MINERVA platform: User’s manual

Table of contents

User view

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

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 Layouts tab in the left panel (functional area), and changing the view to Network (see also Section Layouts).

Candidate interactions

If provided (see Admin manual - Add project and Admin manual - Source file), candidate interactions are displayed in the area that have been identified by exploratory analyses, like text mining in network analysis. Elements, for which candidate interactions are suggested, have Candidates bar below their annotation (see below).

Candidates-compact

After expanding with the “+” button, a list is revealed with candidate molecules, pathways, or publications pertinent to the selected element (see below). The table of candidates for PARK2 involves a gene suggested by PathExpand analysis (left column) and interactions with genes and pathways suggested by text mining (right column). As text mining allows to link to the source article, the referenced papers were also provided. Some elements are duplicated (ATXN2), as they are suggested by different articles.

Candidates-expanded

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 layouts and browse submaps.

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

The panel is used in the following way:

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

Drug tab in the functional panel allows to search for known drug targets and display them in the map. Targets will be marked by bubbles in the display area. Please, note that they have different shape than the search result bubbles.

Layouts

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

Layouts

In the figure above:

Layouts2

Custom layouts part contains the following elements (above):

Upload custom data

Format

For examples of basic and advanced data upload, see Examples - Custom 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 look for 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: red for negative values, green for positive values, with the saturation proportional to the value.

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 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 Generate button will invoke a comment, initiate generation and reduce the amount of available custom layouts (see below, left). The progress status will automatically update (see below, right) and when the progress reaches 100%, your custom layout is ready to be displayed.

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

Important reminder:

Upload

Login/Profile

The Login tab is visible for an anonymous user, upon immediate access to a project hosted on your MINERVA instance. 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, the tab name changes to Profile, displaying information on the registered, logged in user. After the successful login the user gains the possibility to upload custom layouts (see Section Layouts).

Submaps

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 layouts are mirrored in the submaps (see figures below).

Submaps

Submaps2

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.

Export

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



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