Outreach for Workflow Run RO-Crate
Please help us expand this list by letting us know if you have published/used/presented Workflow Run RO-Crate!
Cite us
Cite Workflow Run RO-Crate
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 (2024) Recording provenance of workflow runs with RO-Crate. PLoS ONE 19(9): e0309210. https://doi.org/10.1371/journal.pone.0309210
Cite RO-Crate
Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, José M. Fernández, Daniel Garijo, Björn Grüning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole Goble (2022): Packaging research artefacts with RO-Crate. Data Science 5(2) https://doi.org/10.3233/DS-210053
Cite WRROC profiles
To cite a particular Workflow Run RO-Crate profile, use its https://w3id.org/ persistent identifier (Permalink) or a citation using the Zenodo DOI:
Workflow Run RO-Crate working group (2023):
Process Run Crate specification. Version 0.4
Zenodo
https://w3id.org/ro/wfrun/process/0.4
https://doi.org/10.5281/zenodo.10203944
Workflow Run RO-Crate working group (2023):
Workflow Run Crate specification. Version 0.4
Zenodo
https://w3id.org/ro/wfrun/workflow/0.4>
https://doi.org/10.5281/zenodo.10203971>
Workflow Run RO-Crate working group (2023):
Provenance Run Crate specification. Version 0.4
Zenodo
https://w3id.org/ro/wfrun/provenance/0.4
https://doi.org/10.5281/zenodo.10203978
Publications
2024
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 (2024) Recording provenance of workflow runs with RO-Crate. PLoS ONE 19(9): e0309210. https://doi.org/10.1371/journal.pone.0309210
Mahnoor Zulfiqar, Michael R. Crusoe, Birgitta König-Ries, Christoph Steinbeck,Kristian Peters Luiz Gadelha (2024): Implementation of FAIR Practices in Computational Metabolomics Workflows—A Case Study. Metabolites 14(2) https://doi.org/10.3390/metabo14020118
David Bouyssié, Pınar Altıner, Salvador Capella-Gutierrez, José M. Fernández, Yanick Paco Hagemeijer, Peter Horvatovich, Martin Hubálek, Fredrik Levander, Pierluigi Mauri, Magnus Palmblad, Wolfgang Raffelsberger, Laura Rodríguez-Navas, Dario Di Silvestre, Balázs Tibor Kunkli, Julian Uszkoreit, Yves Vandenbrouck, Juan Antonio Vizcaíno, Dirk Winkelhardt, Veit Schwämmle (2024):
WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows.
Journal of Proteome Research 23(1)
https://doi.org/10.1021/acs.jproteome.3c00636
2023
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 de Paula Kinoshita, Stian Soiland-Reyes (2023): Recording provenance of workflow runs with RO-Crate. arXiv:2312.07852 https://doi.org/10.48550/arXiv.2312.07852
Ignacio Eguinoa, Marek Suchánek, Vojtěch Knaisl, Jan Slifka, Paul De Geest, David López, Bjorn Gruning, Simone Leo, Stian Soiland-Reyes (2023):
BioHackEU22 Report: Enhancing Research Data Management in Galaxy and Data Stewardship Wizard by utilising RO-Crates.
BioHackrXiv
https://doi.org/10.37044/osf.io/24jst
José M. Fernández, Laura Rodriguez-Navas, Salvador Capella-Gutiérrez (2023):
WfExS-backend in the WRROC world?.
ELIXIR All Hands meeting 2023 (poster), Dublin, Ireland, 2023-06-05/–08
F1000Research 12(ELIXIR):616 (poster)
https://doi.org/10.7490/f1000research.1119457.1
Simone Leo, Laura Rodríguez-Navas, José M. Fernández, Paul De Geest, Luca Pireddu, Michael R. Crusoe, Daniel Garijo, Iacopo Colonnelli, Raül Sirvent, Stian Soiland-Reyes (2023):
Making workflow provenance FAIR across workflow systems with Workflow Run RO-Crate.
ELIXIR All Hands meeting 2023 (poster), Dublin, Ireland, 2023-06-05/–08
F100Research 12(ELIXIR):592 (poster)
https://doi.org/10.7490/f1000research.1119445.1
Simone Leo (2023):
RO-Crate for workflow run provenance.
CWL Conference 2023, 2023-02-27
[video (YouTube)]
[video (ConfTube)]
[slides]
Hirotaka Suetake, Tsukasa Fukusato, Takeo Igarashi, Tazro Ohta (2023):
A workflow reproducibility scale for automatic validation of biological interpretation results.
GigaScience 12:giad031
https://doi.org/10.1093/gigascience/giad031
2022
Paul De Geest, Frederik Coppens, Stian Soiland-Reyes, Ignacio Eguinoa, Simone Leo (2022):
Enhancing RDM in Galaxy by integrating RO-Crate.
1st International Conference on FAIR Digital Objects (FDO 2022) (poster)
Research Ideas and Outcomes 8:e95164
https://doi.org/10.3897/rio.8.e95164
Alex Hardisty, Paul Brack, Carole Goble, Laurence Livermore, Ben Scott, Quentin Groom, Stuart Owen, Stian Soiland-Reyes (2022): The Specimen Data Refinery: A canonical workflow framework and FAIR Digital Object approach to speeding up digital mobilisation of natural history collections. Data Intelligence 4(2) https://doi.org/10.1162/dint_a_00134
Florence Bietrix, José Maria Carazo, Salvador Capella-Gutierrez, Frederik Coppens, Maria Luisa Chiusano, Romain David, Jose Maria Fernandez, Maddalena Fratelli, Jean-Karim Heriche, Carole Goble, Philip Gribbon, Petr Holub, Robbie P. Joosten, Simone Leo, Stuart Owen, Helen Parkinson, Roland Pieruschka, Luca Pireddu, Luca Porcu, Michael Raess, Laura Rodriguez-Navas, Andreas Scherer, Stian Soiland-Reyes, Jing Tang, Gary Saunders (2022):
EOSC-Life Methodology framework to enhance reproducibility within EOSC-Life – revised version.
Zenodo, EOSC-Life project deliverable
https://doi.org/10.5281/zenodo.7137743