Appendix B: Contributions

(This thesis chapter will show my contributions for each chapter and list all the other contributors)

My 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](../acknowledgements/) for acknowledgements beyond authorship covered below.

For all chapters except section 5.2, 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
Conceptualization, Data Curation, Formal Analysis, Funding acquisition, Investigation, Methodology, Software, Writing – original draft, Writing – review and editing
Carole Goble
Funding acquisition, Supervision, Writing – review and editing
Paul Groth
Conceptualization, Methodology, Supervision, Writing – original draft, Writing – review and editing

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 of the corresponding manuscript and have contributed to all aspects of the research. Subsection 4.1.4.1 was primarily authored by Simone Leo. Subsection 4.1.4.5 with figure 4.4 was authored by Mercè Crosas and Ana Trisovic and edited by me.

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.

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 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.

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

Supplement 2: Enhancing RDM in Galaxy by integrating RO-Crate

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

Supplement 4: Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language

Supplement 5: Semantic micro-contributions with decentralized nanopublication services

Supplement 6: Perspectives on automated composition of workflows in the life sciences

Supplement 7: ISO 23494: Biotechnology - Provenance Information Model for Biological Specimen and Data

Supplement 8: Towards a Common Standard for Data and Specimen Provenance in Life Sciences

Supplement 9: A Community Roadmap for Scientific Workflows Research and Development

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

Supplement 11: FAIR Computational Workflows (Main contribution pre-dates UvA affiliation)

Supplement 12: Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv (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

Supplement 14: BioHackEU22 Project 22: Plant data exchange and standard interoperability

I have been involved in All Aspects of the research for supplement 1, 2, 3, 4, 11, 12.

Contributor affiliations

Sanne Abeln https://orcid.org/0000-0002-2779-7174
Department of Computer Science, VU Amsterdam, Amsterdam, The Netherlands
Peter Amstutz https://orcid.org/0000-0003-3566-7705
Curii Corporation, Sommerville, MA, USA
Pau Andrio https://orcid.org/0000-0003-2116-3880
The Spanish National Bioinformatics Institute (INB), Barcelona Supercomputing Center (BSC), Barcelona, Spain
Haris Antonatos
SciFY, Athens, Greece
Finn Bacall https://orcid.org/0000-0002-0048-3300
Department of Computer Science, The University of Manchester, Manchester, UK
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
Salvador Capella-Gutierrez https://orcid.org/0000-0002-0309-604X
Life Sciences Department. Barcelona Supercomputing Center (BSC), Barcelona, Spain
Eoghan Ó Carragáin https://orcid.org/0000-0001-8131-2150
University College Cork, Ireland
John Chilton https://orcid.org/0000-0002-6794-0756⁴⁵,
Department of Biochemistry and Molecular Biology, Pennsylvania State University, PA, USA
Galaxy Project
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
Institute for Quantitative Social Science, Harvard University, Cambridge, MA, USA
Secretària de Govern Obert, Catalunya, Barcelona, ES
Peter Crowther https://orcid.org/0000-0002-2222-9418
Melandra Limited, Stockport, UK
Michael R. Crusoe https://orcid.org/0000-0002-2961-9670
Department of Computer Science, VU Amsterdam, Amsterdam, The Netherlands
Common Workflow Language project, Software Freedom Conservancy, Brooklyn, NY, USA
Mathias Dillen https://orcid.org/0000-0002-3973-1252
Meise Botanic Garden, Meise, Belgium
Bert Droesbeke https://orcid.org/0000-0003-0522-5674
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
VIB Center for Plant Systems Biology, Ghent, Belgium
Michel Dumontier https://orcid.org/0000-0003-4727-9435
Institute of Data Science, Maastricht University, Maastricht, The Netherlands
Ignacio Eguinoa https://orcid.org/0000-0002-6190-122X
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
Vincent Emonet https://orcid.org/0000-0002-1501-1082
Institute of Data Science, Maastricht University, Maastricht, The Netherlands
Philip Ewels https://orcid.org/0000-0003-4101-2502
Science for Life Laboratory (SciLifeLab), Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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
Bogdan Gavrilović https://orcid.org/0000-0003-1550-1716⁶
Seven Bridges, Charlestown, MA, USA
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
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
Alexandru Iosup https://orcid.org/0000-0001-8030-9398¹,
Department of Computer Science, VU Amsterdam, Amsterdam, The Netherlands
Leyla Jael Castro https://orcid.org/0000-0003-3986-0510
ZB MED Information Centre for Life Sciences, Cologne, Germany
Tobias Kuhn https://orcid.org/0000-0002-1267-0234
Department of Computer Science, VU Amsterdam, Amsterdam, The Netherlands
Simone Leo https://orcid.org/0000-0001-8271-5429
Center for Advanced Studies, Research, and Development in Sardinia (CRS4), Pula (CA), Italy
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
Douglas Lowe https://orcid.org/0000-0002-1248-3594
Research IT, The University of Manchester, Manchester, UK
Hervé Ménager https://orcid.org/0000-0002-7552-1009
Hub de Bioinformatique et Biostatistique, Département Biologie Computationnelle, Institut Pasteur, Paris, France
Ania Niewielska https://orcid.org/0000-0003-0989-3389
European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
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
Life Sciences Department. Barcelona Supercomputing Center (BSC), Barcelona, Spain
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
Faculty of Science, University Technology Sydney, Australia
The University of Queensland School of Languages and Cultures, The University of Queensland, Brisbane, Queensland, Australia
Beatriz Serrano-Solano https://orcid.org/0000-0002-5862-6132
Bioinformatics Group, Albert-Ludwigs-University Freiburg, Freiburg, Germany
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
Ruben Taelman https://orcid.org/0000-0001-5118-256X
IDLab, Ghent University, Ghent, Belgium
Nebojša Tijanić https://orcid.org/0000-0001-8316-4067
Seven Bridges, Charlestown, MA, USA
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
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 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.

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.

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

For section 5.1 and Supplement 4) I am a member of the Common Workflow Language leadership team.

For Supplement 13 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

Training material contributions

Dataset contributions

Presentation contributions

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]

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
(presentation 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]

Poster contributions