The MetaboLights repository: curation challenges in metabolomics

Area of Science:

• Metabolomics
• Bioinformatics
• Data Science

Background:

• MetaboLights is a leading open-access repository for metabolomic study data and metadata.
• The repository faces challenges in ensuring data quality and standardization with growing deposition numbers and data complexity.

Purpose of the Study:

• To describe the MetaboLights curation pipeline.
• To highlight the challenges encountered during data curation.
• To demonstrate the pipeline's application in quality control for complex metabolomic data.

Main Methods:

• Development and refinement of a data curation pipeline for metabolomic datasets.
• Implementation of quality control measures for raw experimental data and metadata.
• Standardization of diverse metabolomic data representations and workflows.

Main Results:

• A functional curation pipeline is established for MetaboLights.
• Key challenges in handling large-scale, diverse metabolomic data have been identified.
• The pipeline effectively supports the quality control of complex data depositions.

Conclusions:

• The MetaboLights curation pipeline is essential for maintaining data integrity and standardization.
• Continuous improvement of the pipeline is necessary to address evolving challenges in metabolomics data management.
• The repository plays a vital role in advancing metabolomic research through accessible, high-quality data.