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Systems biology diagrams

MINERVA platform visualises diagrams using three formats: SBGN-compliant, SBML and GPML.

SBGN-compliant format

MINERVA handles SBGN-compliant format produced either by CellDesigner (click) or SBGN editors like SBGN-ED (click). Moreover, a number of additional functionalities of MINERVA operates on metadata, that can be provided in the SBGN-compliant file itself. These are the following:

  • Processing of existing annotations: annotations to the elements or the interactions embedded within CellDesigner file are automatically parsed and processed. They can be used to extensively annotate elements during adding a new project. Also, MINERVA platform can verify these annotations against a set of predefined content-governing rules during adding a new project either.

  • Procedural generation of semantic zoom: the information on the complexes and the overlaying compartments is extracted from SBGN-compliant files to generate Pathways and compartments view. These are compartments (SBGN/SBML/GPML) and layers (CellDesigner). In this particular view, on the high level of zoom, the bigger compartments overlay smaller ones and the contents of complexes are masked. Read more in semantic zoom. If your content is created in CellDesigner, you can draw layers (see CellDesigner user manual, p 76), which will be incorporated into the generation of the semantic zoom as well.

  • Cross-platform SBGN translation: CellDesigner files can be uploaded to be displayed in pure SBGN notation, and SBGN-displayed content can be downloaded as a pure SBGN file.

SBML format

SBML file contains the text information about the elements, the reactions and the annotations. MINERVA takes the annotations from SBML file as the inputs and transforms them to the element/interaction annotations which can be displayed in the map. Use of SBOTerms is necessary to determine the type of the elements/interactions. Moreover, SBOTerms must be inputted into the SBML file by a user manually. Without updating SBML file on SBOTerms, all elements are displayed on map as small molecules and all reactions are represented by state transitions.

See here the list of CellDesigner types matching SBOTerms and check the example 2 - SBML file modifications to find out more about modifying SBML format file.

MINERVA handles below SBML packages:

  • layout
  • render (partially)
  • multi

GPML format

GPML files store pathways content at WikiPathways, this format is compatible with PathVisio diagram editor.
GPML is unconstrained by a systems biology data model. It allows ‘free-hand’ drawing of reactions and elements. The MINERVA Platform displays diagrams inspired by CellDesigner SBML scheme, constrained by SBML-based data model. Thus, to handle GPML display in MINERVA, the elements and the reactions in GPML format are mapped onto SBML-based format. Find out in GPML:CellDesigner mapping section how MINERVA imports (display) and exports GPML format files.