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.
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
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="β-galactosidase" reversible="false"> <enzyme id="ENSG00000163521-MONOMER" name="beta-galactosidase precursor"> <protein id="ENSG00000163521-MONOMER" name="beta-galactosidase precursor"> <gene id="ENSG00000163521" name="MGC10771"/> </protein> <enzyme> <enzyme id="ENSG00000166103-MONOMER" name="beta-galactosidase precursor"> <protein id="ENSG00000166103-MONOMER" name="beta-galactosidase precursor"> <gene id="ENSG00000166103" name="NA"/> <protein> </enzyme> ...
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"> ... <side-compounds> <speciesReference species="ADP" /> <speciesReference species="ATP" /> </side-compounds> ...
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.
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
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.
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.