Appendix B: Contributions

Here I detail my contributions for each chapter of this thesis, and list all the other contributors and their affiliations.

Thesis contributions

Below are the author contributions to published articles that form part of this thesis. Contributions are classified primarily according to the Contributor Roles Taxonomy (CASRAI CrEDiT. See also Appendix A for acknowledgements beyond authorship covered below.

For all chapters except Section 5.2 and Section 5.4, I am the main author of the corresponding manuscripts and have contributed to all aspects of the research. See details below:

Contributions for Evaluating FAIR Digital Object as a distributed object system

Chapter 2 and section 3.1 were co-authored by:

Stian Soiland-Reyes
Conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article; contributed Conceptualization, Data Curation, Formal Analysis, Funding acquisition, Investigation, Methodology, Software, Writing – original draft, Writing – review and editing; and approved the final draft.
Carole Goble
conceived and designed the experiments, authored or reviewed drafts of the article; contributed Funding acquisition, Supervision, Writing – review and editing; and approved the final draft.
Paul Groth
conceived and designed the experiments, authored or reviewed drafts of the article; contributed Conceptualization, Methodology, Supervision, Writing – original draft, Writing – review and editing; and approved the final draft.

I am the main author of the corresponding manuscript and have contributed to all aspects of the research.

Contributions for Updating Linked Data practices for FAIR Digital Object principles

Section 3.2 was co-authored by:

Stian Soiland-Reyes
Conceptualization, Formal Analysis, Funding acquisition, Investigation, Software, Writing – original draft, Writing – review and editing
Leyla Jael Castro
Writing – original draft
Daniel Garijo
Conceptualization, Funding acquisition, Writing – review and editing
Marc Portier
Investigation, Writing – original draft, Writing – review and editing
Carole Goble:
Funding acquisition, Supervision
Paul Groth
Supervision

This work was presented as talk by Stian Soiland-Reyes at First International Conference on FAIR Digital Objects, Leiden, The Netherlands.

Contributions for Packaging research artefacts with RO-Crate

Section 4.1 was co-authored by:

Stian Soiland-Reyes
Conceptualization, Data curation, Formal Analysis, Funding acquisition, Investigation, Methodology, Project administration, Software, Visualization, Writing – original draft, Writing – review & editing
Peter Sefton
Conceptualization, Investigation, Methodology, Project administration, Resources, Software, Writing – review & editing
Mercè Crosas
Writing – review & editing
Leyla Jael Castro
Methodology, Writing – review & editing
Frederik Coppens
Writing – review & editing
José M. Fernández
Methodology, Software, Writing – review & editing
Daniel Garijo
Methodology, Writing – review & editing
Björn Grüning
Writing – review & editing
Marco La Rosa
Software, Methodology, Writing – review & editing
Simone Leo
Software, Methodology, Writing – review & editing
Eoghan Ó Carragáin
Investigation, Methodology, Project administration, Writing – review & editing
Marc Portier
Methodology, Writing – review & editing
Ana Trisovic
Software, Writing – review & editing
RO-Crate Community
Investigation, Software, Validation, Writing – review & editing
Paul Groth
Methodology, Supervision, Writing – original draft, Writing – review & editing
Carole Goble
Conceptualization, Funding acquisition, Methodology, Project administration, Supervision, Visualization, Writing – review & editing

I am the main author and editor of the corresponding manuscript and have contributed to all aspects of the research. Section 4.1.4.1 was primarily authored by Simone Leo. SubSection 4.1.4.4 was primarily authored by Leyla Jael Castro. Section 4.1.4.5 with figure 4.4 was authored by Mercè Crosas and Ana Trisovic and edited by me.

The co-authors would also like to acknowledge contributions from:

Finn Bacall
Software, Methodology
Herbert Van de Sompel
Writing – review & editing
Ignacio Eguinoa
Software, Methodology
Nick Juty
Writing – review & editing
Oscar Corcho
Writing – review & editing
Stuart Owen
Writing – review & editing
Laura Rodríguez-Navas
Software, Visualization, Writing – review & editing
Alan R. Williams
Writing – review & editing

Contributions for Creating lightweight FAIR Digital Objects with RO-Crate

Section 4.2 was co-authored by:

Stian Soiland-Reyes
Conceptualization, Funding acquisition, Project administration, Software, Writing – original draft, Writing – review & editing
Peter Sefton
Funding acquisition, Project administration, Software
Leyla Jael Castro
Writing – original draft, Writing – review & editing
Frederik Coppens
Funding acquisition, Supervision, Writing – review & editing
Daniel Garijo
Software, Writing – review and editing
Simone Leo
Conceptualization, Project administration, Software, Writing – original draft
Marc Portier
Writing – review & editing
Paul Groth
Supervision

I am the main author of the corresponding manuscript and have contributed to all aspects of the research.

Contributions for Formalizing RO-Crate in First Order Logic

Section 4.3 was published as an appendix in Packaging research artefacts with RO-Crate.

I am the sole author of the corresponding appendix and have contributed to all aspects of the research.

Contributions for Making Canonical Workflow Building Blocks interoperable across workflow languages

Section 5.1 was co-authored by:

Stian Soiland-Reyes
Conceptualization, Funding acquisition, Investigation, Methodology, Project administration, Supervision, Writing – original draft, Writing – review & editing
Genís Bayarri
Software, Software Documentation
Pau Andrio
Methodology, Software, Validation, Software Documentation
Robin Long
Software, Software Documentation
Douglas Lowe
Software, Software Documentation
Ania Niewielska
Methodology, Resources, Software
Adam Hospital
Methodology, Project administration, Resuorces, Software, Validation, Visualization, Writing – original draft, Writing – review & editing
Paul Groth
Methodology, Supervision, Writing – review & editing

I am the main author of the corresponding manuscript and have contributed to all aspects of the research.

Contributions for The Specimen Data Refinery

Section 5.2 was co-authored by:

Alex Hardisty
Conceptualization, Investigation, Supervision, Validation, Writing – original draft, Writing – review & editing, Approval.
Paul Brack
Investigation, Writing – original draft, Writing – review & editing.
Carole Goble
Conceptualization, Supervision, Writing – review & editing
Laurence Livermore
Conceptualization, Funding acquisition, Investigation, Writing – original draft, Writing – review & editing.
Ben Scott
Investigation, Writing – original draft, Writing – review & editing.
Quentin Groom
Funding acquisition, Investigation, Writing – original draft, Writing – review & editing.
Stuart Owen
Investigation, Writing – original draft, Writing – review & editing.
Stian Soiland-Reyes
Investigation, Writing – original draft, Writing – review & editing.

My main contributions are to section 5.2.2.2, 5.2.2.3, 5.2.4.1, 5.2.7. In the corresponding research I have contributed to designing, technical advice, insight and supervision.

Contributions for Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows

Section 5.3 was co-authored by:

Oliver Woolland
Data curation, Resources, Software, Visualization, Writing – review & editing
Paul Brack
Conceptualization, Software
Stian Soiland-Reyes
Investigation, Methodology, Supervision, Writing – original draft, Writing – review & editing
Ben Scott
Data curation, Software, Validation
Laurence Livermore
Conceptualization, Data curation, Funding acquisition, Methodology, Project administration, Resources, Writing – review & editing

I am the main author of the corresponding manuscript and have contributed to all aspects of the research.

This work was presented as a poster by Stian Soiland-Reyes at First International Conference on FAIR Digital Objects, Leiden, The Netherlands.

Contributions for Recording provenance of workflow runs with RO-Crate

Section 5.4 was co-authored by:

Simone Leo
Conceptualization, Data Curation, Investigation, Methodology, Resources, Software, Supervision, Validation, Visualization, Writing – Original Draft preparation, Writing – Review & Editing
Michael R. Crusoe
Conceptualization, Investigation, Software, Supervision
Laura Rodríguez-Navas
Software, Writing – Original Draft preparation
Raül Sirvent
Data Curation, Software, Writing – Original Draft preparation, Writing – Review & Editing
Alexander Kanitz
Writing – Original Draft preparation, Writing – Review & Editing
Paul De Geest
Data Curation, Software, Writing – Original Draft preparation
Rudolf Wittner
Data Curation, Writing – Original Draft preparation, Writing – Review & Editing
Luca Pireddu
Funding acquisition, Project Administration, Supervision, Writing – Review & Editing
Daniel Garijo
Conceptualization, Formal Analysis, Writing – Original Draft preparation, Writing – Review & Editing
José M. Fernández
Data Curation, Software, Writing – Original Draft preparation
Iacopo Colonnelli
Data Curation, Software, Writing – Original Draft preparation
Matej Gallo
Data Curation, Software
Tazro Ohta
Data Curation, Software, Writing – Original Draft preparation
Hirotaka Suetake
Data Curation, Software, Writing – Original Draft preparation
Salvador Capella-Gutierrez
Funding Acquisition, Resources, Supervision, Writing – Original Draft preparation
Renske de Wit
Software, Writing – Original Draft preparation, Writing – Review & Editing
Bruno de Paula Kinoshita
Data Curation, Software, Writing – Original Draft preparation, Writing – Review & Editing
Stian Soiland-Reyes
Conceptualization, Formal Analysis, Funding Acquisition, Investigation, Methodology, Resources, Software, Supervision, Visualization, Writing – Original Draft preparation, Writing – Review & Editing

I am the last author of this manuscript, and have contributed to all aspects of the research. My main contributions are in Section 5.4.1, Section 5.4.5, Section 5.4.5.3, Section 5.4.5.4.

Supplementary publications

I have also contributed as co-author to these articles during the PhD period, provided as supplements:

Supplement 1: Ten Simple Rules for making a software tool workflow-ready [Brack 2022a]

Supplement 2: Enhancing RDM in Galaxy by integrating RO-Crate [De Geest 2022]

Supplement 3: Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory Zenodo white paper [Goble 2021]

Supplement 4: Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language [Crusoe 2022]

Supplement 5: Semantic micro-contributions with decentralized nanopublication services [Kuhn 2021]

Supplement 6: Perspectives on automated composition of workflows in the life sciences [Lamprecht 2021]

Supplement 7: ISO 23494: Biotechnology - Provenance Information Model for Biological Specimen and Data [Wittner 2020]

Supplement 8: Towards a Common Standard for Data and Specimen Provenance in Life Sciences [Wittner 2023a]

Supplement 9: A Community Roadmap for Scientific Workflows Research and Development [Ferreira da Silva 2021]

Supplement 10: Unique, Persistent, Resolvable: Identifiers as the Foundation of FAIR [Juty 2020] (Main contribution pre-dates UvA affiliation)

Supplement 11: FAIR Computational Workflows [Goble 2020] (Main contribution pre-dates UvA affiliation)

Supplement 12: Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv [Khan 2019] (Main contribution pre-dates UvA affiliation)

Supplement 13: IEEE Standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication: IEEE Std 2791-2020 [IEEE 2791-2020]

Supplement 14: BioHackEU22 Project 22: Plant data exchange and standard interoperability [Arend 2022]

Supplement 15: RO-Crate, a lightweight approach to Research Object data packaging [Ó Carragáin 2019b] (Main contribution pre-dates UvA affiliation)

Supplement 16: Federated causal inference based on real-world observational data sources: application to a SARS-CoV-2 vaccine effectiveness assessment [Meurisse 2023]

Supplement 17: Linking provenance and its metadata in multi-organizational environments of life sciences [Wittner 2023b]

Supplement 18: BioHackEU22 Report: Enhancing Research Data Management in Galaxy and Data Stewardship Wizard by utilising RO-Crates [Eguinoa 2023]

Supplement 19: BioHackEU23 report: Enabling continuous RDM using Annotated Research Contexts with RO-Crate profiles for ISA [Beier 2024]

Supplement 20: BioHackEU23 report: Enabling FAIR Digital Objects with RO-Crate, Signposting and Bioschemas [[Soiland-Reyes 2024a]]

Supplement 21: Report on “FAIR Signposting” and its uptake by the community [Wilkinson 2024]

Supplement 22: Practical webby FDOs with RO-Crate and FAIR Signposting: Experiences and lessons learned [Soiland-Reyes 2024c]

I have been involved in All Aspects of the research for supplements 1, 2, 3, 4, 11, 12, 15, 18, 20, 22.

Contributor affiliations

Pau Andrio https://orcid.org/0000-0003-2116-3880
The Spanish National Bioinformatics Institute (INB), Barcelona
Supercomputing Center (BSC), Barcelona, Spain
Genís Bayarri https://orcid.org/0000-0003-0513-0288
Institute for Research in Biomedicine (IRB Barcelona), The Barcelona
Institute of Science and Technology (BIST), Barcelona, Spain
Paul Brack https://orcid.org/0000-0002-5432-2748
Department of Computer Science, The University of Manchester, Manchester, UK (former)
Eoghan Ó Carragáin https://orcid.org/0000-0001-8131-2150
University College Cork, Ireland
Iacopo Colonnelli https://orcid.org/0000-0001-9290-2017
Computer Science Dept., Università degli Studi di Torino, Torino, Italy
Frederik Coppens https://orcid.org/0000-0001-6565-5145
Department of Plant Biotechnology and Bioinformatics, Ghent University,Ghent, Belgium
VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
Mercè Crosas https://orcid.org/0000-0003-1304-1939
Barcelona Supercomputing Center (BSC), Barcelona, Spain
The Committee on Data of the International Science Council (ISC) (CODATA)
Secretària de Govern Obert, Catalunya, Barcelona, Spain (former)
Institute for Quantitative Social Science, Harvard University, Cambridge, MA, USA (former)
Michael R. Crusoe https://orcid.org/0000-0002-2961-9670
Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
DTL Projects, The Netherlands
Forschungszentrum Jülich, Jülich, Germany
Common Workflow Language project, Software Freedom Conservancy, Brooklyn, NY, USA
Matej Gallo https://orcid.org/0000-0002-1119-1792
Faculty of Informatics, Masaryk University, Brno, Czech Republic
Paul De Geest https://orcid.org/0000-0002-8940-4946
VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
Ignacio Eguinoa https://orcid.org/0000-0002-6190-122X
Showpad, Ghent, Belgium
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium (former)
VIB-UGent Center for Plant Systems Biology, Ghent, Belgium (former)
José Mª Fernández https://orcid.org/0000-0002-4806-5140
Barcelona Supercomputing Center, Barcelona, Spain
Daniel Garijo https://orcid.org/0000-0003-0454-7145
Ontology Engineering Group, Universidad Politécnica de Madrid, Madrid, Spain
Carole Goble https://orcid.org/0000-0003-1219-2137
Department of Computer Science, The University of Manchester, Manchester, UK
Quentin Groom https://orcid.org/0000-0002-0596-5376
Meise Botanic Garden, Meise, Belgium
Paul Groth https://orcid.org/0000-0003-0183-6910
Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands
Björn Grüning https://orcid.org/0000-0002-3079-6586
Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany
Alex Hardisty https://orcid.org/0000-0002-0767-4310
School of Computer Science and Informatics, Cardiff University, Cardiff, UK (former)
Adam Hospital https://orcid.org/0000-0002-8291-8071
Institute for Research in Biomedicine (IRB Barcelona), The Barcelona
Institute of Science and Technology (BIST), Barcelona, Spain
Leyla Jael Castro https://orcid.org/0000-0003-3986-0510
ZB MED Information Centre for Life Sciences, Cologne, Germany
Simone Leo https://orcid.org/0000-0001-8271-5429
Center for Advanced Studies, Research, and Development in Sardinia (CRS4), Pula (CA), Italy
Alexander Kanitz https://orcid.org/0000-0002-3468-0652
Biozentrum, University of Basel, Basel, Switzerland
Swiss Institute of Bioinformatics, Lausanne, Switzerland
Bruno de Paula Kinoshita https://orcid.org/0000-0001-8250-4074
Barcelona Supercomputing Center (BSC), Barcelona, Spain
Laurence Livermore https://orcid.org/0000-0002-7341-1842
The Natural History Museum, London, UK
Robin Long https://orcid.org/0000-0003-2249-645X
Lancaster University, Lancaster, UK
Research IT, The University of Manchester, Manchester, UK (former)
Douglas Lowe https://orcid.org/0000-0002-1248-3594
Research IT, The University of Manchester, Manchester, UK
Ania Niewielska https://orcid.org/0000-0003-0989-3389
European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
Tazro Ohta https://orcid.org/0000-0003-3777-5945
Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Shizuoka, Japan
Institute for Advanced Academic Research, Chiba University, Chiba, Japan
Stuart Owen https://orcid.org/0000-0003-2130-0865
Department of Computer Science, The University of Manchester, Manchester, UK
Luca Pireddu https://orcid.org/0000-0002-4663-5613
Center for Advanced Studies, Research and Development in Sardinia (CRS4), Pula, Italy
Marc Portier https://orcid.org/0000-0002-9648-6484
Vlaams Instituut voor de Zee (VLIZ), Oostende, Belgium
Laura Rodriguez-Navas https://orcid.org/0000-0003-4929-1219
Universitat Oberta de Catalunya (UOC), Barcelona, Spain
Life Sciences Department. Barcelona Supercomputing Center (BSC), Barcelona, Spain (former)
Marco La Rosa https://orcid.org/0000-0001-5383-6993
PARADISEC, Melbourne, Australia
Ben Scott https://orcid.org/0000-0002-5590-7174
The Natural History Museum, London, UK
Peter Sefton https://orcid.org/0000-0002-3545-944X
School of Languages and Cultures, The University of Queensland, Brisbane, Queensland, Australia
Faculty of Science, University Technology Sydney, Australia (former)
Raül Sirvent https://orcid.org/0000-0003-0606-2512
Barcelona Supercomputing Center (BSC), Barcelona, Spain
Stian Soiland-Reyes https://orcid.org/0000-0001-9842-9718
Department of Computer Science, The University of Manchester, Manchester, UK
Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands
Hirotaka Suetake https://orcid.org/0000-0003-2765-0049
Department of Creative Informatics, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo, Japan
Ana Trisovic https://orcid.org/0000-0003-1991-0533
Institute for Quantitative Social Science, Harvard University, Cambridge, MA, USA
Alan R Williams https://orcid.org/0000-0003-3156-2105
Department of Computer Science, The University of Manchester, Manchester, UK (former)
Renske de Wit https://orcid.org/0000-0003-0902-0086
Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
Rudolf Wittner https://orcid.org/0000-0002-0003-2024
Faculty of Informatics, Masaryk University, Brno, Czech Republic
Institute of Computer Science, Masaryk University, Brno, Czech Republic
BBMRI-ERIC, Neue Stiftingtalstrasse 2, 8010, Graz, Austria
Oliver Woolland https://orcid.org/0000-0002-4565-9760
Research IT, The University of Manchester, Manchester, UK

Community roles

For Chapter 2 and Section 5.1 I am a member of FAIR Digital Object Forum working groups FDO-CWFR, FDO-SEM, FDO-TSIG2 and have contributions to FDO specifications Anders 2023, Ivonne 2023, and to the FDO demonstrator paper Wittenburg 2022b. I am a member of the FDO 2024 programme committee and the Research Data Alliance (RDA)’s FAIR Digital Object Fabric Interest Group.

For Chapter 3 I co-chair the RO-Crate community (see appendix A) together with Peter Sefton. We are the main editors and authors of the RO-Crate specifications [RO-Crate 1.0,RO-Crate 1.1,RO-Crate 1.1.3,RO-Crate 1.2]

For section 5.1 I was deputy work package leader in BioExcel-2, with Adam Hospital as work package leader.

For Section 5.4 I am a member of the Workflow Run RO-Crate community as well as the Workflows Community Initiative working group FAIR Computational Workflow.

For Supplement 4 [Crusoe 2022] and Supplement 12 [Khan 2019] I am a member of the Common Workflow Language leadership team.

For Supplement 13 [IEEE 2791-2020] I am a member of the BioCompute Object technical steering committee and was a member of the IEEE 2791-2020 cworking group.

Software contributions

During this PhD I have contributed to several software applications and libraries:

Standard contributions

RO-Crate profiles

Training material and training events

Dataset contributions

Presentation contributions

Stian Soiland-Reyes, Herbert van de Sompel (2024):
Signposting and RO-Crate: experiences and lessons learned.
International FAIR Digital Objects Implementation Summit 2024, Berlin, Germany, 2024-03-20/–21.
https://doi.org/10.5281/zenodo.10847062

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

Stian Soiland-Reyes, Herbert Van De Sompel (2023):
Enabling FAIR Signposting and RO-Crate for content/metadata discovery and consumption.
FAIR-IMPACT Open Call for Support (Webinar), 2023-03-27
https://doi.org/10.5281/zenodo.7774582

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

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
(presented by Justin Clark-Casey)
https://doi.org/10.5281/zenodo.7323480

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 (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

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

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

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

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

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

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

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]

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

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

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]

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]

Workshop organizing

Carole Goble, Raul Palma, Stian Soiland-Reyes, Daniel Garijo (2019):
Workshop on Research Objects 2019 (RO2019). eScience 2019, San Diego, California, US, 2019-09-24.
http://www.researchobject.org/ro2019/

Ignacio Eguinoa, Carole Goble, Michael R Crusoe, Stian Soiland-Reyes, Salvador Capella-Gutierrez, Sarah Cohen-Boulakia, Björn Grüning, Alexander Peltzer, Simone Leo, Frederik Coppens, Mateusz Kuzak (2020):
{Workshop on FAIR Computational Workflows}.
19th European Conference on Computational Biology ({ECCB 2020}).

Carole Goble, Stian Soiland-Reyes, Salvador Capella-Gutierrez, José Mª Fernández, Frederik Coppens (2021):
Workflow Life Cycle workshop.
ELIXIR All Hands 2021 (virtual) 2021-06-11. https://workflowhub.eu/events/4

Stian Soiland-Reyes, Leyla Jael Castro, Núria Queralt Rosinach (2023):
Building lightweight FAIR data packages with Bioschemas and RO-Crate.
Workshop at ELIXIR All Hands meeting 2023 (AHM2023), Dublin, Ireland, 2023-06-06
https://elixir-events.eventscase.com/EN/elixirallhands2023/Agenda https://docs.google.com/document/d/1Vh9mUBWvNEsvC5YZRITtZxsyE6Wr18rJUgp9KweJFNg

Tom Giles, Stian Soiland-Reyes, Jonathan Couldridge (2023):
Approaching Five Safes with TRE-FX Trusted Workflow Run Crate.
TRE-FX Virtual Stakeholder Workshop, 2023-07-11
https://trefx.uk/2023-07-11-tre-stakeholder-workshop

Stian Soiland-Reyes, Leyla Jael Castro, Dietrich Rebholz-Schuhmann (2023):
Data exchange with RO-Crates and Knowledge Graphs.
Workshop at Open Science Festival 2023, Cologne, Germany, 2023-07-05.
https://www.zbmed.de/vernetzen/veranstaltungen/open-science-festival/data-exchange-with-ro-crates-and-knowledge-graphs https://tinyurl.com/osfcrate

Poster contributions

References

See chapter references.