end to ensure reproducibility of results described in publications. However, there is a lack of interoperable representation of end-to-end provenance of scientific experiments that interlinks data, processing steps, and results from an experiment’s computational and non-computational processes.ResultsWe present the “REPRODUCE-ME” data model and ontology to describe the end-to-end provenance of scientific experiments by extending existing standards in the semantic web. The ontology brings together different aspects of the provenance of scientific studies by interlinking non-computational data and steps with computational data and steps to achieve understandability and reproducibility. We explain the important classes and properties of the ontology and how they are mapped to existing ontologies like PROV-O and P-Plan. The ontology is evaluated by answering competency questions over the knowledge base of scientific experiments consisting of computational and non-computational data and steps.ConclusionWe have designed and developed an interoperable way to represent the complete path of a scientific experiment consisting of computational and non-computational steps. We have applied and evaluated our approach to a set of scientific experiments in different subject domains like computational science, biological imaging, and microscopy.

【 授权许可】

CC BY