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Example 2 - SBML file modifications




The SBML file should be customized before uploading to MINERVA, see more in admin manual - SBML file.


SBML file exported from MINERVA map

Click here to download a file with an SBML map exported from MINERVA map, see image below: Main
Creating a new project using this file, will generate an identical map as the exported one (annotations, elements, reactions and their positions are preserved), since SBML file exported by MINERVA contains <layout> block and assigned SBOTerms, matching CellDesigner element and reaction types.


SBML model from miscellaneous sources

Click here to download an example, which is an SBML model downloaded form biomodels website and add project to MINERVA. On the generated map, all elements are small molecules and all reactions are state transitions. Note that without <layout> xml block, the diagram follows a random circular layout. Below are two independent uploads of the biomodel example.


Generated maps


Applying SBOTerms to SBML file

Providing SBOTerms into the SBML file allows to define particular reactions and elements type.

When the new project is added to MiNERVA with the file amended as described above (file with SBOTerms assigned), the generated map looks as shown below. Note that in the left panel the small molecules are annotated automatically by name and the reaction type is provided.

Map with SBOTerms added


MIRIAM annotations in the SBML file

MINERVA automatically annotates elements by name, if proper annotators are configured (see section Configure automatic annotation). On above image, F - fluorine and others small molecules are annotated with ChEBI by name.

To annotate elements with MIRIAM, place them in the SBML <annotation> (species, reactions and compartments). Now, we will add to the SBML file new species gene named FOS and annotate it with HGNC:3796 as below:

Annotation block

Find here the file with FOS added, see image below:

Annotated map

Remarks

SBML file might be a complex one. MINERVA is being developed to support all SBML functions. See below the SBML blocks (within <model>), which are sufficient to create a new MINERVA project:

  • <listOfCompartments>
  • <listOfSpecies>
  • <listOfReactions>
  • <layout>

If MINERVA throws errors on upload of an SBML file, simplify the file to these blocks.