MINERVA configuration: Examples

Table of contents

##Table of Contents

CellDesigner file upload and annotation

This section provides examples of usage of automatic annotators, atomatic verifiers and construction of procedural semantic zoom.

This is Example File 1, containing a CellDesigner file. The file is quite simple, and has the following properties:

Automatic annotation

See Admin manual - Configure automatic annotation for details on annotators.

  1. Upload the Example File 1 to your MINERVA instance using Add project button
  2. Configure automatic annotations by:
    1. checking the checkbox Annotate model automatically
    2. pressing the Advanced button; set the following:
      1. for Element > Species > Gene, set HGNC annotator
      2. for Element > Species > Phenotype, set Gene Ontology annotator
      3. for Element > Species > Rna, set Entrez annotator
      4. for Element > Species > Protein > GenericProtein, set Uniprot annotator
  3. Press Submit

Examine the generated content. Please note that:

Automatic verification

See Section Configure automatic verification for details on annotators.

NOTE: Your MINERVA instance remembers the settings from the previous run, so keep annotation settings as above.

  1. Upload the Example File 1 to your MINERVA instance again. Make sure to either remove previously uploaded example, or to name the uploaded project differently (use Add project button button)
  2. Configure automatic verification by:
    1. checking the checkbox Verify manual annotations
    2. pressing the Advanced button; set the following:
      1. for Element > Species > Gene
        • set HGNC, HGNC symbol and Entrez Gene as Valid
        • check Require annotations checkbox and as Required set HGNC, HGNC symbol and Entrez Gene
      2. for Element > Species > Phenotype, set Gene Ontology annotator
        • set Gene Ontology as Valid
        • check Require annotations checkbox and as Required set Gene Ontology
      3. for Element > Species > Rna
        • set HGNC, HGNC symbol and Entrez Gene as Valid
        • check Require annotations checkbox and as Required set HGNC, HGNC symbol and Entrez Gene
      4. for Element > Species > Protein > GenericProtein
        • set Uniprot as Valid
        • check Require annotations checkbox and as Required set Uniprot
      5. for Reaction > StateTransitionReaction
        • set Pubmed as Valid
        • check Require annotations checkbox and as Required set Pubmed
      6. for Reaction > TranslationReaction
        • set Pubmed as Valid
        • uncheck Require annotations checkbox
      7. for Reaction > TranscriptionReaction
        • set Pubmed as Valid
        • uncheck Require annotations checkbox
      8. Make sure no items in upper hierarchy levels (e.g. Element, Species or Protein for GenericProtein) have different sets of verification rules
  3. Press Submit

Upon upload, an exclamation mark icon will appear next to the project. After clicking, the popup window will look like this:

ExampleWarnings

Examine the generated warnings. Please note that:

NOTE: Valid and Required settings for lower hierarchy levels are overridden by settings for upper hierarchy levels. For instance, if no PubMed annotation is required for TranslationReaction, but Reaction requires PubMed, reactions re1 and re2 raise a warning.

Procedural semantic zoom

Example File 1 after upload and submit will generate a view with procedurally-generated semantic zoom. Please, note that on the highest zoom out level only one compartment, cell, is visible. After zoom-in, two gray areas become visible, describing functional areas in the map. After another zoom-in, they are revealed and the nucleus compartment becomes visible. After a final zoom-in, nucleus becomes transparent as well. See also Add project button.

Custom data upload by registered users

This section provides examples of data upload by registered users. Two subsection provide detailed examples for uploading basic and advanced formats.

Basic format

The file in basic format has two tab-separated columns Name and Value (see also Upload custom data - format):

This is Example File 2, containing a custom coloring for an example map above (Example File 1).

To upload this data set, do the following:

  1. Make sure you have the priviledges to generate layouts in the example map
    1. Click on Projct detail (magnifying glass icon in the rightmost column)
    2. See that by your name the View project checkbox is checked
  2. Enter the User view of the example map: from the Admin view > Map viewer, click on the name of the uploaded project (example_map by default)
  3. Make sure that you are logged in by checking the Profile tab in the left panel
  4. In Layouts > Custom layouts tab, use +Choose button to select Example File 2 and press generate
  5. In Layouts > Custom layouts tab, use the View icon (magnifying glass) to examine generated view

Examine the generated coloring and the uploaded data set. Please note that:

Advanced format

Advanced format foresees two parts of the uploaded dataset - header and body (see also Upload custom data - format).

Header lines have to start with ‘#’. It can contain the following elements:

Body is a table with a following set of columns:

By-identifier coloring

This is Example File 3, containing a custom coloring for an example map above (Example File 1).

Upload this data set similarly as in basic format upload.

Examine the generated coloring and the uploaded data set. Please note that:

Custom colors and interaction coloring

Advanced format foresees assigning user-defined colors to both elements and interactions.

This is Example File 4, containing a custom coloring for an example map above (Example File 1).

Upload this data set similarly as in basic format upload.

Examine the generated coloring and the uploaded data set. Please note that:

Remarks

Alternatively: you can always extract an area of interest as a CellDesigner file, open it in CellDesigner and colour it there.

Advanced file upload

This is Example File 5, containing a .zip archive withe following structure:

  1. Upload the Example File 1 to your MINERVA instance using Add project button
  2. Examine the upload window, note the automatically filled positions
  3. Make sure that in the Complex section proper checkboxes are checked for the main map and the mapping file $. In the Complex section, you can set the names of uploaded submaps

Examine the generated project. Please note that:



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