Chapter 10: Contributions

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

My 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:

Except for chapter 8, I am the main author of the corresponding manuscripts and have contributed to all aspects of the research.

For Chapter 4 and 5 I co-chair the RO-Crate community together with Peter Sefton.

For Chapter 6 I am deputy work package leader in BioExcel, with Adam Hospital as work package leader.

For Chapter 7 I have contributed to all aspects of the research, including supervision, and wrote the original manuscript.

In Chapter 8 my main contributions are to section 2.2, 2.3.2, 4.1, 7.1, 7.2. In the corresponding research I have contributed to designing, technical advice, insight and supervision.

Chapter contributions

Chapter 2: Updating Linked Data practices for FAIR Digital Object principles:

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

Chapter 3: Evaluating FAIR Digital Object as a distributed object system

Stian Soiland-Reyes
Conceptualization, 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
Methodology, Supervision, Writing – original draft, Writing – review and editing

Chapter 4: Creating lightweight FAIR Digital Objects with RO-Crate

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

Chapter 5: Packaging research artefacts with RO-Crate

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

Chapter 6: Making Canonical Workflow Building Blocks interoperable across workflow languages

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

Chapter 7: Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows

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

Chapter 8: The Specimen Data Refinery: A canonical workflow framework and FAIR Digital Object approach to speeding up digital mobilisation of natural history collections

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.

Supplementary publications

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

TODO: Prune this list!

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

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

For Supplement 4 I am a member of the Common Workflow Language leadership team.

For Supplement 14 I am a member of the BioCompute Object technical steering committee and was a member of the IEEE 2791-2020 cworking group.

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/0000-0003-1550-1716
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