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
- 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 5: Semantic micro-contributions with decentralized nanopublication services
Supplement 6: Perspectives on automated composition of workflows in the life sciences
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)
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/0000-0003-1550-1716⁶
- 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