ResearchObject.org (RO)
Published February 28, 2025 | Version v2
Project deliverable Open

EuroScienceGateway D2.2: Publishing workflow enriched FDOs to EOSC

Creators

  • 1. ROR icon University of Manchester
  • 2. ROR icon University of Göttingen
  • 3. ROR icon University of Freiburg
  • 4. EPFL
  • 5. University of Geneva

Description

The concept of publishing workflows as scholarly is being recognised and practiced through repositories like WorkflowHub and principles for FAIR Computational Workflow. This deliverable describes how the evolving landscape of the European Open Science Cloud (EOSC) can facilitate workflow publishing in a federated and distributed manner, exemplified by how workflows for Galaxy are published.

Files

ESG-D2.2 Publishing workflow enriched FDOs to EOSC.pdf

Files (3.7 MB)

Additional details

Cites
Other: 21.11166/1bO1by (Handle)
Other: 21.11166/GEp8Ry (Handle)
10.25504/FAIRsharing.07cf72 (DOI)
21.15125/6BFVdN (Handle)
10.5281/zenodo.13225792 (DOI)
https://eosc.eu/wp-content/uploads/2024/05/EOSC-A_GA8_20240527-28_Paper-G_Update_EOSC_Nodes_requirements-DRAFT-v240524.pdf (URL)
10.3030/101188248 (DOI)
10.3030/101188256 (DOI)
10.14454/mzv1-5b55 (DOI)
10.48546/workflowhub.workflow.676.1 (DOI)
Other: 10.3030/101059492 (DOI)
https://github.com/ResearchObject/ro-crate-inveniordm/blob/main/docs/mapping.md (URL)
Software: https://github.com/ResearchObject/ro-crate-zenodo (URL)
https://galaxyproject.org/news/2024-08-03-workflow-publisher-forum/ (URL)
10.1038/s41597-025-04451-9 (DOI)
https://github.com/esg-epfl-apc/astro-paper-workflow-parsing?tab=readme-ov-file (URL)
https://documents.egi.eu/document/3470 (URL)
Report: https://eosc.eu/eosc-federation-handbook/ (URL)
Project deliverable: 10.5281/zenodo.7886545 (DOI)
https://galaxyproject.org/news/2024-08-03-workflow-publisher-forum/ (URL)
10.1051/0004-6361/202037850 (DOI)
Project deliverable: https://eoscfuture.eu/wp-content/uploads/2023/07/01_EOSC-Portal-and-Onboarding-to-the-EOSC-Marketplace_20230612.pdf (URL)
Conference paper: 10.1109/eScience.2018.00018 (DOI)
10.5281/zenodo.13225792 (DOI)
References
https://web.archive.org/web/20240301011637/https://marketplace.eosc-portal.eu/ (URL)
https://wiki.eoscfuture.eu/display/PUBLIC/D.+v4.00+EOSC+Data+Source+Profile (URL)
https://wiki.eoscfuture.eu/display/PUBLIC/EOSC+Portal+Profiles (URL)
https://wiki.eoscfuture.eu/display/PUBLIC/E.+v4.00+EOSC+Research+Product+Profile (URL)
https://openaire-guidelines-for-literature-repository-managers.readthedocs.io/en/v4.0.0 (URL)
https://marketplace.eosc-portal.eu/ (URL)
https://digital-strategy.ec.europa.eu/en/news/commission-announces-winners-eosc-procurement (URL)
https://usegalaxy.eu/ (URL)
https://workflowhub.eu/ (URL)
https://about.workflowhub.eu/#retention-and-end-of-life-policy (URL)
https://www.openaire.eu/ (URL)
https://www.openaire.eu/openaire-and-eosc (URL)
https://explore.openaire.eu/ (URL)
https://zenodo.org/ (URL)
https://graph.openaire.eu/ (URL)
https://graph.openaire.eu/docs (URL)
https://graph.openaire.eu/docs/category/downloads (URL)
https://graph.openaire.eu/docs/data-model (URL)
https://graph.openaire.eu/docs/data-model/entities/research-product (URL)
http://api.openaire.eu/vocabularies/dnet:result_typologies/other (URL)
https://explore.openaire.eu/search/project?projectId=corda_____he::2641f1fd24670a0dda126225c89c1273 (URL)
https://galaxyproject.org/news/2023-05-05-eosc-esg-openaire/ (URL)
https://galaxyproject.org/news/2024-05-03-inveniordm-integration/ (URL)
https://galaxyproject.org/news/2023-02-23-structured-data-exports-ro-bco/ (URL)
https://galaxyproject.org/news/2022-11-21-add-task-based-history-export-tracking/ (URL)
https://github.com/galaxyproject/galaxy_codex (URL)
https://open-science-cloud.ec.europa.eu/news/european-commission-announces-eosc-eu-nodes-transition-full-production (URL)
https://open-science-cloud.ec.europa.eu/news/european-commission-announces-eosc-eu-nodes-transition-full-production (URL)
https://open-science-cloud.ec.europa.eu/resources (URL)
https://datacite.org/ (URL)
https://open-science-cloud.ec.europa.eu/services (URL)
https://galaxyproject.org/news/2023-11-13-run-in-galaxy-button-workflowhub/ (URL)
https://open-science-cloud.ec.europa.eu/resources/software?q=workflow (URL)
https://galaxyproject.org/news/2025-01-29-esg-eosc/ (URL)
Other: https://open-science-cloud.ec.europa.eu/resources/services/21.11166%2F1bO1by (URL)
Other: https://open-science-cloud.ec.europa.eu/resources/datasources/21.11166%2FGEp8Ry (URL)
https://open-science-cloud.ec.europa.eu/resources/interoperability/21.15125%2F6BFVdN (URL)
https://elixir-europe.org/how-we-work (URL)
https://elixir-europe.org/commissioned-services (URL)
https://elixir-europe.org/about-us/governance/handbook-operations (URL)
https://www.nfdi.de/ (URL)
10.3030/101058785 (DOI)
https://elixiruknode.org/services/ (URL)
https://commons.datacite.org/doi.org?query=client.uid:borq.00002-2021 (URL)
https://explore.openaire.eu/search/software?pid=10.48546%2Fworkflowhub.workflow.160.1 (URL)
Workflow: 10.48546/workflowhub.workflow.160.1 (DOI)
https://github.com/workflowhub-eu/workflowhub-graph (URL)
https://github.com/galaxyproject/planemo (URL)
https://github.com/galaxyproject/planemo/pull/1458 (URL)
https://about.workflowhub.eu/docs/citable/ (URL)
https://training.galaxyproject.org/ (URL)
https://github.com/galaxyproject/training-material/blob/eacc45a0d548cf0f3e2f6c077d3966443e567821/topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing.ga#L5 (URL)
https://github.com/iwc-workflows/allele-based-pathogen-identification/blob/main/ro-crate-metadata.json (URL)
https://gxy.io/GTN:W00002 (URL)
https://iwc.galaxyproject.org/ (URL)
https://w3id.org/workflowhub/workflow-ro-crate/ (W3ID)
https://workflowhub.eu/workflows/676?version=1 (URL)
https://schema.datacite.org/meta/kernel-4.0/ (URL)
https://explore.openaire.eu/search/software?pid=10.48546%2Fworkflowhub.workflow.676.1 (URL)
https://commons.datacite.org/doi.org/10.48546/workflowhub.workflow.676.1 (URL)
https://open-science-cloud.ec.europa.eu/resources/software/50%7Cdoi_________::273b50fa5999dbd353c89c90e9d5d4bc (URL)
Software documentation: https://www.ga4gh.org/product/tool-registry-service-trs/ (URL)
https://github.com/galaxyproject/galaxy/pull/18820 (URL)
https://github.com/galaxyproject/galaxy/issues/18927 (URL)
https://github.com/galaxyproject/galaxy/pull/19215 (URL)
https://github.com/galaxyproject/galaxy/issues/18995 (URL)
https://github.com/galaxyproject/gxformat2/pull/106 (URL)
https://training.galaxyproject.org/training-material/news/2023/05/11/ro-crate.html (URL)
Event: https://gallantries.github.io/video-library/events/smorgasbord3/ (URL)
Event: https://training.galaxyproject.org/training-material/events/galaxy-academy-2024.html (URL)
Software: 10.5281/zenodo.8127634 (DOI)
Software: https://github.com/ResearchObject/ro-crate-inveniordm (URL)
Software: https://gitlab.com/solidipes/solidipes/ (URL)

Funding

European Commission
EuroScienceGateway - leveraging the European compute infrastructures for data-intensive research guided by FAIR principles 101057388
UK Research and Innovation
EuroScienceGateway: leveraging the European compute infrastructures for data-intensive research guided by FAIR principles 10038963

References

  • EOSC Federation Handbook – FULL DRAFT. Version of 2 December 2024