MINERVA v15.0
Manual

MINERVA platform: User’s manual#

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

You can also see the brief summary of this page in the MINERVA Quick Reference Guide or you can follow the guide.

MAIN VIEW#

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

Main{:width=“900px”}

Main components of this view are:

Accessing the project#

Your instance of MINERVA platform can host many projects, which are uploaded by the administrators (see add project). Every project project can be accessed by a dedicated web address.

Exploring the display area#

MINERVA platform displays molecular interaction diagrams, their annotations and links to databases.

Systems biology diagrams#

MINERVA platform visualises diagrams using three formats: SBGN-compliant, SBML and GPML. Read more about customising the content here.

The content is visualized using Google Maps API or Open Layers Library (chosen on the project upload), and allows for similar pan-and-zoom functionalities. The content is interactive, the user can click on an element or an interaction to examine additional details, which are displayed in the left panel (functional area). More exploration tools are available via right click on the map. Moreover, MINERVA allows to color the map’s elements with glyphs provided by user (check section glyphs) and to precisely set the elements order (check section Z-Index). The map content is by default displayed in semantic zoom mode, which enhances map’s clarity. In that view, the compartments and the pathways areas are displayed in a particular order, regulated by the zoom level.

Semantic zoom is a default view of the map. It makes the compartments and pathways cover underlying elements on higher levels of zoom. This view is generated procedurally, directly from the uploaded content. MINERVA calculates which areas cover others, and assigns them to the appropriate zoom levels. Note: In the tab Overlays tab in the left panel (functional area), semantic zoom is activated via Pathways and compartments overlay. You can turn it off by changing the view on Network or Empty.

Find out more here: procedural generation of the semantic zoom.

Basic exploration tools#

Right-click in the display area invokes a contextual menu (image below). The menu allows to:

Right click menu{:width=“400px”}

Add comment#

This functionality allows to comment on contents in the display area. Clicking on Add comment invokes a form that can be filled out by the user and sent to the administrators of the project (see below left). 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 below middle). If particular type is selected, its name is displayed (see below right). The field Pinned controls, whether the comment will be visible in the map.

Comment{:width=“900px”}

After sending, if the Pinned box was ticked, the comment bubble becomes visible in the display area (see below left). If the comment is placed in a submap, the main map shows that bubble also. It is placed on the anchor element. Note that the checkbox Comments located in Information bar must be ticked to make the comments visible at all.

Pinning comment{:width=“900px”}

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 Administrator’s manual - Comments).

Select mode#

Clicking the Select mode enables the functionality supported by Google Maps API and Open Layers Library. It allows to select an arbitrary shape in the display area. To select the area: choose Select mode and click on the map, it is your start point. Draw all of your polygon’s points. To close the polygon choose the end point of the polygon the same as the start point, or double click on the end point. Right click on the selected area allows to remove the selection or download it in various formats, either as a map or an image.

Select mode{:width=“900px”}

Export as image#

This option creates an image of the part of map on your display area. Export to vector and raster graphics is supported, allowing to modify and enhance the downloaded image.

Export as map#

This option allows to produces a file acceptable by either CellDesigner, pure SBGN or SBML editors. The exported file contains the editable fragment of your display area, together with its contents and layout. Importantly, in the case of CellDesigner or SBML export, all additional annotations provided by MINERVA platform are downloaded as well.

Open MolArt#

This option is active only for the protein annotated with UniProt ID (see image below). MolArt (MOLeculAR structure annoTator) is a JavaScript tool and library. It visualizes sequence-related annotations over available experimental or predicted structures (click here for MolArt documentation). MolArt{:width=“900px”}

MolArt opens a new window, which displays in the left panel the molecule’s sequence, relevant annotations (including variation data) and the list of available structures (either experimental or predicted) for a given molecule. The right panel of MolArt window shows selected 3D structure over which any of the sequence annotations can be color-overlaid. See image below:

MolArt{:width=“900px”}

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 the submaps.

Search tab#

Search tab allows to search for a particular elements or interactions in the displayed map. Also, under this tab, the panel displays the detailed information on selected elements or interactions, such as: element’s compartment and full name, symbols, annotations and their source (automatic or manual by curator), see below:

Search{:width=“900px”}

There are four subtabs available in the Search tab, offering different scopes:

GENERIC#

The generic scope works as follows:

Search filed{:width=“900px”}

The reaction kinetics, if available, is displayed after clicking on chosen reaction in the display area. Information about element’s interactions is available for any element by clicking on its pin, see image below:

Search pin dialog{:width=“900px”}

Search pins indicate hits in the display area. Similar search results are merged (marked with the same number) and the left panel contains information about size of that group of x elements. If search pin is be blank (no number), it would mean that aggregated search results exceed 100. For multiple elements search, the results have icons of different color and shape (see image below) which are clickable and show information in the popup window. When searching for different targets (e.g. generic target and drug target) common targets are highlighted with a special icon. The same icon indicates search results that are found in a submap. See more in Submaps tab.

Multiple search results{:width=“900px”}

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 has to be manually constructed, directly into web browser, as below:

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 (target)#

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. The pins have specific shape, different than the results of other search scopes.

CHEMICAL (target)#

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. The pins have specific shape, different than the results of other search scopes.

MiRNA (target)#

The microRNA scope works as follows. MiRNA subtab under the the Search tab allows to look for miRNAs and display their targets in the map. The pins 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 user-provided overlays (which becomes visible upon login).

General Overlays#

The table located in the top of the left panel (see image below), it contains:

Overlays provide additional information about elements and interactions. Hover over the overlay name/view/data to display a short description of the dataset, if provided on upload. Overlays are also visible in the popup window, displayed after clicking on the element’s pin, showing the value and the sign marked on the horizontal color bars. The popup contains information about Interacting drugs, chemicals and MicroRNA with selected element, available after ticking check box Show all.

Overlays main{:width=“900px”}

In the figure above:

User-provided overlays#

User-provided overlays are the overlays uploaded by and visible to the currently logged user. Available overlays can be reordered by name or number. Hover over any of them display short description, if one was provided on the upload. Adding a new overlay is available via Add overlay button (see below image on the left side), which opens the dialog window (see below image on the right side):

User-provided overlays{:width=“700px”}

There are two types of overlays the user can provide: generic and genetic variant.

The list of user-provided overlays contains columns (image above):

The user-provided overlays are displayed identically as default general overlays. The genetic variant overlays additionally contain the genome browser in the popup window (see below):

Genetic variant browser{:width=“900px”}

The genome browser allows to view the position of a variant in the sequence of the corresponding gene. In Gene variants section (see image above) user can choose the location in chromosome, zoom the scale in/out by clicking on +/- buttons and swipe the base pairs axis. The popup window contain following:

Upload user-provided overlay data#

Here, we describe how the data overlays files should look like, so MINERVA can handle them and color the map as needed. To learn more about uploading data sets go to example 3 - Custom data upload.

Basic generic format#

The file in a basic format is a two-column, tab-separated text file, with the columns Name and Value. Please note that the basic format does not have a header.

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.

EXAMPLE: Click here to download an example of basic format overlay. You can upload it to Parkinson’s disease map.

Advanced generic format#

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

EXAMPLE: Click here download an example of generic advanced overlay. You can also upload it to Parkinson’s disease map.

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 element_identifier and line_width for elements, and leaving blank fields in name for interactions.

All data columns work as an intersection to narrow down the coloring. Example: if your map contains only protein SNCA, and you put RNA SNCA, there will be no coloring even though the SNCA is displayed in the map.

Genetic variant format#

It is a particular type of advanced format, it contains the header and the body, see below:

EXAMPLE: Click here to download an example of genetic variant overlay, to have an insight on the file’s content. You can also upload it to Parkinson’s disease map.

Upload Choose the dataset to upload and press the Upload button. You will be notified by email when your overlay is ready. The email will also contain the list of elements in your dataset and the number of elements they colored in the map.

Important reminder:

Submaps tab#

The Submaps tab summarizes all the submaps linked to the main map of this project hosted by your MINERVA instance. See Administrator manual - advanced upload to learn how to upload the submaps together with the main file. The tab Submaps is visible in the left panel only if the map contains at least one submap. The tab contains names of the submaps, + to show maps’ description, if one is provided, and the buttons to display them.

Submaps{:width=“900px”}

The submaps show as a pop-up window on top of the main map, and are synchronized with respect to search queries and displaying data overlays. This means that search results and search pins will be visible in the main map and the active submaps. Similarly, overlays are mirrored in the submaps. Also, on the main map there is an icon informing that search results hit submap. See figures below:

Submaps search results{:width=“900px”}

Submaps2{:width=“900px”}

Info tab#

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

Project info#

Displays name, version and the details of the map.

The Data section features the links to:

The Description section contains information from the CellDesigner file from Model Notes and Model Description (if provided).

Export#

The Export page contains three tabs (Elements, Network and Graphics), allowing to download the map contents in different formats.

User data#

If registered, users can login here, or request for an account from the administrators of this MINERVA instance. Platform administrators can register new users (see Administrator’s manual - USERS) and configure Request an account functionality (see Administrator’s 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 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 helping to understand the underlying map, 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:

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 Add comment).

Legend#

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

PLUGINS#

Plugins allow for creating client-side custom visualizations, independent from the core functionalities of MINERVA. After clicking on the plugin icon a popup window becomes available (see images below).

Plugins icon{:width=“400px”}

Plugins dialog{:width=“600px”}

The user can choose any of the plugins that are available on the MINERVA platform, uploaded on the instance by the admin. Also, in the URL field one can supply a URL to the plugin, written in JavaScript. To learn how to write your own plugins, visit the “Plugin starter kit” repository.

Example plugin: you can upload below URL into the plugin dialog to find out more:

https://raw.githubusercontent.com/davidhoksza/minerva-plugins-starter-kit/master/dist/plugin.js

Afterwards, a plugin panel becomes available on the right (see image below). To close that panel, click the plugin icon to open the window and click Unload button.

Plugins panel{:width=“900px”}

Please find below the list of available plugins, click at plugin’s name for its details.

— |
Name of the plugin | Address URL and the short description of the plugin |
Disease variants associations | https://minerva-dev.lcsb.uni.lu/plugins/disease-associations/plugin.js |
  | Provide the information about genes associated with the given disease in the context of the selected disease map. |
Drug reactions | https://minerva-dev.lcsb.uni.lu/plugins/drug-reactions/plugin.js |
  | Explore the adverse reactions of the drugs which are interacting with the presented entities in a disease map. |
Exploration | https://minerva-dev.lcsb.uni.lu/plugins/exploration/plugin.js |
  | Enhance the visualization and exploration of molecular interaction in the map. |
Guide | https://minerva-dev.lcsb.uni.lu/plugins/guide/plugin.js |
  | Provide the introductory guide through various aspects of the MINERVA platform. |
GSEA | https://minerva-dev.lcsb.uni.lu/plugins/gsea/plugin.js |
  | Calculate the enrichment of the elements from the selected overlay in the pathway. |

This documentation does not correspond to the latest official release of MINERVA (v19.0).
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