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

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hasPart [?]	Chapter 1: Introduction Chapter 2: Background Chapter 3: FAIR Digital Objects and Linked Data Chapter 4: RO-Crate Chapter 5: Computational Workflows Chapter 6: Discussion and conclusions Appendix A: Acknowledgement Appendix B: Contributions Supplemental material FAIR Research Objects and Computational Workflows – A Linked Data Approach Cover of thesis (SVG)
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Go to: Stian Soiland-Reyes

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author [?]	Supplement 22: Practical webby FDOs with RO-Crate and FAIR Signposting: Experiences and lessons learned Packaging research artefacts with RO-Crate Section 5.1: Making Canonical Workflow Building Blocks interoperable across workflow languages Chapter 6: Discussion and conclusions Section 6.1: Discussion Section 6.2: Conclusion Section 4.2: Creating lightweight FAIR Digital Objects with RO-Crate Section 5.3: Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows Chapter 1: Introduction Section 4.1: Packaging research artefacts with RO-Crate Section 4.3: Formalizing RO-Crate in First Order Logic Section 5.2: The Specimen Data Refinery: A canonical workflow framework and FAIR Digital Object approach to speeding up digital mobilisation of natural history collections Section 3.2: Updating Linked Data practices for FAIR Digital Object principles Chapter 2: Background Section 3.1: Evaluating FAIR Digital Object and Linked Data as distributed object systems Section 5.4: Recording provenance of workflow runs with RO-Crate FAIR Research Objects and Computational Workflows – A Linked Data Approach FAIR Research Objects and Computational Workflows – A Linked Data Approach Cover of thesis (SVG)
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Go to: FAIR Research Objects and Computational Workflows – A Linked Data Approach

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author [?]	Stian Soiland-Reyes
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identifier [?]	doi: 10.5281/zenodo.8113625 Handle: 11245.1/d7fcc474-fcd1-4f2e-b5c0-1fd53a88f11d ISBN: 9789493391789
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Go to: University of Amsterdam

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affiliation [?]	Stian Soiland-Reyes prof. dr. ir. C.T.A.M. de Laat dr. Z. Zhao dr. V.O. Degeler
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Go to: Chapter 1: Introduction

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hasPart [?]	RQ1 RQ2 RQ3
hasPart [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach

Go to: Chapter 2: Background

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@id	https://s11.no/2023/phd/background/
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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
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Go to: Chapter 3: FAIR Digital Objects and Linked Data

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@id	https://s11.no/2023/phd/fdo-and-linked-data/
name [?]	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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about [?]	RQ1
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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.
hasPart [?]	Section 4.1: Packaging research artefacts with RO-Crate Section 4.2: Creating lightweight FAIR Digital Objects with RO-Crate Section 4.3: Formalizing RO-Crate in First Order Logic
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Go to: Chapter 5: Computational Workflows

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@id	https://s11.no/2023/phd/workflows/
name [?]	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.
hasPart [?]	Section 5.1: Making Canonical Workflow Building Blocks interoperable across workflow languages Section 5.2: The Specimen Data Refinery: A canonical workflow framework and FAIR Digital Object approach to speeding up digital mobilisation of natural history collections Section 5.3: Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows Section 5.4: Recording provenance of workflow runs with RO-Crate
about [?]	RQ3
hasPart [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach

Go to: Chapter 6: Discussion and conclusions

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author [?]	Stian Soiland-Reyes
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hasPart [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach

Go to: Appendix A: Acknowledgement

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Go to: Appendix B: Contributions

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Supplemental material

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hasPart [?]	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 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 Supplement 11: FAIR Computational Workflows Supplement 12: Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv 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 Supplement 15: RO-Crate, a lightweight approach to Research Object data packaging Supplement 16: Federated causal inference based on real-world observational data sources: application to a SARS-CoV-2 vaccine effectiveness assessment Supplement 17: Linking provenance and its metadata in multi-organizational environments of life sciences Supplement 18: BioHackEU22 Report: Enhancing Research Data Management in Galaxy and Data Stewardship Wizard by utilising RO-Crates Supplement 19: BioHackEU23 report: Enabling continuous RDM using Annotated Research Contexts with RO-Crate profiles for ISA Supplement 20: BioHackEU23 report: Enabling FAIR Digital Objects with RO-Crate, Signposting and Bioschemas Supplement 21: Report on "FAIR Signposting" and its uptake by the community Supplement 22: Practical webby FDOs with RO-Crate and FAIR Signposting: Experiences and lessons learned
hasPart [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach

Go to: Cover of thesis (SVG)

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Review of PhD thesis

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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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about [?]	#laymanspeak Defence of PhD thesis
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Go to: doi

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Go to: Creative Commons Attribution 4.0 International License

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Go to: s11

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