Metabolic Database

The metabolic database was assembled to annotate metabolic pathways inferred with the Metabolic Pathfinder and Pathway extraction tools in NeAT. It unites data from KEGG (version 55), MetaCyc (version 14.1) and aMAZE, and contains in total 2,012 reference pathways.

The data model is described in this doctoral thesis (p. 191).

The metabolic database is provided as a postgres backup file and can be downloaded here.

To load the metabolic database into postgres, start postgres on command line:

  >psql -U postgres

In postgres, create a database user (here named 'metabolic') and the database:

  create user metabolic with password 'metabolic';
  create database "metabolicdb" with owner "metabolic" encoding='TF8';

Quit postgres and restore the database from the backup file on command line:

  >pg_restore -d metabolicdb metabolicdb_dump_03_10_2010.backup -U postgres

You can then enter the metabolic database with the following command line:

  >psql -U metabolic -d metabolicdb

To display some information on the tables and the data content, type:

  metabolicdb=> \dt
  metabolicdb=> \d databases;
  metabolicdb=> select * from databases; 

In the following, a few commands are given to get some statistics on the data content. The commands below provide the number of reactions (15,802), RPAIRs (12,287), compounds (13,195) and genes (3,981).

  metabolicdb=> select distinct transformation_type from transformations;
  metabolicdb=> select distinct bioentity_type from bioentities;
  metabolicdb=> select count(*) from transformations where transformation_type='REACTION';
  metabolicdb=> select count(*) from transformations where transformation_type='SUBREACTION';
  metabolicdb=> select count(*) from bioentities where bioentity_type='COMPOUND';
  metabolicdb=> select count(*) from bioentities where bioentity_type='GENE';

To obtain the number of pathways from KEGG (144), MetaCyc (1752) and aMAZE (116), the following commands can be used:

  metabolicdb=> select count(*) from pathway_versus_database where database_unid=3;
  metabolicdb=> select count(*) from pathways where name like '%map%';
  metabolicdb=> select count(*) from pathway_versus_database where database_unid=4;
  metabolicdb=> select count(*) from pathway_versus_database where database_unid=6;

Metabolic Pathfinding Supplement

This is the supplement for the article: "Metabolic Pathfinding Using RPAIR Annotation"

  1. Reference pathways
    The 116 reference pathways were obtained from the aMAZE database and can be downloaded in gdl format here. The gdl files can be loaded into Cytoscape with the CoNet app. For the display, the style "Directed" and the hierarchical layout are recommended. To differentiate compounds and reactions, the network style can be modified by mapping node shape to ObjectType with a discrete Mapper and selecting different shapes for compounds and reactions.
  2. Statistics on reference pathways and on path finding
  3. Metabolic Pathfinder web interface
    The web interface is available at NeAT tools. Open the sub menu Path finding by clicking the white triangle and select Metabolic path finding.
    Alternatively, the command line version of the pathfinding and pathway inference tools in NeAT can be downloaded from here.
  4. Metabolic networks
    The networks are available via the Metabolic Pathfinder web interface. Go to the Metabolic Pathfinder web interface, then click Manual and go to the KEGG graph repository. The Metabolic Pathfinder manual also provides information on the networks, under Graph type.
    Metabolic networks can also be downloaded from here.
  5. List of excluded compounds

KEGG version 41.0 has been used to generate the results.