Workflow Run RO-Crate is a working group for defining RO-Crate profiles for capturing the provenance of an execution of a computational workflow.
Profiles
The Workflow Run RO-Crate profile collection is the main outcome of the group’s activities.
Community
The Workflow Run RO-Crate working group is part of the RO-Crate community.
We coordinate using the channel #ro-crate on seek4science.slack.com (join) and the RO-Crate mailing list. Material from or related to the group’s activity is available from the GitHub repository.
Currently we have bi-weekly meetings you are welcome to attend.
Post here to join the working group.
Co-chairs: Simone Leo, Laura Rodríguez-Navas
Members:
- Simone Leo https://orcid.org/0000-0001-8271-5429
- Laura Rodríguez-Navas https://orcid.org/0000-0003-4929-1219
- Stian Soiland-Reyes https://orcid.org/0000-0001-9842-9718
- Paul Brack https://orcid.org/0000-0002-5432-2748
- José María Fernández https://orcid.org/0000-0002-4806-5140
- Alan R Williams https://orcid.org/0000-0003-3156-2105
- Ignacio Eguinoa https://orcid.org/0000-0002-6190-122X
- Daniel Garijo https://orcid.org/0000-0003-0454-7145
- Paul De Geest https://orcid.org/0000-0002-8940-4946
- Raül Sirvent https://orcid.org/0000-0003-0606-2512
- Alexander Kanitz https://orcid.org/0000-0002-3468-0652
- Michael R Crusoe https://orcid.org/0000-0002-2961-9670
- LJ Garcia Castro https://orcid.org/0000-0003-3986-0510
- Rudolf Wittner https://orcid.org/0000-0002-0003-2024
- Wolfgang Maier https://orcid.org/0000-0002-9464-6640
- Sebastiaan Huber https://orcid.org/0000-0001-5845-8880
- Kevin Jablonka https://orcid.org/0000-0003-4894-4660
- Haris Zafeiropoulos https://orcid.org/0000-0002-4405-6802
- Iacopo Colonnelli https://orcid.org/0000-0001-9290-2017
- Jake Emerson https://orcid.org/0000-0003-0617-9219
- Abigail Miller https://orcid.org/0000-0001-9228-2882
- Stelios Ninidakis https://orcid.org/0000-0003-3898-9451
- Tazro Ohta https://orcid.org/0000-0003-3777-5945
- Hirotaka Suetake https://orcid.org/0000-0003-2765-0049
- Johannes Köster https://orcid.org/0000-0001-9818-9320
- Luiz Gadelha https://orcid.org/0000-0002-8122-9522
- Mahnoor Zulfiqar https://orcid.org/0000-0002-8330-4071
- Romain David https://orcid.org/0000-0003-4073-7456
- Maciek Bąk https://orcid.org/0000-0003-1361-7301
- Petr Holub https://orcid.org/0000-0002-5358-616X
- Milan Markovic https://orcid.org/0000-0002-5477-287X
- Bruno P. Kinoshita https://orcid.org/0000-0001-8250-4074
- Renske de Wit https://orcid.org/0000-0003-0902-0086
- Jasper Koehorst https://orcid.org/0000-0001-8172-8981
- … you?
Examples
These RO-Crates are being co-developed as examples of using the Workflow Run profiles:
- Provenance Run Crate Example, converted from the CWLProv example
- Baseline Use Case: COVID-19 vaccine effectiveness assessment – a process run crate from the BY-COVID project showing how synthetic dataset generation using Jupyter Notebook can be tracked
- Workflow Run RO-Crate for a ML prediction pipeline run (pipeline repo – part of the DeepHealth digital pathology platform)
- Machine learning pipeline example (conceptual draft from EOSC-Life WP6)
Other resources
- Requirements for the Workflow Run RO-Crate profiles
- Workflow RO-Crate profile – for describing workflows as reusable objects. (extended by workflow run profile)
- Profile for recording workflow runs (conceptual ideas from RO-Crate paper)
- Example of CreateAction and Docker Image (tool invocation)
RO-Crate links
- RO-Crate homepage
- RO-Crate specification 1.1
- RO-Crate profiles (from 1.2-DRAFT – feedback welcome)
- Workflow Crate (profile for a workflow definition)
- Workflow Testing Crate (profile for defining workflow tests)
- Adding a ComputationalWorkflow in RO-Crate
- ComputationalWorkflow profile in BioSchemas
- ComputationalTool profile in BioSchemas
- Provenance of software run in RO-Crate
- BioComputeObject in RO-Crate
Related Work
- Packaging research artefacts with RO-Crate (RO-rate article)
- Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv (RO-Bundle+PROV for CWL, – see also examples)
- Towards a Common Standard for Data and Specimen Provenance in Life Sciences (article on ISO 23494 Common Provenance Model)
- ISO 23494: Biotechnology - Provenance Information Model for Biological Specimen and Data (poster article on ISO 23494)
- EOSC-Life Common Provenance Model (deliverable showing ISO 23494 model)
- P-Plan ontology, OPMW ontology and OPMW-PROV
- ProvONE+: A Provenance Model for Scientific Workflows (not Open Access) [PROV-One ontology]