Implementation of FAIR Practices in Computational Metabolomics Workflows—A Case Study-Reference-Cited by-同舟云学术

Implementation of FAIR Practices in Computational Metabolomics Workflows—A Case Study

Published:2024-02-10 Issue:2 Volume:14 Page:118
ISSN:2218-1989
Container-title:Metabolites
language:en
Short-container-title:Metabolites

Author:

Zulfiqar Mahnoor¹²,Crusoe Michael R.³^ORCID,König-Ries Birgitta²⁴⁵^ORCID,Steinbeck Christoph¹²^ORCID,Peters Kristian⁵⁶⁷^ORCID,Gadelha Luiz¹²⁴⁸

Affiliation:

1. Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany

2. Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany

3. ELIXIR (The European Life-Sciences Infrastructure for Biological Information) Germany, Institute of Bio- and Geosciences (IBG-5)—Computational Metagenomics, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany

4. Institute for Informatics, Friedrich Schiller University Jena, 07743 Jena, Germany

5. iDiv—German Centre for Integrative Biodiversity Research, Halle-Jena-Leipzig, 04103 Leipzig, Germany

6. Geobotany and Botanical Gardens, Martin-Luther University of Halle-Wittenberg, 06108 Halle, Germany

7. Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany

8. German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany

Abstract

Scientific workflows facilitate the automation of data analysis tasks by integrating various software and tools executed in a particular order. To enable transparency and reusability in workflows, it is essential to implement the FAIR principles. Here, we describe our experiences implementing the FAIR principles for metabolomics workflows using the Metabolome Annotation Workflow (MAW) as a case study. MAW is specified using the Common Workflow Language (CWL), allowing for the subsequent execution of the workflow on different workflow engines. MAW is registered using a CWL description on WorkflowHub. During the submission process on WorkflowHub, a CWL description is used for packaging MAW using the Workflow RO-Crate profile, which includes metadata in Bioschemas. Researchers can use this narrative discussion as a guideline to commence using FAIR practices for their bioinformatics or cheminformatics workflows while incorporating necessary amendments specific to their research area.

Funder

Deutsche Forschungsgemeinschaft

Publisher

MDPI AG

Link

https://www.mdpi.com/2218-1989/14/2/118/pdf

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