Publications

What is a Publication?
6 Publications visible to you, out of a total of 6
An Ecosystem of Services for FAIR Computational Workflows

Abstract (Expand)

Computational workflows, regardless of their portability or maturity, represent major investments of both effort and expertise. They are first class, publishable research objects in their own right. … They are key to sharing methodological know-how for reuse, reproducibility, and transparency. Consequently, the application of the FAIR principles to workflows [goble_2019, wilkinson_2025] is inevitable to enable them to be Findable, Accessible, Interoperable, and Reusable. Making workflows FAIR would reduce duplication of effort, assist in the reuse of best practice approaches and community-supported standards, and ensure that workflows as digital objects can support reproducible and robust science. FAIR workflows also encourage interdisciplinary collaboration, enabling workflows developed in one field to be repurposed and adapted for use in other research domains. FAIR workflows draw from both FAIR data [wilkinson_2016] and software [barker_2022] principles. Workflows propose explicit method abstractions and tight bindings to data, hence making many of the data principles apply. Meanwhile, as executable pipelines with a strong emphasis on code composition and data flow between steps, the software principles apply, too. As workflows are chiefly concerned with the processing and creation of data, they also have an important role to play in ensuring and supporting data FAIRification. The FAIR Principles for software and data mandate the use of persistent identifiers (PID) and machine actionable metadata associated with workflows to enable findability, reusability, interoperability and reusability. To implement the principles requires a PID and metadata framework with appropriate programmatic protocols, an accompanying ecosystem of services, tools, guidelines, policies, and best practices, as well the buy-in of existing workflow systems such that they adapt in order to adopt. The European EOSC-Life Workflow Collaboratory is an example of such a digital infrastructure for the Biosciences: it includes a metadata standards framework for describing workflows (i.e. RO-Crate, Bioschemas, and CWL), that is managed and used by dedicated new FAIR workflow services and programmatic APIs for interoperability and metadata access such as those proposed by the Global Alliance for Genomics and Health (GA4GH) [rehm_2021]. The WorkflowHub registry supports workflow Findability and Accessibility, while workflow testing services like LifeMonitor support long-term Reusability, Usability and Reproducibility. Existing workflow management systems/languages and packaging solutions are incorporated and adapted to promote portability, composability, interoperability, provenance collection and reusability, and to use and support these FAIR services. In this chapter, we will introduce the FAIR principles for workflows, the connections between FAIR workflows, and the FAIR ecosystems in which they live, using the EOSC-Life Collaboratory as a concrete example. We will also introduce other community efforts that are easing the ways that workflows are shared and reused by others, and we will discuss how the variations in different workflow settings impact their FAIR perspective.

Authors: Sean R. Wilkinson, Johan Gustafsson, Finn Bacall, Khalid Belhajjame, Salvador Capella, José María Fernández González, Jacob Fosso Tande, Luiz Gadelha, Daniel Garijo, Patricia Grubel, Björn Grüning, Farah Zaib Khan, Sehrish Kanwal, Simone Leo, Stuart Owen, Luca Pireddu, Line Pouchard, Laura Rodriguez-Navas, Beatriz Serrano-Solano, Stian Soiland-Reyes, Baiba Vilne, Alan Williams, Merridee Ann Wouters, Frederik Coppens, Carole Goble

Date Published: 21st May 2025

Publication Type: InBook

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

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

FAIR Computational Workflows

Abstract

Not specified

Authors: Carole Goble, Sarah Cohen-Boulakia, Stian Soiland-Reyes, Daniel Garijo, Yolanda Gil, Michael R. Crusoe, Kristian Peters, Daniel Schober

Date Published: 2020

Publication Type: Journal

Perspectives on automated composition of workflows in the life sciences

Abstract

Not specified

Authors: Anna-Lena Lamprecht, Magnus Palmblad, Jon Ison, Veit Schwämmle, Mohammad Sadnan Al Manir, Ilkay Altintas, Christopher J. O. Baker, Ammar Ben Hadj Amor, Salvador Capella-Gutierrez, Paulos Charonyktakis, Michael R. Crusoe, Yolanda Gil, Carole Goble, Timothy J. Griffin, Paul Groth, Hans Ienasescu, Pratik Jagtap, Matúš Kalaš, Vedran Kasalica, Alireza Khanteymoori, Tobias Kuhn, Hailiang Mei, Hervé Ménager, Steffen Möller, Robin A. Richardson, Vincent Robert, Stian Soiland-Reyes, Robert Stevens, Szoke Szaniszlo, Suzan Verberne, Aswin Verhoeven, Katherine Wolstencroft

Date Published: 2021

Publication Type: Journal

WorkflowHub: a registry for computational workflows

Abstract (Expand)

The rising popularity of computational workflows is driven by the need for repetitive and scalable data processing, sharing of processing know-how, and transparent methods. As both combined records of … analysis and descriptions of processing steps, workflows should be reproducible, reusable, adaptable, and available. Workflow sharing presents opportunities to reduce unnecessary reinvention, promote reuse, increase access to best practice analyses for non-experts, and increase productivity. In reality, workflows are scattered and difficult to find, in part due to the diversity of available workflow engines and ecosystems, and because workflow sharing is not yet part of research practice. WorkflowHub provides a unified registry for all computational workflows that links to community repositories, and supports both the workflow lifecycle and making workflows findable, accessible, interoperable, and reusable (FAIR). By interoperating with diverse platforms, services, and external registries, WorkflowHub adds value by supporting workflow sharing, explicitly assigning credit, enhancing FAIRness, and promoting workflows as scholarly artefacts. The registry has a global reach, with hundreds of research organisations involved, and more than 800 workflows registered.

Authors: Ove Johan Ragnar Gustafsson, Sean R. Wilkinson, Finn Bacall, Stian Soiland-Reyes, Simone Leo, Luca Pireddu, Stuart Owen, Nick Juty, José M. Fernández, Tom Brown, Hervé Ménager, Björn Grüning, Salvador Capella-Gutierrez, Frederik Coppens, Carole Goble

Date Published: 1st Dec 2025

Publication Type: Journal

Powered by
 (v.1.17.0-main)
About WorkflowHub | Acknowledgements | Credits | Terms & Conditions | Privacy Policy | Cite us | Contact us
Copyright © 2008 - 2025 The University of Manchester and HITS gGmbH