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Example 2 - SBML file modifications
SBML file exported from MINERVA map
The SBML file should be customized before uploading to the MINERVA Platform, see more in admin manual - SBML file.
Click here to download SBML map, which was created by export as SBML from the MINERVA Platform. See image below:
Adding a new project using SBML map, will generate an identical map as the exported one (annotations, elements, reactions and their positions are preserved), since SBML file exported by the MINERVA Platform contains <layout> block and assigned SBOTerms, matching CellDesigner element and reaction types.
SBML model from miscellaneous sources
Click here to download biomodel example map, which is an SBML model downloaded form biomodels website. Then, add new project to the MINERVA Platform.
On the generated map, all elements are small molecules and all reactions are state transitions. Note that without <layout> block, the diagram follows a random circular layout. Below are two independent uploads of biomodel example map.
Applying SBOTerms to SBML file
Providing SBOTerms into the SBML file allows to define particular reactions and elements type.
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Add to each species element in listOfSpecies a corresponding SBOTerm, following the mapping of CellDesigner - SBOTerms
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Add to each reaction in listOfReactions a corresponding SBOTerm, following the mapping of CellDesigner - SBOTerms
When the new project is added with the 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.
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:
Find here the file with FOS added, see image below:
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.