Recording provenance of workflow runs with RO-Crate
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.
Authors
- Hirotaka Suetake (ORCID: https://orcid.org/0000-0003-2765-0049)
- Paul De Geest (ORCID: https://orcid.org/0000-0002-8940-4946)
- Alexander Kanitz (ORCID: https://orcid.org/0000-0002-3468-0652)
- Iacopo Colonnelli (ORCID: https://orcid.org/0000-0001-9290-2017)
- Matej Gallo (ORCID: https://orcid.org/0000-0002-1119-1792)
- Michael R. Crusoe (ORCID: https://orcid.org/0000-0002-2961-9670)
- Stian Soiland‐Reyes
- Daniel Garijo (ORCID: https://orcid.org/0000-0003-0454-7145)
- Simone Leo (ORCID: https://orcid.org/0000-0001-8271-5429)
- Luca Pireddu (ORCID: https://orcid.org/0000-0002-4663-5613)
- Salvador Capella-Gutiérrez (ORCID: https://orcid.org/0000-0002-0309-604X)
- Raül Sirvent (ORCID: https://orcid.org/0000-0003-0606-2512)
- Rudolf Wittner (ORCID: https://orcid.org/0000-0002-0003-2024)
- Renske de Wit (ORCID: https://orcid.org/0000-0003-0902-0086)
- Bruno P. Kinoshita (ORCID: https://orcid.org/0000-0001-8250-4074)
- José M. Fernández (ORCID: https://orcid.org/0000-0002-4806-5140)
- Tazro Ohta (ORCID: https://orcid.org/0000-0003-3777-5945)
- Laura Rodríguez‐Navas (ORCID: https://orcid.org/0000-0003-4929-1219)
Institutions
- SIB Swiss Institute of Bioinformatics (CH)
- Chiba University (JP)
- Forschungszentrum Jülich (DE)
- University of Basel (CH)
- Masaryk University (CZ)
- Barcelona Supercomputing Center (ES)
- Center for Advanced Studies Research and Development in Sardinia (IT)
- University of Manchester (GB)
- Biobanking and Biomolecular Resources Research Infrastructure Consortium (AT)
- VIB-UGent Center for Plant Systems Biology (BE)
- Dutch Techcentre for Life Sciences (NL)
- SATO (Japan) (JP)
- Czech Academy of Sciences, Institute of Computer Science (CZ)
- Research Organization of Information and Systems (JP)
- University of Turin (IT)
- Vrije Universiteit Amsterdam (NL)
- Universidad Politécnica de Madrid (ES)
- University of Amsterdam (NL)
- Universitat Politècnica de Catalunya (ES)
Publication Details
- Journal
- PLoS ONE
- Published
- 2024-09-10
- DOI
- https://doi.org/10.1371/journal.pone.0309210
- Citations
- 25
- Primary Topic
- Scientific Computing and Data Management
- Type
- article
- Field-Weighted Citation Impact
- 26.27
Funders
- Comunidad de Madrid
- UK Research and Innovation
- European Commission
- Generalitat de Catalunya
- Fonds Wetenschappelijk Onderzoek
- Universidad Politécnica de Madrid
- Regione Autonoma della Sardegna
- Vlaamse regering
- Horizon 2020 Framework Programme
- HORIZON EUROPE Framework Programme
- Medical Research Council
- Japan Science and Technology Agency
- Agencia Estatal de Investigación
- National Bioscience Database Center