This is a previous version of the manual » v12 || Go to

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

  • Display area (1): where the contents of the projects are visualized.
  • Functional area (2): allowing for advanced interaction with explored content.
  • Information bar (3): containing additional overlay functions.
  • Admin login and Plugins (4): allowing administrator login. To login as user go to Overlays or Info tab.
    Plugins are set of methods allowing to store some data for plugin infrastructure.

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 or Open Layers Library (depending on user preferences). It 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 - the layouts 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 tab).

Basic exploration tools

Right-click in the display area invokes a contextual menu (see below), which allows to annotate, select or download displayed area and also visualize the proteins’ structure.

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).

Pinned comment

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 and Open Layers Library, allowing to select an arbitrary shape in the display area. The shape then can be downloaded in various formats, either as a map (.xml file) or as an image (see below).

Select mode

  • Export as image produces a rectangular image containing the selection. Export to vector and raster graphics is supported, allowing to modify and enhance the downloaded image.

  • Export as map produces a file acceptable by either CellDesigner or pure SBGN editors, containing the editable fragment of the selected display area. Importantly, in the case of CellDesigner export, all additional annotations provided by MINERVA platform are downloaded as well.

Export as image

This option creates an image of the part of map on your display area. Export to vector 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 containing the editable fragment of the selected display area. Importantly, in the case of CellDesigner export, all additional annotations provided by MINERVA platform are downloaded as well.

Open MolArt

This option is active only for protein annotated with UniProt ID (see image below). MolArt (MOLeculAR structure annoTator) is a JavaScript tool and library. It assists users in the visualization of sequence-related annotations over available experimental or predicted structures (click here for MolArt documentation). Select mode


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

Select mode


Content curation

MiNERVA framework handles SBGN-compliant format and SBML format - these two are externally curated content which MINERVA relies on. In case of SBML format it is essential to modify the file before the upload to MINERVA.

SBGN-compliant format

MINERVA handles SBGN-compliant format produced either by CellDesigner (click) or SBGN editors, like SBGN-ED (click). 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:

  • Processing of existing annotations: annotations to elements or interactions embedded within CellDesigner file (MIRIAM > Add relation) are automatically parsed and processed. They can be used to extensively annotate elements (see Admin manual - Configure automatic annotation) and they can be verified by MINERVA platform against a set of predefined content-governing rules (see Admin manual - Configure automatic verification).
  • Procedural generation of semantic zoom : information on complexes and overlaying compartments is extracted from SBGN-compliant files to generate Pathways and compartments view, where on the high level of zoom bigger compartments overlay smaller ones, and on the middle levels of zoom contents of complexes are masked. Moreover, in CellDesigner, TextArea elements can be used to draw named rectangles covering functionally important areas. These will be incorporated into the generation of the semantic zoom as well. For this, you will need to create an additional area by:
    • clicking Edit > Add layer
    • enabling Layer toolbox by checking View > Change toolbar visible > Layer
    • drawing TextArea objects using a corresponding button
  • Cross-platform SBGN translation: CellDesigner files can be uploaded to be displayed in pure SBGN notation (see Admin manual - Fields of the Add project window), and SBGN-displayed content can be downloaded as a pure SBGN file.

For explanation and examples on content curation and annotation, see Example 01 - CellDesigner file upload and annotation.

SBML format

SBML file contains text information about elements, reactions and annotations. MINERVA takes annotations from SBML file as the inputs and transforms them to element/interaction annotations which can be displayed in the map. Use of SBOTerms is necessary to determine the type of elements/interactions. Moreover, SBOTerms must be inputted into the SBML file by user manually. Without updating SBML file on SBOTerms, all elements are displayed on map as small molecules and all reactions are represented by state transitions.
See here the list of CellDesigner types matching SBOTerms.

For explanation on modifying SBML file, see Example 02 - SBML file modifications.


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, such as: full name of element, symbols annotations and their source (automatic or manual), 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:

  • Search field: Type your search query here, separating multiple elements with a semicolon ‘;’. Searches for separate terms will be visible in separate tabs. Search will look for similar names and synonyms of elements in the map.
    You can also search for an identifier of an interaction. (It is described by a number, to be found on the left panel after choosing a particular reaction you are interested in.) To do this, you need to add reaction: prefix to the searched identifier, e.g. for a reaction with and id “re944” you will search for a term “reaction: re944” (see below).

Select mode


The reaction results are supported with information about reaction kinetics. It is available after clicking on chosen reaction in the display area. Select mode

The search pins indicate hits in the display area. Similar search results are merged (marked with the same number). Also, for multiple elements search, the results have different color and shape icons (see image below) which are clickable and show information in popup window. In case of searching for different targets (i. e. generic target and drug target) the overlaying results are highlighted with different icon. The same icon on main map informs that searching results hit in the submap. See more in Submaps tab.
Select mode


  • Perfect match tick box: If this box is ticked, terms with an exact match to the query will be returned. In the case of large networks or broad queries the search results may be capped to ensure the performance of the system. The limit of displaying search results can be configured via the Admin view (see Admin manual - Configuration).

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. 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.

  • Search field: type your search query here, separating multiple drug names or their brand names with a semicolon ‘;’. DrugBank (click) and ChEMBL (click) will be queried for known targets to be displayed in the map.
  • Drug description, synonyms and all known targets will be displayed in the left panel.

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. 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.

  • Search field: type your search query here, separating multiple chemical names or their synonyms with a semicolon ‘;’. Clinical Toxicogenomics Database (click) will be queried for known targets to be displayed in the map.
  • Drug description, synonyms and all known targets will be displayed in the left panel.

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. 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.

  • Search field: type your search query here, separating multiple miRNAs with a semicolon ‘;’. miRTarBase (click) will be queried for known targets to be displayed in the map. Use only mature sequence IDs according to miRBase (click) (e.g., hsa-miR-125a-3p)
  • known targets will be displayed in the left panel.


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).

  • View column allows to
    • Change to viewing mode (click the magnifying glass icon) allowing to switch between
      • Pathways and compartments (hierarchically masked content)
      • Network (only colored network structure shown)
      • Empty (only network structure, no coloring, recommended for data display)
    • Display multiple overlays (tick chosen boxes) - choosing that option automatically turns the viewing mode to Empty to emphasize the overlay’s colors
    • Data column contains buttons, where applicable, allowing to download the dataset used to generate the overlay. Hover over the button to display a short description of the dataset, if provided on upload

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

Overlays


In the figure above:

  • General overlays are overlays accessible for every user viewing the content
  • User-provided overlays menu becomes available upon login (see below)

Overlays2


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

  • List of uploaded overlays containing
    • View column with buttons enabling switching between User-provided overlays
    • Data column with buttons allowing the user to download the dataset used to generate the overlay. The users have access only to their respective datasets.
    • Edit column with buttons allowing the user to provide description to the uploaded datasets.

    Reordering user-provided overlays list is available - drag and drop particular one to change its order.

  • Add overlay button invoking the dialog window with the following components
    • Name field for the new overlay
    • Description: description of the dataset
    • Upload file - Choose file button to select a file with overlay data
    • List of elements field - instead of providing an overlay file, the user can provide a list of named elements to highlight in the map (e.g. list of genes)
    • Google Maps API terms of use checkbox
    • Upload button to generate the user-define


Upload user-provided overlay data

Format

For examples of basic and advanced data upload, see Example 03 - 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.

  • Name column contains the names of elements to be colored
  • Value column contains the values normalized to [-1,1] range.

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:

  • Version # VERSION=xyz - a version of this custom overlay
  • Name # NAME=xyz - a name that will be automatically assigned upon upload
  • Description # DESCRIPTION=xyz - a description that will be automatically assigned upon upload

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

  • Name, Value - same as in basic overlay
  • Compartment - name of a compartment in which coloring should take place
    Warning! Coloring compartments works ONLY for separate (not nested) compartments. Setting a color for elements in a compartment that encloses other compartments sets the color in the nested compartments as well.
  • ChEBI - ChEBI identifiers of elements to be colored
  • Entrez gene - Entrez identifiers of elements to be colored
  • Gene ontology - Gene Ontology identifiers of elements to be colored
  • Ensembl - Ensembl identifiers of elements to be colored
  • HGNC symbol - HGNC symbols of elements to be colored
  • UniProt - UniProt identifiers of elements to be colored
  • ReactionIdentifier - ID of interaction to be colored (interactions coloring only)
  • LineWidth - lineWidth of the colored interaction (interactions coloring only)
  • Color - color of the colored element.

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:

  • The number of available overlays is configured in the Admin view (see Admin manual - Users)
  • The number of available overlays is common for all projects hosted on your MINERVA instance. If a user is registered in a number of projects and uploads custom datasets in all of them, the global number of available custom overlays will be reduced with each uploaded overlay.

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 tab Submaps is visible in the left panel, only if the map contains any submap.

The Submaps tab contains the Name column, and the column with the buttons invoking corresponding submaps.


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. Moreover, on the main map there is icon informing that search results hit submap. 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.

  • Elements export tab allows to narrow down and download the list of elements in the hosted networks. Available filters include:
    • Type - filters the exported elements by the SBGN-compliant type
    • Columns - filters the contents of exported file by selecting, which columns should be included (see below).
      • Name - name of the element
      • Compartment - compartment containing the element
      • Component - CellDesigner specific, TextArea covering the element, see also Section Content curation
      • Type - SBGN type of the element
      • Id - identifier in the system
      • Parent complex - complex element containing this element
    • Submodel - name of the subnetwork containing this element
    • Annotations - filters the annotations of elements in the downloaded file; by default all annotation types are considered
    • Included/excluded compartments - filters the elements by compartments they are in; by default all compartments are considered as “included”, none as “excluded”.
  • Network export tab allows to narrow down and download the interactions in the hosted networks. Importantly, the exported network file is not a fixed-column table. As interactions are in fact hyperedges, each line may contain different number of reactants, products and identifiers. Available filters include:
    • Nodes - filters the nodes of exported interactions by the SBGN-compliant type
    • Annotations - filters the annotations of elements and interactions in the downloaded file; by default all annotation types are considered
    • Included/excluded compartments - filters the elements by compartments they are in; by default all compartments are considered as “included”, none as “excluded”.
  • Graphics export tab allows to download graphics of the map in the SVG format.

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 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 underlying 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:

  • another static image to be displayed next
  • a defined area in the displayed content
  • a set of elements or interactions.

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.

Admin login

Options available in top left corner of the map. Padlock shape icon allowing administrator login or request for an account. To login as user go to Overlays or Info tab.

Plugins

Plugins allow for creating client-side custom visualizations, independent from the core functionalities of MINERVA. After clicking on the plugin icon (see image below) a popup window becomes available. Plugins
In the URL field one needs to supply a URL to the plugin, written in JavaScript. To learn how to write your own plugins, visit the “Plugin starter kit” repository here

For example, you can use a link for an example plugin:
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, go to plugin icon and click Unload button.

Plugins panel

Exploration plugin

Exploration plugin is a particular plugin providing more focused way of molecular interaction network exploration than a default searching, zooming and panning provided by MINERVA.
It is a helpful tool in case a user wants to explore a neighbourhood of a molecule appearing multiple times in a network in different compartments or context. In large networks certain entities need to be duplicated to obtain more readable layout or the entity might be very prevalent and significant in different pathways (e.g. “regular” searching for SNCA gives more than 100 results in different compartments, involved in various roles in different processes).

With the exploration plugin, the user can:

  • See in which (sub)maps an interacting partners of the EOI are present
  • See in which cell’s compartments interacting partners of the EOI are present
  • Iterative exploration of partners’ neighbourhood in given compartment (localized exploration)
  • Restrict types of interacting partners
  • Highlight identified interactions in the map
  • Locate interacting entities in the map
  • Trace back list of interactions to the EOI
  • Search for entities or reaction type by keyword
  • Export the current state of the exploration


Start the plugin

Entering the below address in the plugin URL box to start:
https://minerva-dev.lcsb.uni.lu/plugins/exploration/plugin.js

To start the exploration, choose a bioentity neighbourhood to explore. We call this bioentity entity of interest - EOI and here we use PRKN gene as EOI example. You can click on particular element in the map or by search for it using the search box. Note that the color of Explore button in the top left corner of the plugin turns to dark green after selecting bioentity and shows its name when hovering over it. Clicking on Explore button creates a node representing the chosen entity on the canvas.

The adjacent buttons, next to the Explore, allow on (from left):

  • Turn on/off map focus by hovering on the tree elements
  • Restart exploration
  • Choose settings of plugin
  • See the manual

By left clicking the initial node (in our example PRKN), the plugin connects to the server and obtains all the entities which are connected to it by any reactions. Please note, that only elements of the selected types (see section Settings below) are visible. The retrieved entities are then visualized as a tree by grouping them firstly by (sub)map and secondly by compartment they reside in. The (sub)map nodes are represented by gray diamond symbols and compartments by gray rectangles with rounded edges. Note that the visualization can be pan and zoom by click and drag or zoom in/out.

The tree in this stage thus has four levels:

  1. The root representing all instances of the the EOI anywhere in the map (including submaps).
  2. The (sub)maps in which the EOI connects by a reaction to any entity (of the selected type).
  3. The compartments in given (sub)map in which the EOI connects by a reaction to any entity (of the selected type).
  4. The entities (of the selected type) connected by a reaction to the EOI. The arrow head connecting the compartment node with the entity node specifies the type of relation of the two connected entities (see below Graphical Symbols for details). If given (sub)map and compartment contain multiple times a pair of entities connected by the same type of reaction in the same role, this pair will be shown only once. But, the information about it can be obtained by hovering over the target (right hand side) node which reveals information on all bioentities represented by that particular node.

Exploration_Plugins1


By left clicking any of the inner nodes, the corresponding subtree gets folded or unfolded making more space for the rest of the nodes.

Exploration_Plugins1Plugins2


By left clicking on a leaf entity node, the plugin connects again to the server and retrieves all bioentities connected to it by a reaction and shows them grouped by compartment.
If there is no connected entity which has not been encountered yet, the node changes to empty node (no color filled).

Please note that here only neighbours connected to the bioentities represented by that specific node are shown. E.g. if a node represents gene G in a compartment C only neighbours of gene G in C are shown irrespective whether G appears also in other compartment D. That is, unlike at the root level, the exploration is restricted to a specific position in the map - localized exploration.

Exploration_Plugins3

Searching

The exploration plugin offers search functionality for entities or reaction types containing entered keyword. The two search boxes are located at the bottom in plugin panel. The non-matched entities become transparent thus highlighting the matched entities and the entities from the roots of the respective trees to the matched entities. See below an example of searching for PINK.

Exploration_Plugins4

Additional features - right click

If you right click on any entity pop up with menu shows, containing four options described below:

  • Spawn new root
  • Locate
  • Locate subtree
  • Backtrack


Spawning multiple trees

To check what are neighbours of an encountered bioentity anywhere in the map, i.e. go from local exploration to global exploration, right click on that node and choose Spawn new root. With this operation a new independent root is spawned and this root node again represent all instances of given bioentity anywhere in the map and submaps. Any node in the previous tree which matches the new root is highlighted by thick black circle around that node.

The spawned trees are tracked by rectangular buttons in the upper part of the visualization. Clicking on any of those, positions the view so that it is centred on the root of the respective tree.

A tree can be removed by right clicking on the root of a node and selecting Remove root. This operation removes not only the respective tree, but also all the following trees since those were spawned from the tree being removed which is not valid any more.

Exploration_Plugins5


Locate - interaction with the map

All bioentities represented by the nodes in the visualization are highlighted in the map. This also holds for all reactions which connect an entity to its predecessor in the exploration. Specifically, the EOI is highlighted by an icon while all other entities and reactions are highlighted by color overlay.

The highlighted parts of the map can be either explored by panning and zooming, but the user can also right click on any node in an exploration tree and select Locate which takes to the corresponding position in the map. By choosing Locate subtree, which is available for non-leaf nodes, one can focus on a part of the map covering all the nodes in the subtree rooted in the respective node.
The locating function can be turned on by default by clicking the bulls eye icon in the upper part of the plugin. If turned on, then every time a user hovers over a node, the corresponding entities will be located in the map.


Backtracking

It might be difficult to see in the map the sequence of reactions which connect certain bioentity with the EOI, especially when multiple roots were spawned. If that is the case, one can right click on any node and select Backtrack. This will highlight all paths from the selected node to the root of the first tree (if the backtrack depth is not specified - see Settings). The path will also be highlighted in the map, temporarily turning off other highlights created by the plugin.
Backtracking will result in multiple paths in situations when the root of one tree corresponds to multiple bioentities in the previous tree.
The backtrack paths can be turned of by right clicking on the node from which the last backtrack was started and selecting Clear backtrack.

Exploration_Plugins6

Export

The export button is located in the lower right corner of the plugin. All currently visible elements in the visualization can be exported either to a CSV or JSON file by clicking on Export button. Please note that the data are hierarchical and therefore the JSON format is more suitable for storing the data. If there are multiple spawned trees, they are all exported and separated by an empty line in the resulting CSV.

Graphical symbols

To distinguish different types of information in the visualization, the exploration plugin uses different graphical symbols for nodes and lines arrow heads.

  • Nodes
    There are three types of nodes:
    • Circles represent bioentities nodes and their color correspond to the exploration tree they appear in. If the the sphere has no fill color, there are no neighbours to explore (all appear in the path from that node to the root of the respective tree)
    • Gray rectangles with rounded corners represent compartment nodes
    • Gray diamonds correspond to (sub)maps nodes
  • Lines
    Lines differ by their arrow heads which represent what is the role of the two connected entities in a reaction. The arrow head can be either circle, arrow, or vertical bar depending on the reaction type and role of the right hand side entity (target). The mapping is as follows:
    • circle: the target modulates the reaction
    • vertical bar: the reaction types is one of Inhibition, Unknown inhibition, Negative influence, Unknown negative influence
    • arrow: the remaining reaction types

    The direction of the arrow/position of the vertical bar determines the reactant/product role of the target. If the arrow goes from left to right or the vertical bar is on the right hand side of the head, the target is a product and otherwise it is a reactant. This does not apply to the circle symbol since modulation is not directional.

Settings

The exploration plugin has several settings which can impact the exploration process. These settings can be accessed by clicking on the Settings button in the upper part of the plugin:

  • Species types: the user can select which types of bioentities will be considered during the exploration. Changing this does not impact the existing exploration state. Thus, for this change to take effect, one needs to restart the exploration (either by clicking on the restart or Explore button)
  • Locate on expansion: if checked, when a node is expanded, the newly shown nodes are located in the map
  • Backtrack depth: If set, the backtracking procedure will go only given number of levels back
  • Highlight by icon/surface: sets the way of how encountered entities are highlighted in the map