Recording provenance of workflow runs with RO-Crate

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Abstract:

Recording the provenance of scientific computation results is key to the support of traceability, reproducibility and quality assessment of data products. Several data models have been explored to address this need, providing representations of workflow plans and their executions as well as means of packaging the resulting information for archiving and sharing. However, existing approaches tend to lack interoperable adoption across workflow management systems. In this work we present Workflow Run RO-Crate, an extension of RO-Crate (Research Object Crate) and Schema.org to capture the provenance of the execution of computational workflows at different levels of granularity and bundle together all their associated objects (inputs, outputs, code, etc.). The model is supported by a diverse, open community that runs regular meetings, discussing development, maintenance and adoption aspects. Workflow Run RO-Crate is already implemented by several workflow management systems, allowing interoperable comparisons between workflow runs from heterogeneous systems. We describe the model, its alignment to standards such as W3C PROV, and its implementation in six workflow systems. Finally, we illustrate the application of Workflow Run RO-Crate in two use cases of machine learning in the digital image analysis domain.

SEEK ID: https://workflowhub.eu/publications/61

DOI: 10.1371/journal.pone.0309210

Teams: ELIXIR Tools platform, EuroScienceGateway, Workflow Run Crate working group

Publication type: Journal

Journal: PLOS ONE

Editors: Ivan Zyrianoff

Citation: PLoS ONE 19(9):e0309210

Date Published: 10th Sep 2024

Registered Mode: by DOI

Authors: Simone Leo, Michael R. Crusoe, Laura Rodríguez-Navas, Raül Sirvent, Alexander Kanitz, Paul De Geest, Rudolf Wittner, Luca Pireddu, Daniel Garijo, José M. Fernández, Iacopo Colonnelli, Matej Gallo, Tazro Ohta, Hirotaka Suetake, Salvador Capella-Gutierrez, Renske de Wit, Bruno P. Kinoshita, Stian Soiland-Reyes

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Stian Soiland-Reyes

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Leo, S., Crusoe, M. R., Rodríguez-Navas, L., Sirvent, R., Kanitz, A., De Geest, P., Wittner, R., Pireddu, L., Garijo, D., Fernández, J. M., Colonnelli, I., Gallo, M., Ohta, T., Suetake, H., Capella-Gutierrez, S., de Wit, R., Kinoshita, B. P., & Soiland-Reyes, S. (2024). Recording provenance of workflow runs with RO-Crate. In I. Zyrianoff (Ed.), PLOS ONE (Vol. 19, Issue 9, p. e0309210). Public Library of Science (PLoS). https://doi.org/10.1371/journal.pone.0309210

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Created: 3rd Oct 2025 at 19:37

Last updated: 3rd Oct 2025 at 19:40

Recording provenance of workflow runs with RO-Crate

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