Updates in Rhea: SPARQLing biochemical reaction data

Area of Science:

• Biochemistry and Bioinformatics
• Systems Biology
• Metabolomics

Background:

• Rhea is an expert-curated database of biochemical reactions, essential for annotating biological knowledgebases like UniProtKB.
• Existing Rhea data is crucial for understanding metabolic pathways and their integration with other biological layers.

Purpose of the Study:

• To describe recent advancements in the Rhea database, focusing on new data representations and access methods.
• To demonstrate how these enhancements facilitate integrative analyses across different biological data types.

Main Methods:

• Developed a Resource Description Framework (RDF) representation for Rhea reaction data.
• Implemented a SPARQL endpoint for querying Rhea's curated biochemical reactions.
• Utilized federated queries combining Rhea's SPARQL endpoint with other resources like UniProt.

Main Results:

• New RDF representation and SPARQL endpoint provide enhanced programmatic access to Rhea data.
• Federated queries enable improved metabolite annotation by linking chemical entities to biological context.
• Demonstrated the utility of integrated data for linking metabolome, proteome, transcriptome, and genome.

Conclusions:

• Recent developments significantly improve Rhea's utility for linking chemical and biological information.
• Enhanced data accessibility supports a more holistic understanding of biological systems in health and disease.
• The new infrastructure promotes integrative research across multiple omics levels.