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).

For questions or issues, please submit an issue on our GitHub site at https://github.com/Mathelab/RaMP-DB

Query Analytes

Input pathway you want to search for

Given a pathway name, it returns all compounds contained in that pathway


Summary



Generate Report

Select type of analytes to be returned


Query Result

Query Analytes

Input a list of pathways, one per line



Summary



Download Results

Query Result

IMPORTANT NOTE/INSTRUCTIONS

When inputting source IDs, it is important to add a prefix to denote the id type. This is important because it is possible for two different metabolites to have the same IDs, although each ID may be from a different database source.
Metabolites can be searched with the following ID types: CAS, chebi, chemspider, hmdb, kegg, LIPIDMAPS, and pubchem. To search for a metabolite, the ID type must be added as a prefix. For example, the compound 'HMDB0000562' must be searched by 'hmdb:HMDB0000562', the compound '16737' must be searched by 'chebi:16737'.
Genes can be searched with the following ID types: enzymeNomenclature, ensembl, entrez, hmdb, kegg, uniprot. Similar to metabolites, prefix ID types must be added to the ID for searching.

Query Analytes

Input compound name or source id

Given a gene/metabolite name or ID,retrieve pathways in which the compound is involved in.


Summary


Download Results

Query Result

Preview of output only display first 20 items.

IMPORTANT NOTE/INSTRUCTIONS

When inputting source IDs, it is important to add a prefix to denote the id type. This is important because it is possible for two different metabolites to have the same IDs, although each ID may be from a different database source.
Metabolites can be searched with the following ID types: CAS, chebi, chemspider, hmdb, kegg, LIPIDMAPS, and pubchem. To search for a metabolite, the ID type must be added as a prefix. For example, the compound 'HMDB0000562' must be searched by 'hmdb:HMDB0000562', the compound '16737' must be searched by 'chebi:16737'.
Genes can be searched with the following ID types: enzymeNomenclature, ensembl, entrez, hmdb, kegg, uniprot. Similar to metabolites, prefix ID types must be added to the ID for searching.
Only one type of ID can be input: either source ID or name, not both

1.Query Analytes

Input a list of metabolites, one per line

Input a list of genes, one per line



Summary

The following number of names/ids were mapped:

The query returned the following number of pathways per query gene/metabolite:

Query results should be visible here



Download Results

Query Result

Table output display

2.Run Pathway Enrichment Analysis

Set Pathway Enrichment Parameters

Processing request...



3.Filter and cluster Pathways

Set Filtering/Clustering Parameters

Clustering Parameters:

Results of Pathway Enrichment Analysis



4.Download Results

Significant pathways are returned under 'Results of Pathway Enrichment Analysis' and can be downloaded by clicking 'Download Results'

Note that only pathways that contain at least 3 analytes from the user input will be output

The following number of pathways per database were processed:

Download Results

IMPORTANT NOTE/INSTRUCTIONS

When inputting source IDs, it is important to add a prefix to denote the id type. This is important because it is possible for two different metabolites to have the same IDs, although each ID may be from a different database source.
Metabolites can be searched with the following ID types: CAS, chebi, chemspider, hmdb, kegg, LIPIDMAPS, and pubchem. To search for a metabolite, the ID type must be added as a prefix. For example, the compound 'HMDB0000562' must be searched by 'hmdb:HMDB0000562', the compound '16737' must be searched by 'chebi:16737'.

Query Analytes

Input metabolite or gene

If a compound is input, all genes that catalyze reactions involving the compound are returned. Conversely, if a gene is input, all compounds in reactions that are catalyzed by that gene are returned


Summary


Download Results

Query Result

Table output display

Visuazlize gene-metabolite interaction network

IMPORTANT NOTE/INSTRUCTIONS

When inputting source IDs, it is important to add a prefix to denote the id type. This is important because it is possible for two different metabolites to have the same IDs, although each ID may be from a different database source.
Metabolites can be searched with the following ID types: CAS, chebi, chemspider, hmdb, kegg, LIPIDMAPS, and pubchem. To search for a metabolite, the ID type must be added as a prefix. For example, the compound 'HMDB0000562' must be searched by 'hmdb:HMDB0000562', the compound '16737' must be searched by 'chebi:16737'.
Genes can be searched with the following ID types: enzymeNomenclature, ensembl, entrez, hmdb, kegg, uniprot. Similar to metabolites, prefix ID types must be added to the ID for searching.
Only one type of ID can be input: either source ID or name, not both

Query Analytes

Input a list of genes or metabolites



Summary


Download Results

Query Result

Table output display

Visuazlize gene-metabolite interaction network

IMPORTANT NOTE/INSTRUCTIONS

When inputting source IDs, it is important to add a prefix to denote the id type. This is important because it is possible for two different metabolites to have the same IDs, although each ID may be from a different database source.
Metabolites can be searched with the following ID types: CAS, chebi, chemspider, hmdb, kegg, LIPIDMAPS, and pubchem. To search for a metabolite, the ID type must be added as a prefix. For example, the compound 'HMDB0000562' must be searched by 'hmdb:HMDB0000562', the compound '16737' must be searched by 'chebi:16737'.

Query Analytes

Input a metabolite or ontology

When metabolites are input, it returns associated ontologies (e.g. biofluid location, cellular location, origins (e.g. drug, food, microbial), and/or tissue location When an ontology name is input, it returns all associated metabolites


Summary


Download Results

Query Result

Table output display

IMPORTANT NOTE/INSTRUCTIONS

When inputting source IDs, it is important to add a prefix to denote the id type. This is important because it is possible for two different metabolites to have the same IDs, although each ID may be from a different database source.

Query Analytes

Input a list of metabolites or ontologies



Summary


Download Results

Query Result

Table output display