MINERVA platform: User’s manual

Table of contents

User view refers to the visualization and functionalities accessed by users of the content hosted by your MINERVA instance.

You can also see the summary of this page in the MINERVA Quick Reference Guide.

Main view

The main view of the MINERVA platform is summarized in the figure below.

Main

Main components of this view are

Accessing the project

Your instance of MINERVA platform can host many projects, which are uploaded via the administrator view (see Admin manual - Add project). They are accessed by a provided, dedicated web address.

Exploring the display area

The content is visualized using Google Maps API, and allows similar pan and zoom functionalities. The content is interactive, the user can click on an element or interaction to examine additional details displayed in the left panel (functional area).

The content is by default displayed in a semantic zoom mode, where compartments and areas in the submitted file cover underlying elements on higher levels of zoom. This view is generated procedurally, directly from the uploaded content. This view is generated automatically from the layout of the CellDesigner file. MINERVA platform calculates coverage of bigger areas by smaller, and assigns them to appropriate zoom levels. For more details see Section Content curation. You can turn off the semantic zoom view by going to the Overlays tab in the left panel (functional area), and changing the view to Network (see also Section Overlays).

Annotating, selecting and downloading the display area

Right-click in the display area invokes a contextual menu with two options - (see below).

Annotating

Add comment

This functionality allows to annotate contents in the display area. Clicking the Add comment button invokes a form that can be filled out by the user and sent to the administrators of the project. The field Pinned controls, whether the comment will be visible in the map (see below, left).

Annotating

Type field is a drop-down menu, listing elements nearby to the click location. This allows to choose and attach the comment to a particular element or interaction (see above, right).

After sending, and if the field Pinned was set to Yes, the comment becomes visible in the display area, as shown below, to the left (after checking the Comments checkbox, see Comments).

Pinning

Clicking on the comment bubble displays annotated element and the text of the comment (see above, right). Name and email are not disclosed, they will be accessible only to project and platform administrators (see Admin manual - Comments).

Select mode

Clicking the Select mode enables the functionality supported by Google Maps API, allowing to select an arbitrary shape in the display area. The shape then can be downloaded in various formats, either as a model (.xml file) or as an image (see below).

Select mode

Content curation

MINERVA framework handles SBGN-compliant format, produced either by CellDesigner (http://www.celldesigner.org) or SGBN editors, like SBGN-ED (https://immersive-analytics.infotech.monash.edu/vanted/addons/sbgn-ed). MINERVA relies on such externally curated content.

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:

For explanation and examples on content curation and annotation, see Examples - CellDesigner file upload and annotation.

Functional area

Functional area (the panel to the left from the display area) displays additional information about selected elements and interactions, allows to query the content, generate custom overlays and browse submaps.

Search tab

Search tab allows to search for particular elements or interactions in the displayed map. Also, under this tab, the panel displays detailed information on selected elements or interactions (see below).

Search

There are four subtabs available in the Search tab, offering different scopes: * GENERIC for regular search * DRUG for drug target search * CHEMICAL for chemical target search * MIRNA for miRNA target search

Generic

The generic scope works as follows:

Direct link to the elements in the display area is possible, as the search query can be provided within the web address of the displayed project. An address constructed as follows:

your.webserver.address/?search='search query'

is a link executing the search for a given search query in the default project of your MINERVA instance. For example, an address

your.webserver.address/?search=reaction:xyz123

will directly point to an interaction with id xyz123. Referring to a given project on your MINERVA instance requires additionally to pass the project identifier in the address, as shown below. Identifiers of projects are accessible using the Admin view.

your.webserver.address/?id='project id'&search='search query'

Drug (targets)

The Drug scope works as follows. Drug subtab under the the Search tab allows to look for known drugs or their brand names and display their targets in the map. Targets will be marked by pins in the display area. Please, note that they have specific shape, different than the results of other search scopes.

Chemical (targets)

The Chemical scope works as follows. Chemical subtab under the the Search tab allows to look for known chemicals or their synonyms and display their targets in the map. Targets will be marked by pins in the display area. Please, note that they have specific shape, different than the results of other search scopes.

microRNA (targets)

The MiRNA scope works as follows. miRNA subtab under the the Search tab allows to look for miRNAs and display their targets in the map. Targets will be marked by pins in the display area. Please, note that they have specific shape, different than the results of other search scopes.

Overlays tab

Overlays tab allows to display or generate custom coloring of elements and interactions in the map. It is composed of two sections - general overlays and custom overlays (see figure below).

Overlays are also visible in the popup menu, with the value and the sign marked on the horisontal color bars (see figure below).

Overlays

In the figure above:

Overlays2

User-provided overlays part contains the following elements (above):

Upload user-provided overlay data

Format

For examples of basic and advanced data upload, see Examples - user-provided overlay data upload by registered users. Description of the format follows below.

Basic format The basic format of file containing the uploaded data is two-column, tab-separated text file, with the columns Name and Value.

Basic format will match names of the elements provided in the Name column among the names of elements in a given network and for the matching ones will assign them colors: blue for negative values, red for positive values, with the saturation proportional to the value. The color range for the data upload is customizable in the admin panel.

Advanced format The advanced format allows for by identifier matching, custom color assignment and coloring of interactions. Advanced format foresees two parts of the uploaded dataset - header and body.

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

Body is a table with a following set of allowed columns:

The dataset for upload may be integrated and sparse, i.e. a document may contain all columns at once, and, where irrelevant, their content may be left blank. In other words, you can color interactions and elements in the same dataset, leaving blank fields in ReactionIdentifier and LineWidth for elements, and leaving blank fields in Name for interactions.

Procedure

After choosing the dataset to upload, pressing Upload button will invoke a comment, initiate generation and reduce the amount of available custom overlays (see below, left).

You will be notified by email when your overlay is ready. The email will also contain the list of elements in your dataset not found in the map.

Important reminder:

Submaps tab

The Submaps tab summarizes all the submap networks uploaded together and linked to the main network of this project hosted by your MINERVA instance. See Admin manual - Source file to learn how to upload the submaps together with the main file.

The Submaps tab contains the Name column, and the column with the buttons invoking corresponding submaps. The submaps show as a pop-up window on top of the main map, and are synchronized with respect to search queries and displaying mapped experimental data. This means that search results and search target bubbles will be visible in the main map and the displayed submaps. Similarly, coloring for overlays are mirrored in the submaps (see figures below).

Submaps

Submaps2

Info tab

The Info tab has two components, displaying Project info and User data (for registered and logged in users).

Project info

Displays Name, Version and Description of the map.

The Data section features four links, allowing the user to: * browse the publications supporting the map. The Publication list dialogue allows to search for articles by title or author names, and contains links to interactions supported by particular articles. * download the source files * export the contents of the map (see below) * open the manual

The export page contains three tabs, allowing to download the hosted content in different formats.

User data

It allows a registered user to type in their login and password, or to request for an account from the administrators of this MINERVA instance. Platform administrators can register new users (see Section 3.4 User manager) and configure Request an account functionality (see Admin manual - Configuration)

After login, this panel displays information about the user. After the successful login the user gains the possibility to upload custom overlays (see Section Overlays).

Information bar

Information bar is the topmost part of the user view, containing the Show overview button, Comment and Legend checkboxes and Clear button. The Clear button clears all search results currently shown in the display area. The remaining functionalities are detailed below.

Show overview

This button invokes a static image associated with the displayed content. It may be a graphics facilitating the understanding of the underlaying network, or any other visual cue that the content curator decided to present. The initial image displayed with the Show overview button can be linked to:

Detailed information on how to configure Show overview images display is provided in Admin manual - Source file.

Comments

If this checkbox is checked, the comments provided by users with Pinned option set to Yes will become visible in the display area (see also Section Add comment).

Legend

If this checkbox is checked, the legend describing element and interaction types will be displayed.



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