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Example 2 - SBML file modifications#
SBML file exported from MINERVA map#
The SBML file should be customised 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.
Adding a new project using this SBML file, 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 BioModels example map, which is an SBML model downloaded from the BioModels website. Then, create a new project in 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 the same file.
Applying SBOTerms to SBML file#
Providing SBOTerms into the SBML file allows to define particular reactions and elements type. Add corresponding SBOTerms using the mapping of CellDesigner - SBOTerms
to each species element in listOfSpecies
to each reaction in listOfReactions
When the new project is created 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.
Annotations in the SBML file#
MINERVA can automatically annotate elements by name, if proper annotators are configured (see section Annotation panel). On above image, F - fluorine and others small molecules are annotated with ChEBI by name.
To annotate elements manually, place annotations in the SBML <annotation> (species, reactions and compartments).
Below is an illustration of how to add to the SBML file new species gene named FOS and annotate it with HGNC:3796:
Find here the file with FOS annotation 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.