2023s

Chapter 2: Background
In this chapter, we discuss the related work with respect to FAIR Digital Objects and Linked Data. We do so by looking through the lens of development of these technologies over time, including future directions.
Chapter 3: FAIR Digital Objects and Linked Data
To investigate RQ1 this chapter evaluates both Linked Data and FAIR Digital Object (FDO) as ways to realize the FAIR principles.
Evaluating FAIR Digital Object and Linked Data as distributed object systems
Journal article published in PeerJ Computer Science
Chapter 4: RO-Crate
This chapter introduces RO-Crate, a pragmatic method of packaging data alongside structured metadata that is inline with the FAIR principles. This has been implemented to investigate RQ2.
Chapter 5: Computational Workflows
In order to investigate RQ3, and considering important parts of the FAIR principles include Reuse and provenance, this chapter examines in closer details how FAIR Digital Objects and RO-Crate can be used with Computational Workflows.
Recording provenance of workflow runs with RO-Crate
Journal article published in PLOS One
Discussion
Discussion of findings from this thesis, relating them to emerging related work and future directions.
Conclusions
Conclusions for the research questions raised in introduction.
References
An aggregated list of references from the chapters of this PhD thesis.
About Stian Soiland-Reyes

Photo of Stian with beard

Overview

tl;dr: Senior Lecturer in FAIR, Open and Reproducible Digital Research. Research interests include Linked Data, FAIR digital objects, metadata, provenance, annotations, open source and software development best practices.

Biography

Stian Soiland-Reyes is a Senior Lecturer in FAIR, Open and Reproducible Digital Research and co-leader of the eScience Lab in the Department of Computer Science at The University of Manchester.
MSc projects ideas (COMP66090)

These are my MSc project ideas that I have supervised or am available to supervise for COMP66090 (login required) for post-graduate students in Computer Science or Data Science at The University of Manchester.
Enhancing Research Data Management in Galaxy and Data Stewardship Wizard by utilising RO-Crates
BioHackrXiv preprint from ELIXIR BioHackathon 2022

FAIR Research Objects and Computational Workflows – A Linked Data Approach

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Go to: Stian Soiland-Reyes

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Go to: FAIR Research Objects and Computational Workflows – A Linked Data Approach

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Go to: Chapter 1: Introduction

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Go to: Chapter 2: Background

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name [?] Chapter 2: Background
@type Chapter
description [?] In this chapter, we discuss the related work with respect to FAIR Digital Objects and Linked Data. We do so by looking through the lens of development of these technologies over time, including future directions.
author [?] Stian Soiland-Reyes
contributor [?] Paul Groth
isBasedOn [?] Section 3.1: Evaluating FAIR Digital Object and Linked Data as distributed object systems
about [?] RQ1
Items that reference this one
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Go to: Chapter 3: FAIR Digital Objects and Linked Data

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description [?] To investigate RQ1 this chapter evaluates both Linked Data and FAIR Digital Object (FDO) as ways to realize the FAIR principles. Section 3.1 compares the two approaches as global distributed object systems, and discusses what lessons can be learnt across the communities, taking into consideration the history covered by section 2. Section 3.2 proposes how the FDO principles can be achieved using Linked Data standards, which is explored further in the following chapters.
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Go to: Chapter 4: RO-Crate

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name [?] Chapter 4: RO-Crate
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description [?] This chapter introduces RO-Crate, a pragmatic method of packaging data alongside structured metadata that is inline with the FAIR principles. This has been implemented to investigate RQ2. Section 4.1 describes the RO-Crate purpose, community effort and tooling and demonstrates how RO-Crate has been applied. Section 4.2 shows how RO-Crate can be used to achieve the FDO principles covered in chapter 3. Section 4.3 contributes a formal definition of RO-Crate using first order logic.
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about [?] RQ2
Items that reference this one
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Go to: Chapter 5: Computational Workflows

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description [?] In order to investigate RQ3, and considering important parts of the FAIR principles are Reuse and provenance, this chapter examines in closer details how FAIR Digital Objects and RO-Crate can be used with Computational Workflows. Section 5.1 proposes that tools in computational workflows, when wrapped as interoperable building blocks, can be considered as FAIR Digital Objects, with a use case from biomolecular simulation. Sections 5.2 and 5.3 explore how FDOs and Research Objects can be constructed incrementally using computational workflows, with a use case from specimen digitization in natural history collections. Section 5.4 presents a profile of RO-Crate to capture workflow execution provenance, with incremental granularity levels and six workflow engine implementations. Use cases include machine learning-aided tumour detection and compatibility with PROV approaches.
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about [?] RQ3
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Go to: Chapter 6: Discussion and conclusions

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Go to: Appendix A: Acknowledgement

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Go to: Appendix B: Contributions

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Supplemental material

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Go to: Cover of thesis (SVG)

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Review of PhD thesis



Go to: PhD defence: FAIR Research Objects and Computational Workflows – A Linked Data Approach

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description [?] Stian Soiland-Reyes will defend the dissertation 'FAIR Research Objects and Computational Workflows – A Linked Data Approach'. Supervisors are Prof. P.T. Groth and Prof. C.A. Goble.
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organizer [?] University of Amsterdam
startTime [?] 2025-01-15T16:00:00+0100
endTime [?] 2025-01-15T17:30:00+0100
location [?] Agnietenkapel, University of Amsterdam
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Go to: s11

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Academic activities

Conferences and workshops

  • 2024: 2nd International FAIR Digital Objects Conference, programme committee
  • 2023: 15th International Conference on Knowledge Engineering and Ontology Development (KEOD 2023), programme committee
  • 2023: Semantic Web Applications and Tools for Healthcare and Life Sciences (SWAT4HCLS 2023), programme committee
  • 2022: 14th International Conference on Knowledge Engineering and Ontology Development (KEOD 2022), programme committee
  • 2022: 18th International Conference on Web Information Systems and Technologies (WEBIST 2022), programme committee
  • 2022: Bioinformatics Open Science Conference (BOSC 2022), programme committee
  • 2022: Semantic Web Applications and Tools in Healthcare and Life Sciences (SWAT4HCLS 2022), programme committee
  • 2021: 13th International SWAT4HCLS Conference, programme committee
  • 2019: Workshop on Research Objects 2019 (RO2019), IEEE eScience 2019, workshop organizer & chair
  • 2018: 7th International Provenance and Annotation Workshop (IPAW 2018), programme committee
  • 2018: The Web Conference 2018, programme committee, “Web Content Analysis, Semantics, and Knowledge”
  • 2018: 11th International Workshop on Linked Data on the Web (LDOW 2018), programme committee
  • 2018: Workshop on Research Objects (RO2018), IEEE eScience 2018, workshop organizer & chair
  • 2017: The 16th International Semantic Web Conference 2017 (ISWC 2017), Resource Track Program Committee (Best Reviewer award)
  • 2016: The 15th International Semantic Web Conference (ISWC 2016), Research Track Senior Program Committee
  • 2016: 6th Workshop on Linked Science 2016-Supporting Collaboration and Learning in e-Research Infrastructures (LISC2016)), Programme committee
  • 2012: European Semantic Web Conference (ESW 2012)

Peer review
Federated causal inference based on real-world observational data sources: application to a SARS-CoV-2 vaccine effectiveness assessment
Journal article in BMC Medical Research Methodology
Linking provenance and its metadata in multi-organizational environments of life sciences
Preprint submitted to PeerJ CS