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

GigaScience, vol. 13

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.

Authors 13

1. Anna Niehues

   Radboud University Nijmegen · Radboud University Medical Center

   Affiliation as printed

   Department of Medical BioSciences, Radboud University Medical Center , 6525 GA Nijmegen ,

   Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center , 6525 GA Nijmegen ,

   Department of Medical BioSciences, Radboud University Medical Center , 6525 GA Nijmegen , The Netherlands

   Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center , 6525 GA Nijmegen , the Netherlands

2. Casper de Visser

   Radboud University Nijmegen · Radboud University Medical Center

   Affiliation as printed

   Department of Medical BioSciences, Radboud University Medical Center , 6525 GA Nijmegen ,

   Department of Medical BioSciences, Radboud University Medical Center , 6525 GA Nijmegen , The Netherlands

3. Fiona A. Hagenbeek

   Amsterdam Public Health · Vrije Universiteit Amsterdam

   Affiliation as printed

   Amsterdam Public Health Research Institute , 1081 BT Amsterdam ,

   Department of Biological Psychology, Vrije Universiteit Amsterdam , 1081 BT Amsterdam ,

   Amsterdam Public Health Research Institute , 1081 BT Amsterdam , The Netherlands

   Department of Biological Psychology, Vrije Universiteit Amsterdam , 1081 BT Amsterdam , The Netherlands

4. Purva Kulkarni

   Radboud University Nijmegen · Radboud University Medical Center

   Affiliation as printed

   Department of Human Genetics, Radboud University Medical Center , 6525 GA Nijmegen ,

   Department of Medical BioSciences, Radboud University Medical Center , 6525 GA Nijmegen ,

   Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center , 6525 GA Nijmegen ,

   Department of Human Genetics, Radboud University Medical Center , 6525 GA Nijmegen , The Netherlands

   Department of Medical BioSciences, Radboud University Medical Center , 6525 GA Nijmegen , The Netherlands

   Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center , 6525 GA Nijmegen , the Netherlands

5. René Pool

   Amsterdam Public Health · Vrije Universiteit Amsterdam

   Affiliation as printed

   Amsterdam Public Health Research Institute , 1081 BT Amsterdam ,

   Department of Biological Psychology, Vrije Universiteit Amsterdam , 1081 BT Amsterdam ,

   Amsterdam Public Health Research Institute , 1081 BT Amsterdam , The Netherlands

   Department of Biological Psychology, Vrije Universiteit Amsterdam , 1081 BT Amsterdam , The Netherlands

6. Naama Karu Aachen Metabolomics and Analytics Centre Leiden Academic Centre for Drug Research

   Leiden University

   Affiliation as printed

   Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University , 2333 AL Leiden ,

   Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University , 2333 AL Leiden , The Netherlands

7. Alida S. D. Kindt Aachen Metabolomics and Analytics Centre Leiden Academic Centre for Drug Research

   Leiden University

   Affiliation as printed

   Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University , 2333 AL Leiden ,

   Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University , 2333 AL Leiden , The Netherlands

8. Gurnoor Singh

   Radboud University Nijmegen · Radboud University Medical Center

   Affiliation as printed

   Department of Medical BioSciences, Radboud University Medical Center , 6525 GA Nijmegen ,

   Department of Medical BioSciences, Radboud University Medical Center , 6525 GA Nijmegen , The Netherlands

9. Robert R. J. M. Vermeiren Aachen Department of Child and Adolescent Psychiatry

   Leiden University Medical Center

   Affiliation as printed

   Department of Child and Adolescent Psychiatry, LUMC-Curium, Leiden University Medical Center , 2342 AK Oegstgeest ,

   Department of Child and Adolescent Psychiatry, LUMC-Curium, Leiden University Medical Center , 2342 AK Oegstgeest , The Netherlands

10. Dorret Irene Boomsma

    Amsterdam Public Health · Amsterdam Reproduction Development · Vrije Universiteit Amsterdam

    Affiliation as printed

    Amsterdam Public Health Research Institute , 1081 BT Amsterdam ,

    Amsterdam Reproduction & Development (AR&D) Research Institute , 1081 BT Amsterdam ,

    Department of Biological Psychology, Vrije Universiteit Amsterdam , 1081 BT Amsterdam ,

    Amsterdam Public Health Research Institute , 1081 BT Amsterdam , The Netherlands

    Amsterdam Reproduction & Development (AR&D) Research Institute , 1081 BT Amsterdam , The Netherlands

    Department of Biological Psychology, Vrije Universiteit Amsterdam , 1081 BT Amsterdam , The Netherlands

11. Jenny van Dongen

    Amsterdam Public Health · Amsterdam Reproduction Development · Vrije Universiteit Amsterdam

    Affiliation as printed

    Amsterdam Public Health Research Institute , 1081 BT Amsterdam ,

    Amsterdam Reproduction & Development (AR&D) Research Institute , 1081 BT Amsterdam ,

    Department of Biological Psychology, Vrije Universiteit Amsterdam , 1081 BT Amsterdam ,

    Amsterdam Public Health Research Institute , 1081 BT Amsterdam , The Netherlands

    Amsterdam Reproduction & Development (AR&D) Research Institute , 1081 BT Amsterdam , The Netherlands

    Department of Biological Psychology, Vrije Universiteit Amsterdam , 1081 BT Amsterdam , The Netherlands

12. Peter A.C. ’t Hoen corresponding

    Radboud University Nijmegen · Radboud University Medical Center

    Affiliation as printed

    Department of Medical BioSciences, Radboud University Medical Center , 6525 GA Nijmegen ,

    Department of Medical BioSciences, Radboud University Medical Center , 6525 GA Nijmegen , The Netherlands

13. Alain J. van Gool

    Radboud University Nijmegen · Radboud University Medical Center

    Affiliation as printed

    Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center , 6525 GA Nijmegen ,

    Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center , 6525 GA Nijmegen , the Netherlands