Import / Export metabolic networks

Import a metabolic network

You must be logged to import a metabolic network. Click on the menu Import to access to the import functions. The three import functions are launched in the same way: after filling the form, click on "Launch". The import will appear in the Jobs panel to the right of the interface. Once the import is complete, you will receive an e-mail at the address indicated in the form that will tell you whether the job has been successful or not. Reload your job list and click on to load the created BioSource. Your BioSource will appear from now on in your private projects.

Import menu

Import from SBML file

MetExplore provides a very complete import tool for SBML files. It is able to import the latest SBML formats with the FBC package as well as the SBML files in the format specific to certain tools such as the Cobra Toolbox. Depending on the format of the information stored in your SBML, you will choose different options in the MetExplore import form. Each option is documented directly in the form.

Main features of the SBML import tool

  • Imports flux constraints and gene reaction associations from FBC package
  • Imports Miriam annotations
  • Imports Metadata annotations from SBML notes. Each metadata is identified thanks to keywords provided by the user in the form.

Extract of the import SBML form and Job list

The import process can take a little time. We advise you to test the validity of your SBML before importing with the online SBML validator.

Import from MetExplore xml file

Specifications of the MetExplore xml format

The MetExplore xml format is based on the SBML format and has been designed for simplifying the annotations associated to metabolites and reactions. As it is not com­pat­i­ble with the sbml spec­i­fi­ca­tions, this for­mat could not be used in main sbml-​using soft­wares. The main differences with the classical sbml format are :

  1. The species element contains three new attributes:

    • mass: the molecular weight of the compound

    • formula: the molecular formula of the compound

    • generic: if generic=true, indicates that this compound reprensents a class of compounds and not an individual compound

  2. The reaction element contains 3 new attributes and 5 new child nodes:

    • The EC number, when available, is indicated in the 'ec' attribute.

    • If in the source database, the reaction is not assigned as spontaneous and no enzyme has been assigned to catalyse it, the reaction is considered as a 'hole'. In the extended sbml format, this information, when available, is indicated in the hole attribute in the reaction tag.

    • The attribute 'generic' indicates if the reaction involve class compounds

    • The gene-protein-reaction (GPR) link is indicated thanks to enzyme elements which contain protein and gene elements.

      <reaction id="KETOLACTOSE__45__RXN" name="&beta;-galactosidase" reversible="false">
          <enzyme id="ENSG00000163521-MONOMER" name="beta-galactosidase precursor">
            <protein id="ENSG00000163521-MONOMER" name="beta-galactosidase precursor">
              <gene id="ENSG00000163521" name="MGC10771"/>
          <enzyme id="ENSG00000166103-MONOMER" name="beta-galactosidase precursor">
            <protein id="ENSG00000166103-MONOMER" name="beta-galactosidase precursor">
              <gene id="ENSG00000166103" name="NA"/>
    • Each pathway where the reaction is involved is indicated in the pathway tag. Example:

      <reaction id="ORNITHINE__45__GLU__45__AMINOTRANSFORASE__45__RXN" name="Ornithine--oxo-acid aminotransferase" reversible="true" hole="true" generic="false" type="small">
        <pathway id="PWY-4981" name="proline biosynthesis V (from arginine)"/>
        <pathway id="ARGININE-SYN4-PWY" name="arginine biosynthesis IV"/>
        <pathway id="PWY-3341" name="proline biosynthesis III"/>
        <pathway id="PWY-5004" name="superpathway of citrulline metabolism"/>
        <pathway id="ARGININE-DEG1-PWY" name="arginine degradation VII"/>
    • When they are available, some compounds are indicated as side-compounds in a reaction.

      <reaction id="ORNITHINE__45__GLU__45__AMINOTRANSFORASE__45__RXN" name="Ornithine--oxo-acid aminotransferase" reversible="true" hole="true" generic="false" type="small">
            <speciesReference species="ADP" />
            <speciesReference species="ATP" />

Import from KEGG

The KEGG import allows all the reactions of the metabolic network of an organism stored in KEGG to be imported in a new MetExplore BioSource. For this, you need to recover the 3-letter identifier of the organism on this site. The KeggSource option allows the recovery of all the metabolites of a reaction (Reaction option) or only the metabolites visible on the metabolic pathway maps.

Export a metabolic network

MetExplore allows to export a metabolic network into 3 formats: SBML, MetExplore xml and Excel. For each one, after launching the export, the resulting file is downloadable by clicking on in the corresponding job in the Job panel.

Export in SBML

The export function in SBML is the symmetric of the import function. It allows to export a metabolic network in the latest version of the SBML format by taking into account the FBC package. If the original metabolic network was imported from an SBML file, the original MIRIAM annotations will also be exported. Finally, the annotations of the metabolites and reactions can also be exported in the form of notes, which allows the SBML file to remain compatible with the particular format of the Cobra-Toolbox.

Form for exporting a metabolic network in a SBML file

Export in MetExplore xml

The MetExplore xml format can be more convenient to parse than a classical SBML file. However, be careful, the produced file won't be compatible with sofware requiring a SBML format.

Export in Excel

All the data grids can be exported in an Excel File. The grids are exported as they appear in the MetExplore interface. This means that hidden columns or rows won't be exported and that new columns added (e.g. by mapping) will be exported. Each grid will correspond to a sheet in the Excel File.

Metabolic network exported in Excel file.