RaMP Metabolite Triples (subset)

2,028,838 RDF triples form a prototype graph dataset derived from RaMP content for exploring metabolite-centered biology. It includes a subset of 100 metabolites connected to 1,307 proteins, 6,032 reactions, 59,361 pathways, 968 reaction classes, and 93 metabolite classes. The dataset was created by Keith Kelleher and last updated on 2026-04-29.

Use Cases

• Testing SPARQL query performance on a linked-data structure based on the described metabolite-protein-reaction network.
• Prototyping graph-based exploration tools for metabolite-centered biology using the provided relationships.
• Evaluating external data sharing and integration methods for a focused set of 100 metabolites and their connected entities.

Strengths

• Contains 2,028,838 RDF triples, providing a substantial graph structure for evaluation.
• Explicitly scoped prototype includes 100 metabolites and their connections to thousands of proteins, reactions, and pathways.
• Released under a permissive CC-BY-4.0 license, facilitating reuse and sharing.

Limitations

• Description metadata is limited; actual data quality and structure require manual inspection after download.
• Column-level documentation is absent; field semantics must be inferred from the RDF structure after download.
• The prototype is intentionally scoped and does not include HMDB ontology content or RaMP chemical property fields for metabolites.

Provenance

Source

Derived from RaMP (Relational Database of Metabolomic Pathways) content.

Collection Method

Prototype RDF dataset creation for SPARQL-based exploration.

Freshness

Last updated 2026-04-29 17:58:51; freshness should be verified.