RaMP: Relational Database of Metabolomics Pathways

To use this software on your local machine, you must have the RaMP SQL database installed locally. For instructions on how to do so, please refer to the RaMP-DB GitHub repository RaMP-DB GitHub repository .

RaMP currently integrates information from 4 different databases:

Of note, RaMP does not import all the information contained in these databases. Instead, RaMP includes pathway names and the genes and metabolites they include. RaMP is a work in progress and we will be expanding its content (reaction-level information, non-human compounds and genes, etc.). Currently, the following queries are supported through this interface:

  • Tab1: Given one or multiple pathway names, retrieve all genes and/or metabolites contained in the pathway(s)
  • Tab2: Given a list of metabolite(s) or gene(s), retrieve all pathways that they are involved in. This tab also support pathway overrepresentation analysis
  • Tab3: Given one or multiple metabolite(s) or gene(s), retrieve all gene(s) or metabolite(s), respectively, that are involved in the same reaction. A network of gene-metabolite relationships can be drawn.
  • Tab4: Given one or multiple metabolite(s), retrieve the ontology (e.g. biofluid location, cellular location, etc.) they belong in.

More details can be found in our manuscript

The Venn diagram below shows the overlap in metabolites and genes from each database source (as of 01/24/2017).