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. 2024 Jan 2:13:giad115.
doi: 10.1093/gigascience/giad115.

A multi-omics data analysis workflow packaged as a FAIR Digital Object

Anna Niehues  1   2 , Casper de Visser  1 , Fiona A Hagenbeek  3   4 , Purva Kulkarni  1   2   5 , René Pool  3   4 , Naama Karu  6 , Alida S D Kindt  6 , Gurnoor Singh  1 , Robert R J M Vermeiren  7 , Dorret I Boomsma  3   4   8 , Jenny van Dongen  3   4   8 , Peter A C 't Hoen  1 , Alain J van Gool  2
Affiliations

A multi-omics data analysis workflow packaged as a FAIR Digital Object

Anna Niehues et al. Gigascience. .

Abstract

Background: Applying good data management and FAIR (Findable, Accessible, Interoperable, and Reusable) data principles in research projects can help disentangle knowledge discovery, study result reproducibility, and data reuse in future studies. Based on the concepts of the original FAIR principles for research data, FAIR principles for research software were recently proposed. FAIR Digital Objects enable discovery and reuse of Research Objects, including computational workflows for both humans and machines. Practical examples can help promote the adoption of FAIR practices for computational workflows in the research community. We developed a multi-omics data analysis workflow implementing FAIR practices to share it as a FAIR Digital Object.

Findings: We conducted a case study investigating shared patterns between multi-omics data and childhood externalizing behavior. The analysis workflow was implemented as a modular pipeline in the workflow manager Nextflow, including containers with software dependencies. We adhered to software development practices like version control, documentation, and licensing. Finally, the workflow was described with rich semantic metadata, packaged as a Research Object Crate, and shared via WorkflowHub.

Conclusions: Along with the packaged multi-omics data analysis workflow, we share our experiences adopting various FAIR practices and creating a FAIR Digital Object. We hope our experiences can help other researchers who develop omics data analysis workflows to turn FAIR principles into practice.

Keywords: FAIR; FDO; RO-Crate; metadata; multi-omics; workflow.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1:
Figure 1:
Overview of analysis steps.
Figure 2:
Figure 2:
Schematic overview of packaged workflow.
See this image and copyright information in PMC

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