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

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@id	https://w3id.org/ro/doi/10.5281/zenodo.8113625
name [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach
@type	Dataset Thesis
description [?]	RO-Crate of PhD thesis submitted to the University of Amsterdam
datePublished [?]	2023-12-17
author [?]	Stian Soiland-Reyes
url [?]	https://s11.no/2023/phd/
publisher [?]	s11
identifier [?]	doi: 10.5281/zenodo.8113625
cite-as [?]	https://doi.org/10.5281/zenodo.8113625
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 Supplement 1: Ten Simple Rules for making a software tool workflow-ready Supplement 2: Ten Simple Rules for making a software tool workflow-ready 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: Recording provenance of workflow runs with RO-Crate Supplement 16: RO-Crate, a lightweight approach to Research Object data packaging
license [?]	Creative Commons Attribution 4.0 International License
about [?]	ro-crate-metadata.json

Go to: Stian Soiland-Reyes

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@id	https://orcid.org/0000-0001-9842-9718
name [?]	Stian Soiland-Reyes
@type	Person
affiliation [?]	Department of Computer Science, The University of Manchester, Manchester, UK Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands
author [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach Evaluating FAIR Digital Object and Linked Data as distributed object systems

Go to: s11

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publisher [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach

Go to: doi

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identifier [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach

Go to: Chapter 1: Introduction

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Go to: Chapter 2: Background

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@id	https://s11.no/2023/phd/background/
name [?]	Chapter 2: 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.
hasPart [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach

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
@type	Chapter
hasPart [?]	Evaluating FAIR Digital Object and Linked Data as distributed object systems https://s11.no/2022/phd/updating-ld-for-fdo/
hasPart [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach

Go to: Chapter 4: RO-Crate

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name [?]	Chapter 4: RO-Crate
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hasPart [?]	https://s11.no/2022/phd/ro-crate/ https://s11.no/2022/phd/fdo-with-ro-crate https://s11.no/2022/phd/ro-crate/formalizing
hasPart [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach

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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hasPart [?]	https://s11.no/2022/phd/canonical-workflow-building-blocks/ https://s11.no/2022/phd/specimen-data-refinery/ https://s11.no/2022/phd/incrementally-building-fdos/
hasPart [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach

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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Go to: Supplement 1: Ten Simple Rules for making a software tool workflow-ready

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@id	https://s11.no/2022/phd/10-simple-rules-for-workflow-tools/
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Go to: Supplement 2: Ten Simple Rules for making a software tool workflow-ready

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name [?]	Supplement 2: Ten Simple Rules for making a software tool workflow-ready
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Go to: Supplement 3: Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory

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@id	https://s11.no/2021/phd/workflow-collaboratory/
name [?]	Supplement 3: Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory
@type	ScholarlyArticle
hasPart [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach

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

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@id	https://s11.no/2022/phd/methods-included/
name [?]	Supplement 4: Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language
@type	ScholarlyArticle
hasPart [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach

Go to: Supplement 5: Semantic micro-contributions with decentralized nanopublication services

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@id	https://s11.no/2021/phd/nanopub/
name [?]	Supplement 5: Semantic micro-contributions with decentralized nanopublication services
@type	ScholarlyArticle
hasPart [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach

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

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@id	https://doi.org/10.12688/f1000research.54159.1
name [?]	Supplement 6: Perspectives on automated composition of workflows in the life sciences
@type	ScholarlyArticle
hasPart [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach

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

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@id	https://doi.org/10.1007/978-3-030-80960-7_16
name [?]	Supplement 7: ISO 23494: Biotechnology - Provenance Information Model for Biological Specimen and Data
@type	ScholarlyArticle
hasPart [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach

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

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@id	https://doi.org/10.1002/lrh2.10365
name [?]	Supplement 8: Towards a Common Standard for Data and Specimen Provenance in Life Sciences
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hasPart [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach

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

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@id	https://doi.org/10.1109/WORKS54523.2021.00016
name [?]	Supplement 9: A Community Roadmap for Scientific Workflows Research and Development
@type	ScholarlyArticle
hasPart [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach

Go to: Supplement 10: Unique, Persistent, Resolvable: Identifiers as the Foundation of FAIR

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@id	https://doi.org/10.1162/dint_a_00025
name [?]	Supplement 10: Unique, Persistent, Resolvable: Identifiers as the Foundation of FAIR
@type	ScholarlyArticle
hasPart [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach

Go to: Supplement 11: FAIR Computational Workflows

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@id	https://doi.org/10.1162/dint_a_00033
name [?]	Supplement 11: FAIR Computational Workflows
@type	ScholarlyArticle
hasPart [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach

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

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@id	https://doi.org/10.1093/gigascience/giz095
name [?]	Supplement 12: Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv
@type	ScholarlyArticle
hasPart [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach

Go to: Supplement 13: IEEE Standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication: IEEE Std 2791-2020

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@id	https://doi.org/10.1109/ieeestd.2020.9094416
name [?]	Supplement 13: IEEE Standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication: IEEE Std 2791-2020
@type	ScholarlyArticle
hasPart [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach

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

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@id	https://doi.org/10.37044/osf.io/c724r
name [?]	Supplement 14: BioHackEU22 Project 22: Plant data exchange and standard interoperability
@type	ScholarlyArticle
hasPart [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach

Go to: Supplement 15: Recording provenance of workflow runs with RO-Crate

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name [?]	Supplement 15: Recording provenance of workflow runs with RO-Crate
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Go to: Supplement 16: RO-Crate, a lightweight approach to Research Object data packaging

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name [?]	Supplement 16: RO-Crate, a lightweight approach to Research Object data packaging
@type	ScholarlyArticle
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Go to: Creative Commons Attribution 4.0 International License

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license [?]	FAIR Research Objects and Computational Workflows – A Linked Data Approach