I would like to get the databases of experimental metabolism data in a computable format - mammalian metabolism, rat liver metabolism, rat S9 and microbial. Are these available as a download, or do I need to extract one chemical at a time through the user interface? The Toolbox documentation indicates that these databases exist, but I just can't see how to get to them.


The metabolic maps are part of Metapath. 

You can visualise them but the data, at the request of the donator, cannot be exported.

There are currently 4 databases with metabolic maps in the Toolbox:

  • Observed Mammalian metabolism
  • Observed Microbial metabolism
  • Observed Rat In vivo metabolism
  • Observed Rat Liver S9  metabolism

All can be used like profilers:

You can view the metabolites by double-clicking on the results in the matrix:

But you can also access the actual metabolic map by performing a right-click on the results in the matrix and selecting "Show metabolite tree". This will give you access to the actual metabolic map:


As well as further details on the study [1]: