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
• Samuel Lampa https://orcid.org/0000-0001-6740-9212
• Samuel Grayson https://orcid.org/0000-0001-5411-356X
• … 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]