WorkflowHub Knowledge Graph

This RO-Crate contains a knowledge graph built from RO-Crates on WorkflowHub, enriched with metadata from additional sources. The source code used to create the knowledge graph, including the enrichments, is also included.

This version: 2025-08-29

Also published on Zenodo: https://doi.org/10.5281/zenodo.16995374

Creators: Eli Chadwick, Oliver Woolland, Alexander Hambley, Stian Soiland-Reyes, Volodymyr Savchenko

Submitter: Eli Chadwick

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Packaging BioCompute Objects using RO-Crate

Tutorial and specification for packaging IEEE 2791-2020 (BioCompute Objects/BCOs) as RO-Crate Research Objects.

BioCompute Object (BCO) is a standard (IEEE 2791-2020) for describing computational workflows for regularory submission, e.g. a genomics workflow as part of personalized medicine.

RO-Crate is a community-based specification for research data packaging of Research Objects with rich metadata, based on open standards and vocabularies like JSON-LD and schema.org.

BCO RO-Crate is the combination ...

Creators: Stian Soiland-Reyes, Jonathon Keeney, Hadley King, Janisha Patel, Alex Coleman

Submitter: Stian Soiland-Reyes

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Recording provenance of workflow runs with RO-Crate

Abstract (Expand)

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: 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

Date Published: 10th Sep 2024

Publication Type: Journal

EuroScienceGateway MS6: Integrated EuroScienceGateway knowledge graph

Abstract (Expand)

Description The Workflowhub Knowledge Graph has been improved and its generation made more robust. When this work was last reported, a complete knowledge graph had been generated but several criticisms …icisms were made. The previous graph was: - Verbose and hard for a human to read or navigate - Had unresolvable URIs as root data entities - Contained many duplicate entries - Contained sparse metadata from only a single source Work has successfully been undertaken to address all of these points. The graph now uses partially resolvable, more human readable, URIs for root data entities. Steps have been added to the generation software to add metadata from additional sources (enrichment) and to remove duplicate entries (consolidation). Several areas of the codebase have been refactored and improved, to help ensure repeatability and longevity. The new knowledge graph still has areas that could be improved. Partially resolvable URIs should be migrated to fully resolvable alternatives. Further enrichment processes should be added which affords greater de-duplication.

Authors: Eli Chadwick, Oliver Woolland, Volodymyr Savchenko, Finn Bacall, Alexander Hambley, José María Fernández González, Armin Dadras, Stian Soiland-Reyes

Date Published: 1st Aug 2025

Publication Type: Tech report

EuroScienceGateway D2.1: Reproducible FAIR Digital Objects for Workflows

Abstract (Expand)

Description This EuroScienceGateway report gives an overview of FAIR Digital Objects (FDO), considering their use for computational workflows as scholarly objects. EuroScienceGateway has progressed the …d the technologies Signposting and RO-Crate for implementing Workflow FDOs with the registry WorkflowHub and the workflow system Galaxy, and initiated work with academic publishers to encourage workflow citation practices. Here we document how WorkflowHub supports research software best practices for workflows, and assist building FAIR Computational Workflows. Provenance of workflow executions has been made possible in an interoperable way across many workflow systems using Workflow Run Crate profiles, including from Galaxy. Finally this report explores how Workflow FDOs are exposed and can be utilised, e.g. gathered in knowledge graphs and having tighter workflow system integration.

Authors: Stian Soiland-Reyes, Eli Chadwick, Finn Bacall, Jose M. Fernandez, Björn Grüning, Hakan Bayındır

Date Published: 28th Aug 2024

Publication Type: Tech report

Workflow Provenance registration with COMPSs

Session during the Innovative HPC workflows for industry (https://eflows4hpc.eu/event/innovative-hpc-workflows-for-industry/) that describes how Workflow Provenance is recorded with COMPSs: the background on the tools used, how the recording has been designed, and how to use it and inspect metadata.

DOI

Creator: Raül Sirvent

Submitter: Raül Sirvent

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FAIR Computational Workflows

Presented at Swedish eResearch Centre meeting, 13 may 2022

Creator: Carole Goble

Submitter: Carole Goble

External Link
FAIR Computational Workflows - FAIReScience 2021

invited presentation at https://researchsoft.github.io/FAIReScience/, FAIReScience 2021 online workshop virtually co-located with the 17th IEEE International Conference on eScience (eScience 2021)

20th Sept 2021

Creator: Carole Goble

Submitter: Carole Goble

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FAIR Computational Workflows - Keynote ICTeSSH 2021

Keynote Presented at the ICTeSSH 2021 Conference to Social Science and Humanities. ICTeSSH 2021, 30th June 2021

https://ictessh.uns.ac.rs/ In data intensive science multi-step tool-chains are widely used to help scientists manage, analyze, and share increasing volumes of complex data. The use of computational workflows to manage these multi-step computational processes has accelerated in the past few years driven by the need for scalable data processing, the exchange of processing know-how, and ...

Creator: Carole Goble

Submitter: Carole Goble

External Link
FAIR Computational Workflows - Keynote JOBIM 2021

Keynote JOBIM 2021 (French Bioinformatics Conference)

FAIR Computational Workflows https://jobim2021.sciencesconf.org/ 8 July 2021

Computational workflows capture precise descriptions of the steps and data dependencies needed to carry out computational data pipelines, analysis and simulations in many areas of Science, including the Life Sciences. The use of computational workflows to manage these multi-step computational processes has accelerated in the past few years driven by the need for ...

Creator: Carole Goble

Submitter: Carole Goble

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FAIR Computational Workflows - Keynote GCB2021

Keynote at German Conference on Bioinformatics 2021 https://gcb2021.de/ FAIR Computational Workflows Computational workflows capture precise descriptions of the steps and data dependencies needed to carry out computational data pipelines, analysis and simulations in many areas of Science, including the Life Sciences. The use of computational workflows to manage these multi-step computational processes has accelerated in the past few years driven by the need for scalable data processing, the ...

Creator: Carole Goble

Submitter: Carole Goble

External Link
Describing and packaging workflows using RO-Crate and BioCompute Objects

BioCompute Object (BCO) is a standard (IEEE 2791-2020) for describing computational workflows for regularory submission, e.g. a genomics workflow as part of personalized medicine.

RO-Crate is a community-based specification for research data packaging of Research Objects with rich metadata, based on open standards and vocabularies like JSON-LD and schema.org.

BCO RO-Crate is the combination of these two approaches, packaging a BCO and the workflow it describes in a RO-Crate.

This webinar describes ...

Creator: Stian Soiland-Reyes

Submitter: Stian Soiland-Reyes

External Link
Build WorkflowHub Knowledge Graph
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WorkflowHub Knowledge Graph

A tool to generate a knowledge graph from a source of RO Crates. By default, this tool sources and generates an RDF graph of crates from WorkflowHub.

Docker build and push [![Python linting and ...

Type: Snakemake

Creators: Alexander Hambley, Oliver Woolland, Eli Chadwick, Volodymyr Savchenko, José Mª Fernández, Stian Soiland-Reyes

Submitter: Eli Chadwick

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