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Example 02 - SBML file modifications

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• SBML file exported from MINERVA map
• SBML model from miscellaneous sources
  • Applying SBOTerms into SBML file
• Miriam annotation in SBML File
• Remarks

The SBML file needs amends before uploading to MINERVA, see more in Admin Manual - SBML file.

SBML file exported from MINERVA map

The file Exported map contains SBML map exported from PD map, see image below:
Adding a new project using Exported map as source 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 block layout and assigned SBOTerms.

SBML model from miscellaneous sources

Download Biomodel 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 elements are connected and displayed randomly. See on the below image, the two independent uploads of Biomodel example.

Applying SBOTerms into SBML file

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

• Add to each species element in listOfSpecies a corresponding SBOTerm, as per the list of CellDesigner types matching SBOTerms
  
  
• Add to each reaction in listOfReactions a corresponding SBOTerm, as per as per the list of CellDesigner types matching SBOTerms
  

Add new project to MiNERVA with the file amended as per the above instructions (Amended SBOTerms file). 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 annotation in 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, below annotation block is necessary to be added inside species. Now, 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>

In case of throwing errors on upload by MINERVA, simplify SBML file to above four blocks.