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Example 1 - CellDesigner file upload and annotation#

This section provides examples of use of automatic annotators when creating a new project in MINERVA.

Description of the example map content#

Click here to download an example map, drawn in CellDesigner file. The file is quite simple, and has the following properties:

Annotations

1. Gene component SNCA is not annotated.
2. RNA component SNCA is annotated with Entrez Gene id (NCBI Gene in CellDesigner MIRIAM tab).
3. Two (of three) protein components SNCA are annotated with UniProt id.
4. Protein component PRKN is not annotated.
5. Phenotype component UPS is annotated with Gene Ontology.
6. Interaction re3 is annotated with PubMed id, while other reactions are not.

Compartments and areas

1. SNCA translation and SNCA degradation areas are drawn on top of the diagram.
2. Cell, synapse and nucleus compartments are drawn.

Creating the project#

Use the example map to create an example project on your MINERVA instance:

1. press Create project button.
2. select Local source and use file selector to upload the file
3. provide necessary project information, default view, and license information
4. press Create Project button in the bottom right corner

Automatic annotation#

See Annotation panel for details about annotators.

1. Create an annotator preset
   • go to Annotation tab (left panel)
   • press Add new button and name your preset (e.g. test)
   • use Add button to add the following annotators to the preset (use search bar to quickly find annotators): Entrez Gene, Gene Ontology, HGNC, UniProt; close the window when finished
   • order the annotators as follows: HGNC, UniProt, Gene Ontology, Entrez Gene; order is important as one annotator may use an output of another
   • configure each annotator by clicking on it and selecting Source, Annotations and Elements, as in the table below
   • press Create button

2. Run automatic annotations:
   • press Manage button next to your project
   • select Annotate and choose your created preset (suggested name test from earlier)
   • observe the Annotation Started prompt in the bottom right corner
   • select Manage > Annotate again to see Annotation in progress note

Examine the annotated content of the map. Please note that:

1. The annotations between SNCA gene, SNCA RNA and SNCA protein differ, because different Annotation fields were selected for different annotators. Also, some annotators cannot provide certain annotations and use different information sources to annotate the elements.

2. Even though SNCA gene had no annotation, it was correctly annotated by name by HGNC annotator.

3. UniProt annotator works only by the identifier, so it was unable to provide annotations for PRKN or ubiquitinated SNCA (no annotation).

4. Gene Ontology annotator retrieved a definition of the annotated Phenotype.