PhD

Beside working at The University of Manchester I am a PhD Candidate in the INDElab at the Informatics Institute of the University of Amsterdam.

My supervisor is Paul Groth and my topic is Using Research Objects to improve reproducibility. I started in July 2019.

As I am doing a thesis by publication, these pages gather the articles submitted/accepted/published so far that will become part of my PhD thesis. Note that some of these articles have been slightly reformatted to fit publication on the Web.

Chapter 1: Introduction TODO: Introduction to PhD
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 ..
Evaluating FAIR Digital Object and Linked Data as distributed object systems Preprint submitted to PeerJ CS
Updating Linked Data practices for FAIR Digital Object principles Talk abstract presented at FAIR Digital Objects conference (FDO2022)
Chapter 4: RO-Crate ..
Packaging research artefacts with RO-Crate Journal article published in Data Science
Creating lightweight FAIR Digital Objects with RO-Crate Poster abstract presented at FAIR Digital Objects conference (FDO2022)
Formalizing RO-Crate in First Order Logic Appendix from Journal article published in Data Science
Chapter 5: Computational Workflows ..
Making Canonical Workflow Building Blocks interoperable across workflow languages Journal article published in Data Intelligence
The Specimen Data Refinery: A canonical workflow framework and FAIR Digital Object approach to speeding up digital mobilisation of natural history collections Journal article published in Data Intelligence
Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows Poster abstract presented at FAIR Digital Objects conference (FDO2022)
Chapter 6: Conclusions TODO: Discussions and conclusions of PhD
References An aggregated list of references from the chapters of this PhD thesis.
Appendix A: Acknowledgements TODO: Acknowledgements of PhD
Appendix B: Contributions TODO: Contributions of PhD
Supplement 1: Ten Simple Rules for making a software tool workflow-ready Journal article published in PLOS Computational Biology
Supplement 2: Enhancing RDM in Galaxy by integrating RO-Crate Poster abstract presented at FAIR Digital Objects conference (FDO2022)
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 Journal article published in Communications of the ACM
Supplement 5: Semantic micro-contributions with decentralized nanopublication services Journal article published in PeerJ Computer Science
Supplement 7: ISO 23494: Biotechnology – Provenance Information Model for Biological Specimen and Data Poster abstract accepted for Provenance Week 2020
Supplement 15: Recording provenance of workflow runs with RO-Crate Working Manuscript, in preparation for PLOS One submission
Supplement 16: RO-Crate, a lightweight approach to Research Object data packaging Conference abstract presented at Workshop on Research Objects 2019 (RO2019)
Supplement 17: Federated causal inference based on real-world observational data sources: application to a SARS-CoV-2 vaccine effectiveness assessment Preprint submitted to BMC Medical Research Methodology
Supplement 18: Linking provenance and its metadata in multi-organizational environments of life sciences Preprint submitted to PeerJ CS
Supplement 19: Enhancing Research Data Management in Galaxy and Data Stewardship Wizard by utilising RO-Crates BioHackrXiv preprint from ELIXIR BioHackathon 2022