MetaboMAPS supports visualizing numerical data from nearly every source. However, it has the following limitations:

  • The data must be in CSV format (tab, comma, semicolon, or space separated)
  • The first row defines the different conditions that are used for legend labeling
  • The first column must contain the identifiers that connects the following data to a plot box
  • The data must be numerical with points as seperator

Data for reactions and metabolites must be seperated from each other. However, you don't have to preselect the data, which means you can keep all your e.g. transcriptome data in a single file. MetaboMAPS picks only those for plotting that were found on the selected map. Everything else will be omitted. Please note that very large files can lead to enhanced loading times.

The answer is short: anything and everything.

Every researcher has their own needs in terms of identifiers that are used during their work. I give you a short list of what comes to my mind, but MetaboMAPS is not limited to those:

  • EC numbers (we like those because we belong to BRENDA)
  • GeneIDs
  • Locus Tags
  • Gene names
  • Database accessions (UniProt, KEGG, MetaCyc, PubChem, Phytozome,... choose whatever you like)
  • Metabolite synonyms (we are working with BKMS to provide synonym matching, e.g. when you assign CoA, also synonyms such as coenzyme A will match.

As you might expect, EC numbers and Metabolite synonyms are treated special, first because they are not organism specific (meaning they don't have to be assigned to every single organism that has the map). Second, because they can be connected to other databases: EC numbers link to BRENDA and metabolites link to BRENDA, KEGG, Metayc, and Sabio-RK (if possible).

You can use the pathways from other contributors or contribute to the community yourself. It is up to you!

Since MetaboMAPS uses the native SVG format, you can keep working with your tool of choice: SVGs can be exported from Adobe Illustrator, Inkscape, Powerpoint, LibreOffice, ChemSketch, just to name a few. And if you cannot export it, you can convert it.

You uploaded your pathway map and then recognized a typo on it? Or maybe your pathway just needs an update because of new findings? Don't worry! You don't have to redraw all plot box nor must you reassign all the identifiers. Just click on the to edit your pathway. Now you see the pathway editor. On the top left, right beneath the name of the pathway, is a button looking like this: When you click on this button, a new window opens, where you can upload the new version of your pathway. Afterwards, a preview shows up, where you can check, if the plot boxes are drawn correctly.

Plot boxes are shifted?

It can happen that the plotboxes are shifted for various reasons. For example, when the dimensions of your SVG changed. However, you don't have to move them one by one. Just click into the SVG to set it in focus. Then use Ctrl+A to select all plot boxes or Ctrl+click on the plot boxes you want to arrange. Afterwards, you can move the selected plot boxes around with the arrow keys on your keyboard.


When you update a private pathway, the old version is completely replaced by the new one. However, when you upload a public pathway, a new version is added. This ensures that users can still see the pathway and is important for reference in publications. If you want to share a specific version of a pathway map, append a dot with a following version number to the accession code (e.g. P61.1).