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

被引：2

作者：

Niehues, Anna ^{[1
,2
,9
]}

de Visser, Casper ^{[1
]}

Hagenbeek, Fiona A. ^{[3
,4
,10
]}

Kulkarni, Purva ^{[1
,2
,5
]}

Pool, Rene ^{[3
,4
]}

Karu, Naama ^{[6
]}

Kindt, Alida S. D. ^{[6
]}

Singh, Gurnoor ^{[1
]}

Vermeiren, Robert R. J. M. ^{[7
]}

Boomsma, Dorret, I ^{[3
,4
,8
]}

van Dongen, Jenny ^{[3
,4
,8
]}

't Hoen, Peter A. C. ^{[1
]}

van Gool, Alain J. ^{[2
]}

机构：

[1] Radboud Univ Nijmegen, Med Ctr, Dept Med BioSci, NL-6525 GA Nijmegen, Netherlands

[2] Radboud Univ Nijmegen, Med Ctr, Dept Lab Med, Translat Metab Lab, NL-6525 GA Nijmegen, Netherlands

[3] Vrije Univ Amsterdam, Dept Biol Psychol, NL-1081 BT Amsterdam, Netherlands

[4] Amsterdam Publ Hlth Res Inst, NL-1081 BT Amsterdam, Netherlands

[5] Radboud Univ Nijmegen, Med Ctr, Dept Human Genet, NL-6525 GA Nijmegen, Netherlands

[6] Leiden Univ, Metabol & Analyt Ctr, Leiden Acad Ctr Drug Res, NL-2333 AL Leiden, Netherlands

[7] Leiden Univ, Med Ctr, Dept Child & Adolescent Psychiat, LUMC Curium, NL-2342 AK Oegstgeest, Netherlands

[8] Amsterdam Reprod & Dev AR&D Res Inst, NL-1081 BT Amsterdam, Netherlands

[9] Leiden Univ, Med Ctr, Leiden, Netherlands

[10] TIMACS, Hobart, TAS, Australia

来源：

GIGASCIENCE | 2024年 / 13卷

关键词：

multi-omics; workflow; metadata; FAIR; RO-Crate; FDO;

D O I：

10.1093/gigascience/giad115

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：12