Table of content



Introduction

The COVID-19 Disease Map is an open-data repository of curated diagrams and models of molecular mechanisms implicated in the disease. The molecular pathophysiology of COVID-19 is complex and spans multiple biological pathways and cell types. The COVID-19 Disease Map helps to understand the disease from a systems perspective. The visualization of the networks is generated by MINERVA Platform - a standalone webserver for visual exploration, analysis and management of molecular networks encoded in systems biology formats. The map is accessible via a web browser here: COVID-19 map.

Further in this section, the basic MINERVA features are described, so you can start browsing and searching through the COVID-19 Disease Map. To find out more about MINERVA Platform functionalities available in the map, go to MINERVA Platform manual.




How to work with the map in the nutshell

This paragraph is a really brief information about how to work with the COVID-19 Disease Map. Details are described in the following sections.
There are two ways to browse and search the COVID-19 Disease Map. After opening the map here, you see in the center the map and the menu on its left, called Left Panel (see image below).
The main view of the map is a glyph with light blue hexagonal interactive buttons (called anchor points). Clicking on any of these buttons displays name of associated submap in the Left Panel. Click on the submap’s name in the Left Panel, to view the submap.
The second way to display the submap is directly from the SUBMAPS tab in Left Panel. Just click SUBMAPS, and then click on the magnifying glass next to submap’s name.

You can also check, for a quick start the MINERVA Quick Reference Guide.




COVID-19 Map display

The COVID-19 Disease Map is available in any browser. The main display of the map is presented on the image below. The main part of the view is the visualization of the networks. You can freely pan and zoom the map with +/- icon in the top left corner of the map.


covid map view


The map main view is a glyph with the interactive buttons, we call these the anchor points. Clicking on any of the anchors allows to view and browse the submaps with a particular pathways. The anchor is represented by as a white background red border rectangular, see below image.

submaps anchors


Click on the anchor is marked with the red pin. To enter the submap, click firstly on the anchor, and then click on the associated button in the left panel (see below).

submaps


The submap is displayed (below image). You can pan and zoom it.

submaps display


You can click on the elements and the interactions between them, their details are displayed in the left panel.

highlight interaction


The legend

The entities (proteins, genes, etc.) and the reactions between them, are explained in the map’s legend. To view the legend, click the checkbox in the top right corner of the map.

legend


Comment the content

MINERVA allows to leave a comment on the map. To create a comment you need to:

  • open context menu with right click on the map area, where you would like to leave a comment;

  • choose form the context menu Add comment;

  • the dialog is open, fill it and click SEND (left bottom corner button).

add comment


To see the comment on the map, click checkbox COMMENTS in the top right corner of the map. You will see ‘bubble’ icon on the map. Click on it, to view the comment content (image below). comment display


Left Panel

On the left side of the map, there is Left Panel. It contains features which enhance the map browsing and the diagram analysing, like search an entity in the map, view a submap or display the omics data.

Search function is divided in four categories. To search for any gene, RNA or protein use search bar in GENERIC tab. If you are interested in checking the targets of the particular drugs or chemicals, use DRUGS or CHEMICALS tab. To search for targets of miRNA, user MiRNA tab.
You can search for multiple entities in one search, use ; between the terms, e.g. ‘TAFI ; PLAU’.
To clear the search results or currently highlighted elements, click CLEAR button (top right corner of the map).

Submaps

The main view of the map is represented as a glyph with anchors to the particular submaps. Go to SUBMAPS tab in the Left Panel to display the list of all available submaps. Click on the magnifying glass next to submap’s name to view the diagram.
The + icon next to the submap’s name reveals its description.

submap anchors

Visualise omics data

You can upload your own omics data, and visualize them on the map. This feature is mostly use to analyse gene expression in the model.
COVID-19 Disease Map contains default COVID19 scRNAseq overlay, available in the OVERLAYS tab (see image below). By clicking on the checkbox View, the map is coloured with the gene expression.

main omics


In the submap view, the display of overlay is presented below. Find out more about uploading your own omics data in MINERVA manual.

submap omics


How to get MINERVA Platform account

MINERVA Platform account provides users with more options, like uploading own omics data, accessing maps hosted on the instance or managing map’s details and privileges.
If you would like to get MINERVA Platform account, go to INFO tab in Left Panel. There is a hyperlink ‘Request an account’ - click on it and send an email with the request.