Overview
RaMP-DB integrates metabolite and gene/protein identifiers with pathway, reaction, chemical and ontology annotations. Researchers can query the resource through a browser, API or R package and perform downstream enrichment on MS-derived metabolite lists. Database coverage, mapping and the chosen background determine what can be interpreted.
What can this tool do?
Common uses
- Map metabolite identifiers across pathway resources.
- Perform pathway enrichment with metabolites or combined gene/metabolite lists.
- Retrieve pathway, reaction and ontology context programmatically.
Scientific fit
Primary function
Pathway and biological interpretation
Other functions
Reference data and database search, Multi-omics integration
Analysis types
Untargeted metabolomics, Targeted metabolomics, Multi-omics
Data compatibility
Inputs
Compound list or annotations, Pathway or reaction data
Outputs
Pathway or reaction data, Statistical results
Input formats
CSV or TSV, Metabolite or gene identifiers with source prefixes; browser or API queries
Output formats
CSV or TSV, JSON
Scope and considerations
Designed for
- Biological interpretation and identifier harmonization after metabolite or gene-level results are available.
Not designed for
- Raw mass-spectrometry preprocessing or primary metabolite identification.
Important requirements
- Mapped metabolite identifiers with database prefixes, or supported gene/protein identifiers.
- For local R use, the package dependencies and a cached RaMP database; use a recorded database version.
Considerations
- Pathway results depend on identifier mapping, source-database coverage, background definition and the biological context of the study.
- Inspect unmapped and multiply mapped identifiers; enrichment does not validate the original MS annotation.
Access and documentation
The R package declares GPL-2 and provides local access through a downloaded SQLite database. Public web and API interfaces are also available. The software license does not replace the terms of contributing source databases; record both package and database versions.
License: GPL-2
Evidence and review
Official project documentation and direct tool publication metadata reviewed on 2026-09-12. No account creation, data upload, installation or independent benchmarking performed.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Zhang B, Hu S, Baskin E, et al. RaMP: a comprehensive relational database of metabolomics pathways for pathway enrichment analysis of genes and metabolites. Metabolites 8, 16 (2018). doi:10.3390/metabo8010016
- Braisted J, et al. RaMP-DB 2.0: a renovated knowledgebase for deriving biological and chemical insight from metabolites, proteins, and genes. Bioinformatics 39, btac726 (2023). doi:10.1093/bioinformatics/btac726
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-09-12 · First committed entry
Add IDBac and RaMP specialist resources
View change · Entry at this revision