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RO-Crate Outreach and Publications

Table of contents

  1. Zenodo community
  2. Cite RO-Crate
  3. Recent publications, presentations, citations
    1. 2024
    2. 2023
    3. 2022
    4. 2021
    5. 2020
    6. 2019
    7. 2018
    8. Research Object publications
  4. Upcoming and recent events

Feel free to add to this page, either edit and raise pull request or raise issue using your GitHub account.

Zenodo community

Please submit your RO-Crate-related contributions (including RO-Crate deposits!) to the Zenodo ResearchObject community.

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

Recent publications, presentations, citations

2024

Dmitry Schigel, Kate Ingenloff, Sharif Islam, Tomas Martinovic, Claus Weiland (2024):
SYM06 Biodiversity Data Standards and FAIR in Prototyping Biodiversity Digital Twins.
Biodiversity Information Standards (SPNHC-TDWG) 2024, 2024-09-02/–06, Okinawa, Japan.
https://www.youtube.com/watch?v=2IJKRQF8H-4

Ove Johan Ragnar Gustafsson, Sean R. Wilkinson, Finn Bacall, Stian Soiland-Reyes, Simone Leo, Luca Pireddu, Stuart Owen, Nick Juty, José Mª Fernández, Tom Brown, Hervé Ménager, Björn Grüning, Salvador Capella-Gutierrez, Frederik Coppens, Carole Goble (2024):
WorkflowHub: a registry for computational workflows.
arXiv:2410.06941 [cs.DL]
https://doi.org/10.48550/arXiv.2410.06941

Sean Wilkinson, Meznah Aloqalaa, Khalid Belhajjame, Michael R. Crusoe, Bruno de Paula Kinoshita, Luiz Gadelha, Daniel Garijo, Ove Johan Ragnar Gustafsson, Nick Juty, Sehrish Kanwal, Farah Zaib Khan, Johannes Köster, Karsten Peters-von Gehlen, Line Pouchard, Randy K. Rannow, Stian Soiland-Reyes, Nicola Soranzo, Shoaib Sufi, Ziheng Sun, Baiba Vilne, Merridee A. Wouters, Denis Yuen, Carole Goble (2024):
Applying the FAIR Principles to Computational Workflows.
arXiv 2410.03490 [cs.DL]
https://doi.org/10.48550/arXiv.2410.03490

Rob Carrillo, Stian Soiland-Reyes, Esteban Gonzalez, Marie Josse, Marc Portier, Gael Lymer (2024):
Webinar: Unlocking the Power of RO-Crate for FAIR Research Data.
FAIR-EASE webinar
[video] [slides]

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 [RO-Crate]

José M. Fernández, Paula Iborra, Sébastien Moretti, Arun Isaac, Paul De Geest, Stian Soiland-Reyes (2024):
BioHackEU23: FAIR Workflow Execution with WfExS and Workflow Run Crate.
BioHackrXiv
https://doi.org/10.37044/osf.io/7f94w

Eli Chadwick, Stian Soiland-Reyes (2024):
RO-Crate: package your research outputs with their metadata.
Version 1: Research Software Engineering Conference (RSECon 2024), Newcastle, UK, 2024-09-03/–05.
https://doi.org/10.5281/zenodo.14007027
Version 2: ELIXIR-UK All Hands 2024, Cardiff, UK, 2024-11-19/–20. https://doi.org/10.5281/zenodo.14228958

Sebastian Beier, Daniel Arend, Cyril Pommier, Kristina Gruden, Patrick König, Stian Soiland-Reyes, Philippe Rocca-Serra, Peter Selby, Leyla Jael Castro, Klaus F. X. Mayer, Uwe Scholtz, Björn Usadel (2024):
Facilitating Interoperability in Agricultural Research through ELIXIR-supported Metadata Standards.
FAIRagro Community Summit, Berlin, Germany, 2024-06-17/–18.
https://doi.org/10.5281/zenodo.12527784

Peter Sefton, Alvin Sebastian, Moises Sacal Bonequi, Rosanna Smith (2024):
Crate-O - a drop-in linked data metadata editor for RO-Crate (and other) linked data in repositories and beyond.
Open Repositories Conference (OR 2024), Göteborg, Sweden, 2024-06-03/–06
https://doi.org/10.5281/zenodo.12542586 [slides] [notes]

Dieuwertje Bloemen, Özgür Karadeniz (2024):
Creating a Dataverse RO-Crate exporter with FAIR-IMPACT support.
Open Repositories Conference (OR 2024), Göteborg, Sweden, 2024-06-03/–06
https://doi.org/10.5281/zenodo.12548334

Peter Sefton, Stian Soiland-Reyes (2024):
Five ways RO-Crate data packages are important for repositories.
Open Repositories Conference (OR 2024), Göteborg, Sweden, 2024-06-03/–06
https://doi.org/10.5281/zenodo.12579432

Eleni Adamidi, Panagiotis Deligiannis, Aikaterina Mastoraki, Thanasis Vergoulis (2024):
Proposing a New RO-Crate Profile for Enhanced Reproducibility in Computational Experiments.
8th World Conference on Research Integrity (WCRI 2024), Athens, Greece, 2024-06-02/–05.
https://doi.org/10.5281/zenodo.11200097

Ben Foley, Peter Sefton, Simon Musgrave, Moises Sacal Bonequi (2024):
Access Control Framework for Language Collections.
Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024), Torino, Italia, 2024-05.
https://aclanthology.org/2024.lrec-main.10

Barbara Magagna, Erik Schultes, Anne Fouilloux, Gerhard Burger, Dirk Devriendt, Robin Bramley, Tobias Kuhn, Joao Moreira, Luiz Olavo Bonino Da Silva Santos, Luís Ferreira Pires (2024):
Ontological analysis of FAIR Supporting Resources.
FOAM 2024: FAIR principles for Ontologies and Metadata in Knowledge Management, Formal Ontology in Information Systems Conference 2024 (FOIS 2024), 15-19 July 2024, Enschede, Netherlands

Otso Ovaskainen, Patrik Lauha, Julian Lopez Gordillo, Ossi Nokelainen, Anis U. Rahman, Allan T. Souza, Jussi Talaskivi, Gleb Tikhonov, Aurélie Vancraeyenest, Ari Lehtiö (2024):
Prototype Biodiversity Digital Twin: Real-time bird monitoring with citizen-science data.
Research Ideas and Outcomes 10:e125523
https://doi.org/10.3897/rio.10.e125523

Simon Rolph, Chris Andrews, Dylan Carbone, Julian Lopez Lopez Gordillo, Tomáš Martinovič, Nick Oostervink, Dirk Pleiter, Kata Sara-aho, John Watkins, Christoph Wohner, Will Bolton, Jan Dick (2024):
Prototype Digital Twin: Recreation and biodiversity cultural ecosystem services. Research Ideas and Outcomes 10:e125450
https://doi.org/10.3897/rio.10.e125450

Desalegn Chala, Erik Kusch, Claus Weiland, Carrie Andrew, Jonas Grieb, Tuomas Rossi, Tomas Martinovic, Dag Endresen (2024):
Prototype biodiversity digital twin: crop wild relatives genetic resources for food security.
Research Ideas and Outcomes 10:e125192
https://doi.org/10.3897/rio.10.e125192

The Galaxy Community (2024):
The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update.
Nucleic Acids Research 52(W1)
https://doi.org/10.1093/nar/gkae410

Martin Starman, Fabian Kirchner, Martin Held, Catriona Eschke, Sayed-Ahmad Sahim, Regine Willumeit-Römer, Nicole Jung, Stefan Bräse (2024):
ELNdataBridge: Facilitating Data Exchange and Collaboration by Linking Electronic Lab Notebooks via API.
ChemRxiv
https://doi.org/10.26434/chemrxiv-2024-41gh4

Jonas Grieb, Claus Weiland, Alexander Wolodkin, Leyla Jael Castro, Stian Soiland-Reyes, Maya Beukes, Martin Jansen (2024):
Using Webby FDOs to Integrate AI Taxon Identification and Citizen Science.
Biodiversity Information Science and Standards 8:e134757
https://doi.org/10.3897/biss.8.134757

Claus Weiland, Jonas Grieb, Daniel Bauer, Desalegn Chala, Erik Kusch, Carrie Andrew, Dag Endresen (2024):
Dataspace Integration for Agrobiodiversity Digital Twins with RO-Crate.
Biodiversity Information Science and Standards 8:e134479
https://doi.org/10.3897/biss.8.134479 [video]

Tomáš Martinovič, Kata Sara-aho, Ondrej Salamon, Simon Rolph, Allan T Souza (2024):
Graphical User Interface for Biodiversity Digital Twins: Data Challenges.
Biodiversity Information Science and Standards 8:e135092
https://doi.org/10.3897/biss.8.135092 [video]

Sharif Islam, Julian Lopez Gordillo, Dag Endresen, Carrie Andrew (2024):
Bridging Data Standards and FAIR Principles in Biodiversity Digital Twinning: Prototyping, Challenges, Lessons Learned, and Future Plans.
Biodiversity Information Science and Standards 8:133089
https://doi.org/10.3897/biss.8.133089 [video]

George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen-Boulakia (2024):
BioFlow-Insight: facilitating reuse of Nextflow workflows with structure reconstruction and visualization.
NAR Genomics and Bioinformatics 6(3):lqae092
https://doi.org/10.1093/nargab/lqae092

Daniel J.B. Clarke, John Erol Evangelista, Zhuorui Xie, Giacomo B. Marino, Mano R. Maurya, Sumana Srinivasan, Keyang Yu, Varduhi Petrosyan, Matthew E. Roth, Miroslav Milinkov, Charles Hadley King, Jeet Kiran Vora, Jonathon Keeney, Christopher Nemarich, William Khan, Alexander Lachmann, Nasheath Ahmed, Sherry L. Jenkins, Alexandra Agris, Juncheng Pan, Srinivasan Ramachandran, Eoin Fahy, Emmanuel Esquivel, Aleksandar Mihajlovic, Bosko Jevtic, Vuk Milinovic, Sean Kim, Patrick McNeely, Tianyi Wang, Eric Wenger, Miguel A. Brown, Alexander Sickler, Yuankun Zhu, Philip D. Blood, Deanne M. Taylor, Adam C. Resnick, Raja Mazumder, Aleksandar Milosavljevic, Shankar Subramaniam, Avi Ma’ayan (2024):
Playbook Workflow Builder: Interactive Construction of Bioinformatics Workflows from a Network of Microservices.
bioRxiv
https://doi.org/10.1101/2024.06.08.598037

Timothy Clark, Jillian Mohan, Leah Schaffer, Kirsten Obernier, Sadnan Al Manir, Christopher P Churas, Amir Dailamy, Yesh Doctor, Antoine Forget, Jan Niklas Hansen, Mengzhou Hu, Joanna Lenkiewicz, Maxwell Adam Levinson, Charlotte Marquez, Sami Nourreddine, Justin Niestroy, Dexter Pratt, Gege Qian, Swathi Thaker, Jean-Christophe Bélisle-Pipon, Cynthia Brandt, Jake Chen, Ying Ding, Samah Fodeh, Nevan Krogan, Emma Lundberg, Prashant Mali, Pamela Payne-Foster, Sarah Ratcliffe, Vardit Ravitsky, Andrej Sali, Wade Schulz, Trey Ideker (2024):
Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines.
bioRxiv
https://doi.org/10.1101/2024.05.21.589311

Davide Fucci (2024):
FAIR enough: a Vision for Research Objects in Empirical Software Engineering Studies.
Proceedings of the 1st IEEE/ACM International Workshop on Methodological Issues with Empirical Studies in Software Engineering (WSESE ‘24)
2024 IEEE/ACM International Workshop on Methodological Issues with Empirical Studies in Software Engineering (WSESE)
https://doi.org/10.1145/3643664.3648201

Eric Hauser, Sebastian Gallenmüller, Georg Carle (2024):
RO-Crate for Testbeds: Automated Packaging of Experimental Results.
2024 IFIP Networking Conference (IFIP Networking)
https://doi.org/10.23919/IFIPNetworking62109.2024.10619057 [preprint] [dataset]

Robert D. Finn, Bachir Balech, Josephine Burgin, Physilia Chua, Erwan Corre, Cymon J. Cox, Claudio Donati, Vitor Martins dos Santos, Bruno Fosso, John Hancock, Katharina F. Heil, Naveed Ishaque, Varsha Kale, Benoit J. Kunath, Claudine Médigue, Evangelos Pafilis, Graziano Pesole, Lorna Richardson, Monica Santamaria, Tim Van Den Bossche, Juan Antonio Vizcaíno, Haris Zafeiropoulos, Nils P. Willassen, Eric Pelletier, Bérénice Batut (2024):
Establishing the ELIXIR Microbiome Community [version 1; peer review: 1 approved, 1 approved with reservations]
F1000Research 13(ELIXIR):50
https://doi.org/10.12688/f1000research.144515.1

George Marchment, Marie Schmit, Clémence Sebe, Frédéric Lemoine, Hervé Ménager, Sarah Cohen-Boulakia (2024):
Representing bioinformatics Nextflow workflows in RO-Crate: challenges and opportunities.
Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS), Leiden, Netherlands. 2024-02-26/–29. https://doi.org/10.5281/zenodo.10822156

Stian Soiland-Reyes, Carole Goble (2024):
WorkflowHub cloud integration in ELIXIR.
ELIXIR All Hands Meeting 2024 (AHM2024), Uppsala, Sweden, 2024-06-12
https://doi.org/10.5281/zenodo.11654943

Tim Beck, Stian Soiland-Reyes (2024):
Potential of ELIXIR cloud methods in EOSC-ENTRUST and HDR UK.
ELIXIR All Hands Meeting 2024 (AHM2024), Uppsala, Sweden, 2024-06-12
https://doi.org/10.5281/zenodo.11654733

Carole Goble (2024):
FAIR Digital Research Objects: Metadata Journeys.
University of Auckland: Centre for eResearch, Auckland, New Zealand, 2024-02-16
https://doi.org/10.5281/zenodo.10710142

Carole Goble (2024):
Handling Health Data: FAIR Research Objects for Trusted Research Environments.
eResearch New Zealand 2024: eResearch New Zealand 2024 (Keynote). Wellington , New Zealand, 2024-02-08
https://doi.org/10.5281/zenodo.10648472

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

Carole Goble, Stian Soiland-reyes, Herbert Van de Sompel, Mark Wilkinson (2024):
RO-Crate, Signposting and Bioschemas.
Lorentz Symposium: The Road to FAIR and Equitable Science. Leiden, The Netherlands, 2024-01-22/–26.
https://doi.org/10.5281/zenodo.10555382

Scott Edmunds (2024):
A Decade of FAIR – and what next? Q&A on FAIR workflows with the Netherlands X-omics Initiative.
GIGAblog
http://gigasciencejournal.com/blog/fair-workflows/

Anna Niehues, Casper de Visser, Fiona A Hagenbeek, Purva Kulkarni, René Pool, Naama Karu, Alida S D Kindt, Gurnoor Singh, Robert R J M Vermeiren, Dorret I Boomsma, Jenny van Dongen, Peter A C ’t Hoen, Alain J van Gool (2024):
A multi-omics data analysis workflow packaged as a FAIR Digital Object.
GigaScience 13:giad115
https://doi.org/10.1093/gigascience/giad115

Stian Soiland-Reyes, Leyla Jael Castro, Rohitha Ravinder, Claus Weiland, Jonas Grieb, Alexander Rogers, Christophe Blanchi, Herbert Van de Sompel (2024): BioHackEU23 report: Enabling FAIR Digital Objects with RO-Crate, Signposting and Bioschemas.
BioHackrXiv
https://doi.org/10.37044/osf.io/gmk2h

Sebastian Beier, Timo Mühlhaus, Cyril Pommier, Stuart Owen, Dominik Brilhaus, Heinrich Lukas Weil, Florian Wetzels, Gavin Chait, Daniel Arend, Manuel Feser, Gajendra Doniparthi, Jonathan Bauer, Sveinung Gundersen, Pável Vázquez (2024):
BioHackEU23 report: Enabling continuous RDM using Annotated Research Contexts with RO-Crate profiles for ISA.
BioHackrXiv
https://doi.org/10.37044/osf.io/7y2jh

Stian Soiland-Reyes, Peter Sefton, Simone Leo, Leyla Jael Castro, Claus Weiland, RO-Crate community (2024):
RO-Crate community update 2024.
(submitted)
https://research.manchester.ac.uk/en/publications/ro-crate-community-update-2024

Stian Soiland-Reyes, Stuart Wheater, Tom Giles, Carole Goble, Phil Quinlan (2024):
Five Safes RO-Crate: FAIR Digital Objects for Trusted Research Environments.
(submitted)
https://research.manchester.ac.uk/en/publications/five-safes-ro-crate-fair-digital-objects-for-trusted-research-env

Herbert Van de Sompel, Stian Soiland-Reyes (2024):
FAIR Signposting: Exposing the Topology of Digital Objects on the Web.
(submitted)
https://research.manchester.ac.uk/en/publications/fair-signposting-exposing-the-topology-of-digital-objects-on-the-

Johannes L. Hörmann, Luis Yanes, Ashwin Vazhappilly, Antoine Sanner, Hannes Holey, Lars Pastewka, Matthew Hartley, Tjelvar S. G. Olsson (2024):
dtool and dserver: A flexible ecosystem for findable data.
PLOS One 19(6):e0306100
https://doi.org/10.1371/journal.pone.0306100

Andrey Vukolov, Erik van Winkle, Vyacheslav Tykhonov, Roberto Pugliese (2024):
Decentralised Persistent Identification - an Emerging Technology for Sustainability Maintenance and Knowledge-driven Processes.
IFAC-PapersOnLine 58(8)
https://doi.org/10.1016/j.ifacol.2024.08.149

2023

Tom Brown, Nick Juty, Stian Soiland-Reyes, Felix Shaw, Rutger Vos (2023):
RO-Crates as a practical implementation of FAIR Digital Object to align biodiversity genomics work streams.
(submitted)
https://research.manchester.ac.uk/en/publications/ro-crates-as-a-practical-implementation-of-fair-digital-object-to

Rudolf Wittner, Matej Gallo, Simone Leo, Cecilia Mascia, Francesca Frexia, Markus Plass, Stian Soiland-Reyes, Heimo Müller, Jörg Geiger, Petr Holub (2023):
Linking provenance and its metadata in multi-organizational environments of life sciences.
(Submitted)
https://research.manchester.ac.uk/en/publications/linking-provenance-and-its-metadata-in-multi-organizational-envir

Ana Trisovic (2023):
Cluster Analysis of Open Research Data: A Case for Replication Metadata.
International Journal of Digital Curation 17(1)
https://doi.org/10.2218/ijdc.v17i1.833

Bogdan Nicolae, Tanzima Z. Islam, Robert Ross, Huub Van Dam, Kevin Assogba, Polina Shpilker, Mikhail Titov, Matteo Turilli, Tianle Wang, Ozgur O. Kilic, Shantenu Jha, Line C. Pouchard (2023):
Building the I (Interoperability) of FAIR for Performance Reproducibility of Large-Scale Composable Workflows in RECUP.
IEEE 19th International Conference on e-Science (e-Science)
https://doi.org/10.1109/e-science58273.2023.10254808 [preprint]

Augustus Ellerm, Mark Gahegan, Benjamin Adams (2023):
LivePublication: The Science Workflow Creates and Updates the Publication.
IEEE 19th International Conference on e-Science (e-Science) (preprint not available)
https://doi.org/10.1109/e-Science58273.2023.10254857

Raül Sirvent (2023):
Workflow Provenance registration with COMPSs.
Innovative HPC workflows for industry, 2023-10-25, Munich, Germany
https://doi.org/10.5281/zenodo.10046567

Maxwell Adam Levinson, Sadnan Al Manir, Christopher Churas, Leah Schaffer, Dexqter Pratt, Trey Ideker, Sarah Ratclliffe, Timothy Clark (2023):
Leveraging FAIR-compliant standards for data management and provenance towards building an interpretable genomic translator for human cellular architecture maps in the Bridge2AI program.
Zenodo
https://doi.org/10.5281/zenodo.8343021

Casper de Visser, Lennart F. Johansson, Purva Kulkarni, Hailiang Mei, Pieter Neerincx, K. Joeri van der Velde, Péter Horvatovich, Alain J. van Gool, Morris A. Swertz, Peter A. C. ‘t Hoen, Anna Niehues (2023):
Ten quick tips for building FAIR workflows.
PLOS Computational Biology 19(9): e1011369
https://doi.org/10.1371/journal.pcbi.1011369

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

Sharif Islam, Hanna Koivula, Dag Endresen, Erik Kusch, Dmitry Schigel, Wouter Addink (2023):
Data Standards and Interoperability Challenges for Biodiversity Digital Twin: A novel and transformative approach to biodiversity research and application.
Biodiversity Information Standards (TDWG 2023), Hobert, Australia, 2023-10-09/–13.
Biodiversity Information Science and Standards 7:e112373
https://doi.org/10.3897/biss.7.112373 [video]

Leyla Jael Castro, Stian Soiland-Reyes, Dietrich Rebholz-Schuhmann (2023):
RO-Crates Meets FAIR Digital Objects.
1st Conference on Research Data Infrastructure (CoRDI 2023), 2023-09-12/–14, Karlsruhe, Germany.
Proceedings of the Conference on Research Data Infrastructure 1
https://doi.org/10.52825/cordi.v1i.396 [poster]

Sebastian Schaaf, Anika Erxleben-Eggenhofer, Bjoern Gruening (2023):
Galaxy and RDM.
1st Conference on Research Data Infrastructure (CoRDI 2023), 2023-09-12/–14, Karlsruhe, Germany.
Proceedings of the Conference on Research Data Infrastructure 1
https://doi.org/10.52825/cordi.v1i.421

Peter Wittenburg, Dimitris Koureas (2023):
FDO to Structure the Domain of Knowledge.
1st Conference on Research Data Infrastructure (CoRDI 2023), 2023-09-12/–14, Karlsruhe, Germany.
Proceedings of the Conference on Research Data Infrastructure 1
https://doi.org/10.52825/CoRDI.v1i.374

Carole Goble, Finn Bacall, Stian Soiland-Reyes, Stuart Owen, Ignacio Eguinoa, Bert Droesbeke, Hervé Ménager, Laura Rodriguez-Navas, José M. Fernández, Björn Grüning, Simone Leo, Luca Pireddu, Michael Crusoe, Johan Gustafsson, Salvador Capella-Gutierrez, Frederik Coppens (2023):
EOSC-Life Workflow Collaboratory for the Life Sciences.
1st Conference on Research Data Infrastructure (CoRDI 2023), 2023-09-12/–14, Karlsruhe, Germany.
Proceedings of the Conference on Research Data Infrastructure 1
https://doi.org/10.52825/cordi.v1i.352 [slides]

Rudolf Wittner, Petr Holub, Cecilia Mascia, Francesca Frexia, Heimo Müller, Markus Plass, Clare Allocca, Fay Betsou, Tony Burdett, Ibon Cancio, Adriane Chapman, Martin Chapman, Mélanie Courtot, Vasa Curcin, Johann Eder, Mark Elliot, Katrina Exter, Carole Goble, Martin Golebiewski, Bron Kisler, Andreas Kremer, Simone Leo, Sheng Lin-Gibson, Anna Marsano, Marco Mattavelli, Josh Moore, Hiroki Nakae, Isabelle Perseil, Ayat Salman, James Sluka, Stian Soiland-Reyes, Caterina Strambio-De-Castillia, Michael Sussman, Jason R. Swedlow, Kurt Zatloukal, Jörg Geiger (2023):
Towards a common standard for data and specimen provenance in life sciences.
Learning Health Systems
https://doi.org/10.1002/lrh2.10365

Ove Johan Ragnar Gustafsson, Nicola Soranzo, Bjoern Gruening, Marius van den Beek, Finn Bacall, Carole Goble, Farah Zaib Khan, Gareth Price, Nigel Ward, Jeff Christiansen (2023):
Finding workflows in the Galaxy universe: integrating a global ecosystem using workflow registries.
2023 Galaxy Community Conference (GCC2023), 2023-07-10/–16, Brisbane, Australia.
https://doi.org/10.5281/zenodo.8157532

Anne Fouilloux, Elisa Trasatti, Federica Foglini, Alejandro Coca-Castro, Jean Iaquinta (2023):
FAIR Research Objects for realising Open Science with the EOSC project RELIANCE.
1st International Conference on FAIR Digital Objects (FDO 2022)
Research Ideas and Outcomes 9:e108765
https://doi.org/10.3897/rio.9.e108765

Alessandro Lotta, Gianmaria Silvello (2023):
How to Cite a Web Ranking and Make it FAIR.
Theory and Practice of Digital Libraries (TPDL 2023), 2023-09-26/–29, Zadar, Croatia.
https://doi.org/10.1007/978-3-031-43849-3_6 [preprint]

Peter Sefton, Stian Soiland-Reyes (2023):
Packaging data with detailed metadata using RO-Crate in FAIR open repositories.
Open Repositories 2023 (OR2023), 2023-06-12/–15, Stellenbosch University, South Africa.
https://doi.org/10.5281/zenodo.8091505

Peter Sefton, Moises Sacal Bonequi, Alvin Sebastian, Mark Raadgever (2023):
Introducing the Oni Repository Stack.
Open Repositories 2023 (OR2023), 2023-06-12/–15, Stellenbosch University, South Africa.
https://doi.org/10.5281/zenodo.8091519

Peter Sefton (2023): Towards a Generic Research Data Commons: A highly scalable standard-based repository framework for Language and other Humanities data.
Open Repositories 2023 (OR2023), 2023-06-12/–15, Stellenbosch University, South Africa.
https://www.ldaca.edu.au/posts/arkisto-stack-or-2023/
https://doi.org/10.5281/zenodo.8091653

Stian Soiland-Reyes, Leyla Jael Garcia (2023):
Overview of FAIR data publishing with Bioschemas & RO-Crate.
ELIXIR All Hands meeting 2023, workshop “Building lightweight FAIR data packages with Bioschemas and RO-Crate”, Dublin, Ireland, 2023-06-05/–08
https://doi.org/10.7490/f1000research.1119459.1

Stian Soiland-Reyes, Carole Goble (2023):
Building diverse collections using RO-Crate.
ELIXIR All Hands meeting 2023, mini-symposium “Biodiversity, Food Security and Pathogens”, Dublin, Ireland, 2023-06-05/–08
https://doi.org/10.7490/f1000research.1119466.1

Stian Soiland-Reyes, Simone Leo, Leyla Jael Castro, Peter Sefton, Carole Goble (2023):
Sharing data as machine-actionable objects using RO-Crate, Bioschemas and Signposting.
ELIXIR All Hands meeting 2023 (poster), Dublin, Ireland, 2023-06-05/–08
F1000Research 12(ELIXIR):572 (poster)
https://doi.org/10.7490/f1000research.1119431.1
https://doi.org/10.5281/zenodo.8004796

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
https://doi.org/10.5281/zenodo.8004793

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

Aikaterina Mastoraki, Panagiotis Deligiannis, Eleni Adamidi, Thanasis Vergoulis (2023):
Improving reproducibility of computational analyses performed on the ELIXIR-GR cloud.
ELIXIR All Hands meeting 2023 (poster), Dublin, Ireland, 2023-06-05/–08
F1000Research 12(ELIXIR):557 (poster) https://doi.org/10.7490/f1000research.1119423.1

Stian Soiland-Reyes, Carole Goble (2023):
Building diverse FDO Collections using RO-Crate.
FAIR Digital Object Forum, workshop “Defining FDO Collections”, 2023-04-14.
[slides] [video]

Line Pouchard (2023):
FAIR enabling reuse of data-intensive workflows and scientific reproducibility.
Keynote, The First Practically FAIR Workshop 2023 (PFAIR 2023)
14th ACM/SPEC International Conference on Performance Engineering (ICPE 23), Coimbra, Portugal, 2023-04-15.
https://doi.org/10.5281/zenodo.7893867 [slides] [abstract]

Juri Hößelbarth, Lennart Hofeditz, Richard Freitag (2023):
Sciebo RDS - reducing friction of FAIR data handling for researchers.
Cloud Storage Synchronization and Sharing (CS3 2023), Barcelona (Catalunya, Spain), 2023-03-06/–08
[abstract] [slides] [video]

Simone Leo (2023):
RO-Crate for workflow run provenance.
CWL Conference 2023, 2023-02-27
[video (YouTube)] [video (ConfTube)] [slides]

Mahnoor Zulfiqar (2023):
Running Reproducible Metabolomics Workflow with CWL.
CWL Conference 2023, 2023-02-27
[video (YouTube)] [video (ConfTube)]

Carole Goble, Stian Soiland-Reyes (2023):
Sharing research artefacts as FAIR Digital Objects using RO-Crate.
Brookhaven National Laboratory, 2023-01-23.
https://doi.org/10.5281/zenodo.7559338 [slides] [video]

Romain David, Audrey S. Richard, Claire Connellan, Katharina B. Lauer, Maria Luisa Chiusano, Carole Goble, Martin Houde, Isabel Kemmer, Antje Keppler, Philippe Lieutaud, Christian Ohmann, Maria Panagiotopoulou, Sara Raza Khan, Arina Rybina, Stian Soiland-Reyes, Charlotte Wit, Rudolf Wittner, Rafael Andrade Buono, Sarah Arnaud Marsh, Pauline Audergon, Dylan Bonfils, Jose-Maria Carazo, Remi Charrel, Frederik Coppens, Wolfgang Fecke, Claudia Filippone, Eva Garcia Alvarez, Sheraz Gul, Henning Hermjakob, Katja Herzog, Petr Holub, Lukasz Kozera, Allyson L. Lister, José López-Coronado, Bénédicte Madon, Kurt Majcen, William Martin, Wolfgang Müller, Elli Papadopoulou, Christine M.A. Prat, Paolo Romano, Susanna-Assunta Sansone, Gary Saunders, Niklas Blomberg, Jonathan Ewbank (2023):
Umbrella Data Management Plans to Integrate FAIR Data: Lessons From the ISIDORe and BY-COVID Consortia for Pandemic Preparedness.
Data Science Journal 22:52
https://doi.org/10.5334/dsj-2023-035

Molly A Bogue, Robyn L Ball, Vivek M Philip, David O Walton, Matthew H Dunn, Georgi Kolishovski, Anna Lamoureux, Matthew Gerring, Hongping Liang, Jake Emerson, Tim Stearns, Hao He, Gaurab Mukherjee, John Bluis, Sejal Desai, Beth Sundberg, Beena Kadakkuzha, Govindarajan Kunde-Ramamoorthy, Elissa J Chesler (2023):
Mouse Phenome Database: towards a more FAIR-compliant and TRUST-worthy data repository and tool suite for phenotypes and genotypes.
Nucleic Acids Research 51(D1)
https://doi.org/10.1093/nar/gkac1007

Andrea L. Berez-Kroeker, Shirley Gabber, Aliya Slayton (2023):
Recent Advances in Technologies for Resource Creation and Mobilization in Language Documentation.
Annual Review of Linguistics 9
https://doi.org/10.1146/annurev-linguistics-031220-120504

Tony Ross-Hellauer, Thomas Klebel, Alexandra Bannach-Brown, Serge P.J.M. Horbach, Hajira Jabeen, Natalia Manola, Teodor Metodiev, Haris Papageorgiou, Martin Reczko, Susanna-Assunta Sansone, Jesper Schneider, Joeri Tijdink, Thanasis Vergoulis (2023):
TIER2: enhancing Trust, Integrity and Efficiency in Research through next-level Reproducibility.
Research Ideas and Outcomes 8:e98457
https://doi.org/10.3897/rio.8.e98457

2022

Haris Zafeiropoulos, Martin Beracochea, Stelios Ninidakis, Katrina Exter, Antonis Potirakis, Gianluca De Moro, Lorna Richardson, Erwan Corre, João Machado, Evangelos Pafilis, Georgios Kotoulas, Ioulia Santi, Robert D Finn, Cymon J Cox, Christina Pavloudi (2022):
metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data.
GigaScience 12:giad078
https://doi.org/10.1093/gigascience/giad078

Sonia Natalie Mitchell, Andrew Lahiff, Nathan Cummings, Jonathan Hollocombe, Bram Boskamp, Ryan Field, Dennis Reddyhoff, Kristian Zarebski, Antony Wilson, Bruno Viola, Martin Burke, Blair Archibald, Paul Bessell, Richard Blackwell, Lisa A. Boden, Alys Brett, Sam Brett, Ruth Dundas, Jessica Enright, Alejandra N. Gonzalez-Beltran, Claire Harris, Ian Hinder, Christopher David Hughes, Martin Knight, Vino Mano, Ciaran McMonagle, Dominic Mellor, Sibylle Mohr, Glenn Marion, Louise Matthews, Iain J. McKendrick, Christopher Mark Pooley, Thibaud Porphyre, Aaron Reeves, Edward Townsend, Robert Turner, Jeremy Walton, Richard Reeve (2022):
FAIR data pipeline: provenance-driven data management for traceable scientific workflows.
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 380(2232)
https://doi.org/10.1098/rsta.2021.0300

Leyla Jael Castro, Zeyd Boukhers, Olga Giraldo, Adamantios Koumpis, Oya Beyan, Dietrich Rebholz-Schuhmann (2022):
NFDI4DataScience registry for reproducible Data Science and Artificial Intelligence.
Workshop On Open Citations And Open Scholarly Metadata 2022 (WOOC2022) 2022-10-05
https://doi.org/10.5281/zenodo.7129715 [video]

José M Fernández, Laura Rodríguez-Navas, Salvador Capella-Gutiérrez (2022):
Secured and annotated execution of workflows with WfExS-backend.
European Conference on Computational Biology (ECCB) 2022, The Global Alliance for Genomics And Health (GA4GH) 10th Plenary Meeting.
F1000Research 11:1318 (poster)
https://doi.org/10.7490/f1000research.1119198.1

Mauro Del Rio, Luca Lianas, Oskar Aspegren, Giovanni Busonera, Francesco Versaci, Renata Zelic, Per H. Vincent, Simone Leo, Andreas Pettersson, Olof Akre & Luca Pireddu (2022):
AI Support for Accelerating Histopathological Slide Examinations of Prostate Cancer in Clinical Studies.
International Conference on Image Analysis and Processing (ICIAP 2022): Image Analysis and Processing.
Lecture Notes in Computer Science (LNCS) 13373
https://doi.org/10.1007/978-3-031-13321-3_48

Daniel Arend, Sebastian Beier, laurent bouri Marco Brandizi, Donald Hobern, Erwan Le Floch, Timo Mühlhaus, Cyril Pommier, Stuart Owen, Philippe Rocca-Serra, Thomas Rosnet, Stian Soiland-Reyes (2022):
BioHackEU22 Project 22: Plant data exchange and standard interoperability.
BioHackrXiv
https://doi.org/10.37044/osf.io/c724r

Justin Clark-Casey, Stian Soiland-Reyes (2022):
Making EOSC Research Objects FAIR with RO-Crate: A common metadata overlay for EOSC repositories.
EOSC Symposium 2022
https://doi.org/10.5281/zenodo.7323480

Raül Sirvent, Javier Conejero, Francesc Lordan, Jorge Ejarque, Laura Rodríguez-Navas, José M. Fernández, Salvador Capella-Gutiérrez, Rosa M. Badia (2022):
Automatic, Efficient and Scalable Provenance Registration for FAIR HPC Workflows.
2022 IEEE/ACM Workshop on Workflows in Support of Large-Scale Science (WORKS)
https://doi.org/10.1109/WORKS56498.2022.00006 [preprint] [slides]

Carole Goble, Stian Soiland-Reyes (2022):
RO-Crate: packaging metadata love notes into FAIR Digital Objects. (Keynote)
Helmholtz Metadata Collaboration conference 2022, virtual, 2022-10-05/–06.
https://doi.org/10.5281/zenodo.7147703

Gerrit Günther, Jan Schweikert, Oonagh Mannix, Wolfgang Süß (2022):
Use Cases in HMC – from Generation to Reuse of Data.
Helmholtz Metadata Collaboration conference 2022, virtual, 2022-10-05/–06.
https://doi.org/10.5281/zenodo.7157694

Roman Gerlach (2022):
Datenverarbeitungsprozesse planen und dokumentieren - Eine Einführung in Research Objects und RO-Crate.
FDM Thuringen Coffee Lecture, 2022-11-30.
https://doi.org/10.5281/zenodo.7385632 [video] [slides]

Fidan Limani (2022):
FAIR Digital Objects and Linked Data.
Semantic Web in Libraries (SWIB22), 2022-11-28/-12-02
https://www.youtube.com/watch?v=BpUrQYIX2IA

Guido Aben, Juri Hößelbarth (2022):
Starting FDO in the Cradle – ROcrating Live Data.
1st International Conference on FAIR Digital Objects (FDO 2022) (poster)
Research Ideas and Outcomes 8: e95972
https://doi.org/10.3897/rio.8.e95972 [poster]

Stian Soiland-Reyes, Leyla Jael Castro, Daniel Garijo, Marc Portier, Carole Goble, Paul Groth (2022):
Updating Linked Data practices for FAIR Digital Object principles.
1st International Conference on FAIR Digital Objects (FDO 2022) (presentation).
Research Ideas and Outcomes 8:e94501
https://doi.org/10.3897/rio.8.e94501 [slides]

Stian Soiland-Reyes, Peter Sefton, Leyla Jael Castro, Frederik Coppens, Daniel Garijo, Simone Leo, Marc Portier, Paul Groth (2022):
Creating lightweight FAIR Digital Objects with RO-Crate.
1st International Conference on FAIR Digital Objects (FDO 2022) (poster)
Research Ideas and Outcomes 8: e93937
https://doi.org/10.3897/rio.8.e93937 [poster]

Oliver Woolland, Paul Brack, Stian Soiland-Reyes, Ben Scott, Laurence Livermore (2022):
Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows.
1st International Conference on FAIR Digital Objects (FDO 2022) (poster)
Research Ideas and Outcomes 8: e94349
https://doi.org/10.3897/rio.8.e94349 [poster]

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 [poster]

Olga Giraldo, Renato Alves, Dimitrios Bampalikis, Jose M Fernandez, Eva Martin del Pico, Fotis E Psomopoulos, Allegra Via, Leyla Jael Castro (2022):
A FAIRification roadmap for ELIXIR Software Management Plans.
1st International Conference on FAIR Digital Objects (FDO 2022) (poster)
Research Ideas and Outcomes 8: e94608
https://doi.org/10.3897/rio.8.e94608 [poster]

Anna Niehues, Casper de Visser, Fiona A. Hagenbeek, Naama Karu, Alida S. D. Kindt, Purva Kulkarni, René Pool, Dorret I. Boomsma, Jenny van Dongen, Alain J. van Gool, Peter A. C. ‘t Hoen (2022):
A Multi-omics Data Analysis Workflow Packaged as a FAIR Digital Object.
1st International Conference on FAIR Digital Objects (FDO 2022) (poster)
Research Ideas and Outcomes 8: e94042.
https://doi.org/10.3897/rio.8.e94042 [poster]

Hirotaka Suetake, Tsukasa Fukusato, Takeo Igarashi, Tazro Ohta (2022):
A workflow reproducibility scale for automatic validation of biological interpretation results bioRxiv 2022.10.11.511695 https://doi.org/10.1101/2022.10.11.511695

Renske de Wit (2022):
A Non-Intimidating Approach to Workflow Reproducibility in Bioinformatics: Adding Metadata to Research Objects through the Design and Evaluation of Use-Focused Extensions to CWLProv.
Master thesis, Vrije Universiteit Amsterdam / Zenodo.
https://doi.org/10.5281/zenodo.7113250 [video] [slides] https://doi.org/10.5281/zenodo.7113250 [video] [slides]

Tazro Ohta, Hirotaka Suetake (2022):
Verifying workflow reproducibility using RO-Crate.
Workflow Run Crate Meeting 2022-09-27
https://youtu.be/LFoX0wnTfuc

Esteban González, Alejandro Benítez & Daniel Garijo (2022):
FAIROs: Towards FAIR Assessment in Research Objects.
TPDL 2022: Linking Theory and Practice of Digital Libraries
https://doi.org/10.1007/978-3-031-16802-4_6 [preprint]

Nikola Tzochev, Andreas Pfeil (2022):
A Java Library for RO-Crate
RO-Crate community call, 2022-08-25.
[video] [slides] https://doi.org/10.5281/zenodo.7025336

Abigail Miller (2022):
BioConnect Data Packages: Use of RO-Crate, ISA model and Frictionless Data.
RO-Crate community call, 2022-07-28.
[video] [slides] [transcript] [example] https://doi.org/10.5281/zenodo.7116702

Carole Goble, Stian Soiland-Reyes (2022):
RO-Crate for Research Reproducibility & Data Management.
ELIXIR All Hands Meeting, Amsterdam, 2022-06-08
https://doi.org/10.5281/zenodo.6793758

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
(see also associated [RO-Crate])

Nick Thieberger, Amanda Harris (2022):
When Your Data is My Grandparents Singing. Digitisation and Access for Cultural Records, the Pacific and Regional Archive for Digital Sources in Endangered Cultures (PARADISEC).
Data Science Journal 21(1)
https://doi.org/10.5334/dsj-2022-009

River Tae Smith, Louisa Willoughby, Trevor Johnston (2022):
Integrating Auslan Resources into the Language Data Commons of Australia.
Proceedings of the LREC2022 10th Workshop on the Representation and Processing of Sign Languages: Multilingual Sign Language Resources
https://aclanthology.org/2022.signlang-1.28

Max Schröder, Susanne Staehlke, Paul Groth, J. Barbara Nebe, Sascha Spors & Frank Krüger (2022):
Structure-based knowledge acquisition from electronic lab notebooks for research data provenance documentation.
Journal of Biomedical Semantics 13:4 https://doi.org/10.1186/s13326-021-00257-x

Stian Soiland-Reyes, Genís Bayarri, Pau Andrio, Robin Long, Douglas Lowe, Ania Niewielska, Adam Hospital, Paul Groth (2022):
Making Canonical Workflow Building Blocks interoperable across workflow languages.
Data Intelligence 4(2)
https://doi.org/10.1162/dint_a_00135

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

Marc Portier, Cedric Decruw, Katrina Exter, Rory Meyer, Lennert Tyberghein, Laurian Van Maldeghem (2022):
Contemporary Data Management for Biodiversity Observation Networks leading to Linked Open Data Publishing through Distributed Techniques applying RO-Crate and GitHub Actions.
Biodiversity Information Standards (TDWG 2022), Sofia, Bulgaria.
Biodiversity Information Science and Standards 6:e94630
https://doi.org/10.3897/biss.6.94630 [video]

Amirpasha Mozaffari, Michael Langguth, Bing Gong, Jessica Ahring, Adrian Rojas Campos, Pascal Nieters, Otoniel José Campos Escobar, Martin Wittenbrink, Peter Baumann, Martin G. Schultz (2022):
HPC-oriented Canonical Workflows for Machine Learning Applications in Climate and Weather Prediction.
Data Intelligence 4(2)
https://doi.org/10.1162/dint_a_00131

Peter Wittenburg, Alex Hardisty, Yann Le Franc, Amirpasha Mozaffari, Limor Peer, Nikolay A. Skvortsov, Zhiming Zhao, Alessandro Spinuso (2022):
Canonical Workflows to Make Data FAIR.
Data Intelligence 4(2)
https://doi.org/10.1162/dint_a_00132

Beatriz Serrano-Solano, Anne Fouilloux, Ignacio Eguinoa, Matúš Kalaš, Björn Grüning, Frederik Coppens (2022):
Galaxy: A Decade of Realising CWFR Concepts.
Data Intelligence 4(2)
https://doi.org/10.1162/dint_a_00136

Thomas Jejkal, Sabrine Chelbi, Andreas Pfeil, Peter Wittenburg (2022):
Evaluation of Application Possibilities for Packaging Technologies in Canonical Workflows.
Data Intelligence 4(2)
https://doi.org/10.1162/dint_a_00137

Nikolay A. Skvortsov, Sergey A. Stupnikov (2022):
A Semantic Approach to Workflow Management and Reuse for Research Problem Solving.
Data Intelligence 4(2)
https://doi.org/10.1162/dint_a_00142

Andreas Pfeil, Thomas Jejkal, Danah Tonne, Germaine Götzelmann (2022): From a Dynamic Image Annotation Process within the Humanities to a Canonical Workflow.
Data Intelligence 4(2)
https://doi.org/10.1162/dint_a_00138

Marc Portier (2022):
Data Publishing with RO-Crate and git.
Open Belgium 2022, 2022-04-29.

Luiz Gadelha, Martin Hohmuth, Mahnoor Zulfiqar, David Schöne, Sheeba Samuel, Maria Sorokina, Christoph Steinbeck, Birgitta König-Ries (2022):
Toward a Framework for Integrative, FAIR, and Reproducible Management of Data on the Dynamic Balance of Microbial Communities.
arXiv 2207.06890 [cs.DB]
https://doi.org/10.48550/arXiv.2207.06890

2021

Jeremy Leipzig, Daniel Nüst, Charles Tapley Hoyt, Karthik Ram, Jane Greenberg (2021):
The role of metadata in reproducible computational research.
Patterns 2(1):100322 https://doi.org/10.1016/j.patter.2021.100322

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 (2021):
Perspectives on automated composition of workflows in the life sciences [version 1; peer review: 2 approved].
F1000Research 10:897 FAIR data pipeline: provenance-driven data management for traceable scientific workflows https://doi.org/10.12688/f1000research.54159.1

Thanasis Vergoulis, Konstantinos Zagganas, Loukas Kavouras, Martin Reczko, Stelios Sartzetakis, and Theodore Dalamagas (2021):
SCHeMa: Scheduling Scientific Containers on a Cluster of Heterogeneous Machines.
arXiv CoRR arXiv:2103.13138

Marco La Rosa (2021):
From endangered languages to the Science Mesh - petascale FAIR data repositories
CS3MESH4EOSC Blog

田辺 浩介, 松田 朝彦 (2021):
RO-Crateを用いた材料研究データのデータリポジトリへの登録
Kosuke Tanabe, Asahiko Matsuda (2021):
Ingesting materials research data into a data repository using RO-Crate.
情報知識学会誌 31(4) p. 497-502.
Journal of Japan Society of Information and Knowledge (Jōhō Chishiki Gakkaishi) 31(4) pp. 497-502.
第26回情報知識学フォーラム予稿
26th Information and Knowledge Study Forum, 2021-12-18, Kyoto University, Kyoto, Japan. https://doi.org/10.2964/jsik_2021_067

Myles Axton (2021):
A network database for the human biobank.
Advanced Genetics **2(2):e10049
https://doi.org/10.1002/ggn2.10049

Sonia Natalie Mitchell, Andrew Lahiff, Nathan Cummings, Jonathan Hollocombe, Bram Boskamp, Dennis Reddyhoff, Ryan Field, Kristian Zarebski, Antony Wilson, Martin Burke, Blair Archibald, Paul Bessell, Richard Blackwell, Lisa A Boden, Alys Brett, Sam Brett, Ruth Dundas, Jessica Enright, Alejandra N. Gonzalez-Beltran, Claire Harris, Ian Hinder, Christopher David Hughes, Martin Knight, Vino Mano, Ciaran McMonagle, Dominic Mellor, Sibylle Mohr, Glenn Marion, Louise Matthews, Iain J. McKendrick, Christopher Mark Pooley, Thibaud Porphyre, Aaron Reeves, Edward Townsend, Robert Turner, Jeremy Walton, Richard Reeve (2021):
FAIR Data Pipeline: provenance-driven data management for traceable scientific workflows.
arXiv CoRR arXiv:2110.07117 [q-bio.QM]

Vernon Gayle (2021):
A practical guide to developing research objects when undertaking reproducible statistically orientated social science research during COVID-19.
National Centre for Research Methods https://eprints.ncrm.ac.uk/id/eprint/4465

Daniel S. Katz, Fotis Psomopoulos, Leyla Jael Castro (2021):
Working Towards Understanding the Role of FAIR for Machine Learning.
2nd Workshop on Data and Research Objects Management for Linked Open Science [article] [slides]
https://doi.org/10.4126/FRL01-006429415

Mario Scrocca, Damiano Scandolari, Gloria Re Calegari, Ilaria Baroni, Irene Celino (2021):
The Survey Ontology: Packaging Survey Research as Research Objects.
2nd Workshop on Data and Research Objects Management for Linked Open Science [article] [slides] [ontology] [ro-crate] https://doi.org/10.4126/FRL01-006429412

Stian Soiland-Reyes (2021):
RO-Crate — A brief “crash course”.
ELIXIR Data-Interoperability Joint Platform F2F Hybrid Meeting, 2021-11-23.

Stian Soiland-Reyes (2021):
Reproducibility; Research Objects (RO-Crate) and Common Workflow Language (CWL).
WoSSS21:Workshop on Sustainable Software Sustainability, 2021-10-07. [video recording]

Stian Soiland-Reyes (2021):
Sharing FAIR Research Objects to improve reproducibility.
ZB-Med Seminar, 2021-07-15.
[video recording] https://doi.org/10.5281/zenodo.5105857

Carole Goble (2021):
FAIR Computational Workflows.
JOBIM 2021 (Journées Ouvertes en Biologie, Informatique et Mathématiques), 2021-07-08

Stian Soiland-Reyes (2021):
RO-Crate, workflows and FAIR Digital Objects.
FAIR Digital Object Forum, CWFR & FDO SEM meeting, 2021-07-02 [video recording], [slides] https://doi.org/10.5281/zenodo.5060283

Laura Rodríguez-Navas (2021):
WfExS: a software component to enable the use of RO-Crate in the EOSC-Life collaboratory.
FAIR Digital Object Forum, CWFR & FDO SEM meeting, 2021-07-02 [video recording], [slides]

Laura Rodríguez-Navas (2021):
WfExS: a software component to enable the use of RO-Crate in the EOSC-Life tools collaboratory.
EOSC Symposium 2021, 2021-06-17 [video recording] [slides

Krzysztof Kurowski, Oscar Corcho, Christine Choirat, Magnus Eriksson, Frederik Coppens, Mark van de Sanden, Milan Ojsteršek (2021):
EOSC Interoperability Framework.
KI-02-21-055-EN-N. Report from the EOSC Executive Board, Working Groups FAIR and Architecture. Publications Office of the EU.
https://doi.org/10.2777/620649

Oscar Corcho, Raúl Palma, Daniel Garijo (2021):
Metadata models and Research Objects for Earth Observation Data Cubes.
EOSC Symposium 2021, 2021-06-18 [video recording] [slides]

Carole Goble (2021):
FAIR Computational Workflows: the what, why how and who.
ICTESSH 2021 (International Conference on ICT enhanced Social Sciences and Humanities 2022), 2021-06-30

Stian Soiland-Reyes (2021):
Capturing “Just enough” Data, Software and Metadata with RO-Crate.
FAIR Festival 2021, FAIR Implementation Challenges & Solutions, 2021-06-21. https://doi.org/10.5281/zenodo.5007432

Peter Sefton, Marco La Rosa, Michael Lynch (2021):
Arkisto: a repository based platform for managing all kinds of research data.
Open Repositories 2021 (OR2021), 2021-06-10. [video recording] [slides]

Peter Sefton, Stian Soiland-Reyes (2021):
Research Object Crate (RO-Crate) Update
Open Repositories 2021 (OR2021), 2021-06-10. [video recording] [slides]

Stian Soiland-Reyes (2021):
Capturing Just Enough Data, Software and Metadata with RO-Crate.
Dataverse community meeting 2021, Software Metadata and Containerization, 2021-06-17. [video recording] https://doi.org/10.5281/zenodo.4973678

Carole Goble (2021): FAIR Workflows and Research Objects get a Workout. Dataverse community meeting 2021, keynote, 2021-06-15

Stian Soiland-Reyes (2021): Capturing workflow life cycle with RO-Crate. ELIXIR All Hands 2021, Workshop: Workflow Life Cycle, 2021-06-11 https://doi.org/10.5281/zenodo.4926088

Carole Goble, Stian Soiland-Reyes, Oscar Corcho (2021):
Packaging and describing Data Collections with RO-Crate.
2nd Workshop of the Data Citation Community of Practice for Earth, Space, and Environmental Sciences (and Related Sciences) (DataCitationCoP), AGU Data Citation Community of Practice, 2021-06-08.
https://doi.org/10.5281/zenodo.4916168

Stian Soiland-Reyes (2021):
Describing and packaging workflows using RO-Crate and BioCompute Objects.
Webinar for U.S. Food and Drug Administration (FDA), 2021-05-12. [Video recording] [slides]
https://doi.org/10.5281/zenodo.4633732

Carole Goble (2021): FAIRy stories: the FAIR Data principles in theory and in practice. NSF Convergence Accelerator Series Tracks A&B, 2021-05-19

Stian Soiland-Reyes (2021):
Data provenance with RO-Crate.
EOSC-Life retreat 2021, Provenance of tools and workflows; FAIRification of workflows, 2021-05-19.

Nick Thieberger, Marco La Rosa (2021):
Collection data management and repatriation of archival materials back to their source communities. 7th International Conference on Language Documentation & Conservation (ICLDC) [video recording]

Carole Goble, Stian Soiland-Reyes (2021): RO-Crate: A framework for packaging research products into FAIR Research Objects.
RDA IG Data Fabric: FAIR Digital Objects 2021-02-25. [Video recording] [slides]

Carole Goble (2021): The swings and roundabouts of a decade of fun and games with Research Objects.
17th Italian Research Conference on Digital Libraries (IRCDL 2021) Padova, Italy, 2021-02-18. [Video recording]

Marc Portier (2021): Open Science: the WorkZones. Open Belgium 2021, 2021-03-24. [video recording [slides]

Stian Soiland-Reyes, Carole Goble (2021):
RO-Crate: Describing and packaging FAIR Research Objects.
Scottish Covid-19 Response Consortium, 2021-03-18 https://doi.org/10.5281/zenodo.4633655

Stian Soiland-Reyes, Carole Goble (2021):
Publishing workflows in WorkflowHub.eu using CWL, and packaging with RO-Crate.
2021 Common Workflow Language Virtual Conference [video recording]

Mike Lynch (2021): Arkisto: an open-source, standards-based framework for digital preservation Linux.conf.au 2021, 2021-01-23. [video recording]

Marco La Rosa, Peter Sefton (2021): Describo and RO-Crate - the FAIR data research helpers.
Cloud Storage Services for Synchronization and Sharing (CS3)

2020

Peter Sefton (2020):
Progress report on using Schema.org, additional vocabularies and ad-hoc terms to describe and package research diverse research data collection using Research Object Crate v.1.1.
Australian Vocabulary Special Interest Group (AVSIG, 2020-12-01. [video recording]

Stephanie Walton, Laurence Livermore, Olaf Bánki, Robert W. N. Cubey, Robyn Drinkwater, Markus Englund, Carole Goble, Quentin Groom, Christopher Kermorvant, Isabel Rey, Celia M Santos, Ben Scott, Alan R. Williams, Zhengzhe Wu (2020):
Landscape Analysis for the Specimen Data Refinery.
Research Ideas and Outcomes 6:e57602 https://doi.org/10.3897/rio.6.e57602

Peter Sefton (2020):
Using schema.org in RO-crate.
Australian Vocabulary Special Interest Group (AVSIG, 2020-06-02. [video recording

Stian Soiland-Reyes (2020): Packaging workflows with RO-Crate FAIR Workflows workshop at International FAIR Convergence Symposium_, 2020-11-30. Video recording Slides

Michael L. Nelson, Herbert Van de Sompel (2020):
A 25 Year Retrospective on D-Lib Magazine.
arXiv:2008.11680 [cs.DL]

Tomasz Miksa, Maroua Jaoua, Ghaith Arfaoui (2020):
Research Object Crates and Machine-actionable Data Management Plans.
First Workshop on Data and Research Objects Management for Linked Open Science (DaMaLOS) at The 19th International Semantic Web Conference (ISWC 2020).
[article] [slides] [video] https://doi.org/10.4126/frl01-006423291

Carole Goble (2020): The swings and roundabouts of a decade of fun and games with Research Objects.
First Workshop on Data and Research Objects Management for Linked Open Science (DaMaLOS) at The 19th International Semantic Web Conference (ISWC 2020).
https://doi.org/10.4126/frl01-006423950

Peter Sefton, Nick Thieberger, Marco La Rosa, Michael Lynch (2020): An open, composable standards–based research eResearch platform: Arkisto.
eResearch Australasia 2020

Stian Soiland-Reyes, Ignacio Eguinoa (2020):
Packaging workflows with RO-Crate.
Workshop on FAIR Computational Workflows, 19th European Conference on Computational Biology (ECCB 2020).
https://doi.org/10.5281/zenodo.4011999

Simone Leo, Salvador Capella-Gutierrez (2020):
Testing workflows: Life Monitor and OpenEBench.
Workshop on FAIR Computational Workflows, 19th European Conference on Computational Biology (ECCB 2020).

Gavin Kennedy (2020):
Interoperable Research Workspaces and the Mesh.
CS3 2020 - Cloud Storage Synchronization and Sharing Services, 2020-01-27 / 2020-01-29, Copenhagen, Denmark.

2019

Peter Sefton, Eoghan Ó Carragáin, Carole Goble, Stian Soiland-Reyes (2019):
Introducing RO-Crate: research object data packaging.
eResearch Australasia 2019, 2019-10-21/2019-10-25, Brisbane, Australia. [slides] [abstract]

Nick Thieberger, Amanda Harris (2019):
Be Not Like the Wind: Access to Language and Music Records, Next Steps.
Proceedings of the 1st International Conference on Language Technologies for All (LT4All), pp. 101-103. Paris, December 2019. European Language Resources Association (ELRA).
https://lt4all.elra.info/proceedings/lt4all2019/pdf/2019.lt4all-1.26.pdf

Mike Lynch:
Publishing versioned datasets using OCFL and nginx.
eResearch Australasia 2019, 2019-10-21/2019-10-25, Brisbane, Australia.

Peter Sefton, Mike Lynch:
FAIR Simple Scalable Static Research Data Repository.
eResearch Australasia 2019, 2019-10-21/2019-10-25, Brisbane, Australia.

Eoghan Ó Carragáin, Carole Goble, Peter Sefton, Stian Soiland-Reyes (2019):
RO-Crate, a lightweight approach to Research Object data packaging..
RO-15 at Workshop on Research Objects (RO 2019), IEEE eScience 2019, 2019-09-24, San Diego, CA, USA.
https://doi.org/10.5281/zenodo.3337883 [slides]

Kyle Chard, Niall Gaffney, Matthew B. Jones, Kacper Kowalik, Bertram Ludäscher, Jarek Nabrzyski, Victoria Stodden, Ian Taylor, Thomas Thelen, Matthew J. Turk, Craig Willis (2019):
Application of BagIt-Serialized Research Object Bundles for Packaging and Re-execution of Computational Analyses.. at Workshop on Research Objects (RO 2019), IEEE eScience 2019, 2019-09-24, San Diego, CA, USA. 2019 IEEE 15th International Conference on e-Science (e-Science). https://doi.org/10.1109/eScience.2019.00068 [preprint]

Eoghan Ó Carragáin; Carole Goble; Peter Sefton; Stian Soiland-Reyes (2019): A lightweight approach to research object data packaging Bioinformatics Open Source Conference (BOSC2019), 2019-07-24/2019-07-25, Basel, Switzerland. https://doi.org/10.5281/zenodo.3250687

Eoghan Ó Carragáin, Carole Goble, Peter Sefton, Stian Soiland-Reyes (2019):
RO-Crate, a lightweight approach to Research Object data packaging [version 1; not peer reviewed].
Poster at Bioinformatics Open Source Conference (BOSC2019). F1000Research 2019, 8(ISCB Comm J):1197 (poster)
https://doi.org/10.7490/f1000research.1117130.1

Eoghan Ó Carragáin, Carole Goble, Peter Sefton, Stian Soiland-Reyes (2019):
RO-Crate, a lightweight approach to Research Object data packaging [version 1; not peer reviewed].
Talk at Bioinformatics Open Source Conference (BOSC2019). F1000Research 2019, 8(ISCB Comm J):1196 (slides)
https://doi.org/10.7490/f1000research.1117129.1 [slides]

Peter Sefton (2019):
DataCrate - a progress report on packaging research data for distribution via your repository.
Talk at Open Repositories (OR2019), Hamburg, 2019-06-11
https://doi.org/10.5281/zenodo.3554281

Peter Sefton (2019):
What’s in a package? Data packaging overview.
[slides] at Open Repositories (OR2019), Hamburg, 2019-06-10

Stian Soiland-Reyes; Carole Goble (2019):
Research Object.
Research Data Packaging Workshop at Open Repositories (OR2019), Hamburg, 2019-06-10.
https://slides.com/soilandreyes/2019-06-10-ro-or2019

Peter Sefton (2019):
Research Data Packaging
Research Data Packaging Workshop at Open Repositories (OR2019), Hamburg, 2019-06-10.
[slides]

2018

Peter Sefton, Michael Lynch, Liz Stokes, Gerard Devine (2018):
Launching DataCrate v1.0 a general purpose data packaging format for research data distribution and web-display.
Talk at eResearch Australasia 2018 https://eresearch.uts.edu.au/2018/11/01/launch_datacrate_1.htm

Peter Sefton, Gerard Devine, Christian Evenhuis, Michael Lynch, Sharyn Wise, Michael Lake, Duncan Loxton (2018):
DataCrate: a method of packaging, distributing, displaying and archiving Research Objects. Talk at Workshop on Research Objects (RO 2018), 29 Oct 2018, Amsterdam, Netherlands. https://doi.org/10.5281/zenodo.1445817 [abstract] [slides]

Research Object publications

See also publications about Research Objects which includes work pre-dating RO-Crate and about Research Objects in general.

Upcoming and recent events

To suggest an event, either edit and raise pull request or raise issue using your GitHub account.

Joint Hackathon of HD UK & ELIXIR-UK, Birmingham, UK, 2025-02-12/–14.

EOSC Winter School 2025, Sevilla, Spain, 2024-01-20/–25.

3rd Biohackathon Germany, Kassel, Germany, 2024-12-09/–13.

BioHackathon Europe, Barcelona, Spain, 2024-11-04/–08.

Webby FDOs with RO-Crates and FAIR Signposting, NFDI4DS hackathon, ZB Med, Cologne, Germany, 2024-11-20/–20.

Webinar: Unlocking the Power of RO-Crate for FAIR Research Data. 2024-08-29, FAIR-EASE Webinar.

Open Repositories 2024 (OR2024), Gothenburg, Sweden, 2024-06-03/–06.

2nd International Conference on FAIR Digital Objects (FDO 2024), 2024-03-21/–24, Berlin, Germany.

Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS), 2024-02-26/–29, Leiden, The Netherlands. Tutorial on RO-Crate, Bioschemas and Signposting.

EOSC Winter School, 2024-01-29 / -02-01, Thessaloniki, Greece.

International Conference on Knowledge Engineering and Ontology Development (KEOD 2023), 2023-11-13/–15, Rome, Italy. Co-located with IC3K/WEBIST.

The 22nd International Semantic Web Conference (ISWC 2023), 2023-11-06/–10, Athens, Greece.

BioHackathon Europe 2023, 2023-10-30/-11-03. Barcelona, Spain.

19th IEEE International Conference on eScience, 2023-10-09/–13, Limassol, Cyprus.

Open Science Fair, 2023-09-25/–27, Madrid, Spain. Papers due 2023-04-17.

Bioinformatics Open Source Conference (BOSC2023)+hackfest, 2023-07-24/–28, ISMB/ECCB 2023, Lyon, France.

Galaxy Community Conference 2023 (GCC2023), 2023-07-17/–23, Minneapolis, Minnesota, US.

Open Science Festival 2023, 2023-07-04/–05, Cologne, Germany. Workshop: Quo vadis Open Standards for Data Management? ORKG meets RO-Crates

Open Repositories 2023 (OR2023), 2023-06-12/–15, Stellenbosch University, South Africa. Presentation by Peter Sefton, Packaging data with detailed metadata using RO-Crate in FAIR open repositories.

3rd Workshop on Metadata and Research (objects) Management for Linked Open Science - DaMaLOS 2023, 2023-06-29, Co-located with ESWC, Hersonissos, Greece. Call for papers due 2023-03-31.

20th IEEE International Conference on Software Architecture (ICSA 2023), L’Aquila, Italy, 2023-03-13/–17.

ELIXIR All Hands 2023, 2023-06-05/–08, Dublin, Ireland + hybrid. Workshop: Building lightweight FAIR data packages with Bioschemas and RO-Crate

Galaxy Smörgåsbord 2023, 2023-05-22/–26, virtual. Training includes Module: FAIR data and provenance with RO-Crate and Galaxy.

2023 Common Workflow Language Conference (CWLCon 2023). 2023-02-27/-03-03, virtual.

1st BioHackathon Germany. 1st BioHackathon Germany, Lutherstadt Wittenberg - Leucorea, GE, 2022-12-12/–16 incl. project on DataPLANT, ELIXIR:GA4GH, FAIR Computational Workflows

ELIXIR Biohackathon 2022 2022-11-07/–11, Paris, France. Projects include Bioschemas, Galaxy w/RO-Crate+RDM, Linked Open Science, Schema.org datafeeds, Workflow Execution Service

International conference on FAIR Digital Objects, 2022-10-26/–28, Leiden, Netherlands incl. talk on Updating Linked Data practices and posters on RO-Crate, Galaxy Workflow Run Crate, Specimen Data Refinery workflows

3rd Workshop on Research Objects, Metadata and Management for Linked Open Science - DaMaLOS 2022 (cancelled)

Workshop on Data and Research Objects Management for Linked Open Science (DaMaLOS) 2021-10-24, 20th International Semantic Web Conference (ISWC 2021).

International Conference on Theory and Practice of Digital Libraries (TPDL), 2022-10-20/2022-10-23, topics incl. FAIR data and software, Research objects, Nanopublications, Linked Data, Digital Preservation.

eResearch Australasia 2022-10-17/–21, Brisbane, Australia

Helmholtz Metadata Collaboration Conference, 2022-10-05/–06, virtual.

ELIXIR Biohackathon Europe 2021 2021-11-08/2020-11-12, Hybrid. Projects proposed for RO-Crate and WorkflowHub.

ELIXIR Biohackathon Europe 2020 2020-11-09/2020-11-13, Virtual. Project on Galaxy export of RO-Crate.

Workshop on Data and Research Objects Management for Linked Open Science (DaMaLOS) 2020-11-02, 19th International Semantic Web Conference (ISWC 2020).

FAIR Computational Workflows workshop (2020-09-02) at the 19th European Conference on Computational Biology (ECCB 2020).

BCC2020 CollaborationFest (2020-07-22 / 2020-07-23) topic Exporting RO-Crate/BioCompute-Object packaged workflows from Galaxy made a first release of the RO-Crate Python library.

Virtual COVID-19 BioHackathon (2020-04-05 / 2020-04-11) topic WorkflowHub launched https://covid19.workflowhub.eu/ with RO-Crate support.

ELIXIR Biohackathon Europe 2019 2019-11-18/2019-11-22, Paris, France. Project on Research Object shape profiles.

eResearch Australasia 2019 2019-10-21/2019-10-25. Data Packaging birds of a feather session.

Workshop on Research Objects 2019 (RO2019). Workshop at IEEE eScience 2019, 2019-09-24, San Diego, CA, USA. http://www.researchobject.org/ro2019/

Research Data Packaging Workshop at Open Repositories (OR2019), 2019-06-10, Hamburg, Germany. [trip report] https://or2019.blogs.uni-hamburg.de/workshops/

Workshop on Research Objects 2018 (RO2018). Workshop at IEEE eScience 2018, 2018-10-29, Amsterdam, The Netherlands. http://www.researchobject.org/ro2018/

Approaches to Research Data Packaging BoF meeting at RDA 11th Plenary 2018-03-22, Berlin, Germany. https://rd-alliance.org/approaches-research-data-packaging-rda-11th-plenary-bof-meeting

The below RO-Crate logos can be used by for application, websites, posters, slides etc. for work that use, implement or support RO-Crate according to the specification, ideally linking to https://w3id.org/ro/crate. To ask permission for any other use, raise an issue.

Logo with RO-Crate in small text below, aspect ratio 1:1. [svg] [png] Logo without text, aspect ratio 1:1 [svg] [png] Logo next to RO-Crate in large text, aspect ratio 3.3:1 [svg] [png]