Development of RIKEN Plant Metabolome MetaDatabase

Area of Science:

• Plant science
• Metabolomics
• Bioinformatics

Background:

• Advancements in metabolomics enable rapid detection and quantification of cellular metabolites.
• Metabolomic data offer insights into plant metabolism, benefiting plant and human health.
• Existing public repositories have limitations in data sharing, reanalysis, reusability, and reproducibility.

Purpose of the Study:

• To address shortcomings in plant metabolomics data sharing.
• To develop a centralized database for plant metabolomic data and associated metadata.
• To facilitate data reanalysis, reusability, and reproducibility in plant metabolomics research.

Main Methods:

• Development of the RIKEN Plant Metabolome MetaDatabase (RIKEN PMM).
• Storage of mass spectrometry-based metabolite profiling data (e.g., gas chromatography-MS).
• Inclusion of detailed, structured experimental metadata using Linked Open Data principles (Resource Description Framework) and standardized vocabularies (Metabolomics Standards Initiative Ontology).

Main Results:

• RIKEN PMM provides a repository for plant metabolomic data, including raw data (netCDF), mass spectra (NIST MSP), and metabolite annotations.
• Metadata are structured and described as Linked Open Data for integration with other life science data.
• The database offers intuitive and interactive operations for data exploration.

Conclusions:

• RIKEN PMM enhances the sharing and usability of plant metabolomics data.
• The database supports biologists interested in metabolomic phenotypes and researchers exploring life sciences through plant metabolomics.
• Improved data accessibility and standardization are crucial for advancing plant science and related fields.