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---
layout: page
title: Minerva
index: minerva:Miverva Title
type: project
nav: userguide:User Guide,userguide2:User Guide 2
---

#### Licensing:

What type of license? What about Google Maps API license?

#### Debian package description:

MINERVA (**M**olecular **I**nteraction **NE**two**R**k **V**isu**A**lization) platform is a standalone webserver for visualization, exploration and management of molecular networks encoded in SBGN-compliant format. After installation, the resource is used and managed via a webbrowser, under the address configured …

CellDesigner ([www.sbi.jp/celldesigner](https://www.google.com/url?q=http://www.sbi.jp/celldesigner&sa=D&usg=AFQjCNEtBcIj5pBHUw2BzRNJK25zhsdT2g))
or SBGN (webref?) format files are accepted. Please, consult the user guide (webref?) for more details.

> DISCLAIMER: to be written up




#### man minerva description:

<dl class="dl-horizontal">
<dt>NAME</dt>
<dd>minerva - a webserver for <b>m</b>olecular <b>i</b>nteraction <b>ne</b>two<b>r</b>k<b>v</b>isu<b>a</b>lization</dd>

<dt>SYNOPSIS</dt>
<dd>mode of use needed</dd>

<dt>DESCRIPTION</dt>
<dd>as above</dd>

<dt>DISCLAIMER</dt>
<dd>as above</dd>

<dt>PARAMETERS</dt>
<dd>mode of use needed</dd>

<dt>OPTIONS</dt>
<dd>mode of use needed</dd>
<dt></dt><dd>start</dd>
<dt></dt><dd>stop</dd>
<dt></dt><dd>restore</dd>
<dt></dt><dd>etc ...</dd>

<dt>NOTES</dt>

<dt>SEE ALSO</dt>
<dd>javac, java, ... </dd>

</dl>


# 1. Introduction

MINERVA (**M**olecular **I**nteraction **NE**two**R**k **V**isu**A**lization)  platform is a standalone
webserver for visualization, exploration and management of molecular networks encoded in SBGN-compliant format (See **Appendix 6.1 source file**).

> Copy from Implementation part of the MINERVA article here.

Visualization of uploaded networks, generated by the platform, is accessible via a web browser to all viewers with the
weblink to the resource. See **Section 4. User panel** for a description of functionalities available in the map.

# 2. Installation

> …

# 3. Administrator view

Administrator view refers to the set of functionalities for web-based management of the content and configuration of your MINERVA instance.

## 3.1. Login
Administrator view is accessible via the “ADMIN” button in the bottom left corner of the user view (see below). See also **Section 4 User view**.

![Login view](images/image22.png){:width="800px"}


Many projects (maps, networks) can be hosted in parallel on a single MINERVA instance (see <b>Section 4.1.1 Accessing the project**).
and a user having administrator rights to at least one of them can log via “ADMIN”. After successful login (see below),
you will have access to the administrator panel to manage your MINERVA instance.

![Successful login](images/image30.png){:width="800px"}

## 3.2. Comments
This panel allows you to manage comments provided by users of your maps (see <b>Section 4.x User panel - Comments**).
The panel to the right (<em>Projects</em>) allows you to switch between different maps.
Current active map will be highlighted. For the current active map, comments will be displayed in the panel to the left.
The field “Title” is a hyperlink to a given comment in the map.

![Comments](images/image24.png){:width="800px"}


Users logged in as administrators have a possibility to remove a comment, as for them an additional button is visible
on the comment pop-up (see below, 1). You can provide a comment associated with the removed comment (see below, 2)
and press the “Remove” button (see below, 3).

![Remove Comments](images/image17.png){:width="800px"}


The removed comment will no longer be visible among the pinned comments, and its status will be updated in the
“Comments” panel (see below).

![Removed Comment status](images/image07.png){:width="800px"}


## 3.3. Map manager

This panel allows you to add new projects and manage existing ones. In the top left corner, the name of current active
project is displayed. The panel allows you to (1) add new projects (2) edit them and (3) examine messages generated
during the upload of the project.

![Map manager](images/image02.png){:width="800px"}


### 3.3.1. Add project

The “ADD PROJECT” button invokes a menu allowing you to upload your project and start its generation in the MINERVA platform.

![Add project](images/image23.png){:width="800px"}

#### 3.3.1.1. Fields of the “ADD PROJECT” window

* File - Choose button: invokes a file upload dialog. For a quick start, CellDesigner files are accepted directly. Available options and configurations of the source file are discussed in <b>Section 6.1 Abppendix - Source file**.

* ProjectId: a working name of the uploaded project on the MINERVA platform

* Project name: the name of the uploaded project displayed in the top left corner of the Admin and User panels; your official name of the project

* Complex: this section describes how main map and uploaded submaps (if any) are related. For more details on how to
upload predefined layouts, data mining datasets, images with biological overview and submaps associated with the main
 map, see <b>Appendix 6.1 Source file**.
Ignore it if you submit a single file.
    * <em>Filename</em>: name of one of multiple files
    * <em>Name/em>: name of the main map, or a submap, in the project
    * <em>Root model/em>: a column of checkboxes; only one position must be checked, corresponding to the main map in the project
    * <em>Mapping file/em>: a column of checkboxes; only one position must be checked, corresponding to the mapping file
    describing relationships between the main map and the submap(s)
    * <em>Model type/em>: whether the submap is a pathway, or a list of downstream targets; currently in development and unused
    * <em>File type/em>:  type of the uploaded file; recognized automatically.
* Additional layouts: this section describes uploaded additional layouts (element and interaction colorings) to be
generated and accessible for all users of the project via “Layouts” tab in the “User panel”.
Ignore it if you submit a single file.
    * <em>Filename</em>: name of one of custom layout files
    * <em>Name</em>: name of the layout visible in the project
    * <em>Description</em>: the text to appear after mouseover on the name of the layout.    
* Data mining: this section describes data mining candidates uploaded for the project. Ignore it if you submit a single file.
    * <em>Filename</em>: name of one of data mining files
    * <em>Name</em>: name of the resource visible in the project
    * <em>Source</em>: (optional) weblink to the source of the data mining set
    * <em>Type</em>: currently in development and unused
* Overview images: this section describes the uploaded overview images and their configuration file. It is a column of
filenames. Ignore it if you submit a single file.
* Version: a text field displayed next to the name of your project in the “User panel”.
* Annotate model automatically: if this checkbox is checked, elements of the uploaded map will be automatically annotated using built in annotators.
Behavior of the annotators can be configured by clicking the “Advanced” button (see <b>Section 3.3.1.1 Configure automatic annotation**).
* Verify manuel annotations: if this checkbox is checked, elements and interactions of the uploaded map will be scanned
for existing annotations; if present these existing annotations will be validated against a set of rules.
Verification rules can be configured by clicking the “Advanced” button (see <b>Section 3.3.1.2 Verify manual annotations**).
* Cache data: if this checkbox is checked, all hyperlinks in the project resolved by MIRIAM repository
(e.g. cross-links to external bioinformatic databases) are resolved and cached.
* Auto margin: if this checkbox is checked, upon generation of the graphics, empty spaces surrounding elements and interactions will be cropped
* Display SBGN: if this checkbox is checked, the uploaded model will be displayed in SBGN format,
instead of default CellDesigner format.

#### 3.3.1.2. Configure automatic annotation
The “Advanced” button, next to the “Annotate model automatically” checkbox under “ADD PROJECT” button, invokes a dedicated configuration window (see below).

![Configuration window](images/image19.png){:width="800px"}

Clicking on each element type (“Object annotators”) in the left panel, an annotator can be assigned in the right panel
that will attempt to automatically retrieve information from external bioinformatic databases for each relevant element,
and annotate them. There are a number annotators available, utilizing either the name, or existing identifier of an object.
These are:
<dl class="dl-horizontal">

<dt>Biocompendium</dt>
<dd>name of an element will be used to retrieve additional information, including: full name, symbols, description and identifiers:
RefSeq, ENSEMBL, Entrez Gene identifier, HGNC symbol, KEGG, Reactome, Pubmed and others</dd>

<dt>HGNC</dt>
<dd>HGNC identifier, if present, or, if absent, name of an element will be used to retrieve additional information,
including full name, symbols, description and identifiers: RefSeq, ENSEMBL and Entrez Gene identifier</dd>

<dt>Uniprot:</dt>
<dd>Uniprot identifier, if present, will be used to retrieve additional information, including HGNC symbol and identifier, and Entrez Gene identifier</dd>

<dt>Entrez Gene</dt>
<dd>Entrez Gene identifier, if present, will be used to retrieve additional information, including full name, synonyms,
description, HGNC symbol and identifier, and ENSEMBL identifier</dd>

<dt>ENSEMBL:</dt>
<dd>ENSEMBL identifier, if present, will be used to retrieve additional information, including symbol, full name, synonyms,
HGNC symbol and identifier, and Entrez Gene identifier</dd>

<dt>ChEBI:</dt>
<dd>Uniprot identifier, if present, will be used to retrieve additional information, including synonyms, parents and
children in the ChEBI ontology tree</dd>

<dt>Gene Ontology</dt>
<dd>Uniprot identifier, if present, will be used to retrieve additional information, including full GO definition for
this identifier.</dd>

</dl>

#### 3.3.1.3. Configure automatic verification
The “Advanced” button, next to the “Verify manual annotations” checkbox under “ADD PROJECT” button, invokes a dedicated configuration window (see below).


![Configuration window](images/image26.png){:width="800px"}

Clicking on each element or interaction type (“Classes”) in the left panel:
<dl class="dl-horizontal">
<dt>top right panels</dt>
<dd>a list of valid MIRIAM identifiers can be assigned. All elements or interactions in the uploaded model, annotated
with an identifier outside of the “Valid” list will be flagged as warnings</dd>

<dt>bottom rb panels</dt>
<dd>a list of mandatory MIRIAM identifiers can be assigned. If checkbox “Require annotations” is checked, all elements
or interactions in the uploaded model, annotated without at least one identifier marked as “Required” list will be
flagged as warnings.</dd>
</dl>

#### 3.3.1.4. “Submit” button: project generation
Clicking “Submit” button at the bottom of the “ADD PROJECT” dialog window will start generation of the project.
The window will refresh automatically, showing status changes during the process. Any warnings raised during the process
will cause an “exclamation mark” icon to appear next to the project status. The list of warnings is extended gradually,
and you need to wait for the project completion to see the full list. You will receive an email notification after the
generation is complete.

It may happen that the project generation will result in a failure. An icon will be displayed, and a mouseover on it
will display the reason for failure. Moreover, you will receive an email message detailing the error you have received.

### 3.3.2. Edit project

![Edit project](images/image02.png){:width="800px"}

Clicking on the magnifying glass icon in the last column with the project parameters (see above, 2) will invoke a dialog
window to modify the configuration of a generated project (see below)

<b>General** is the first configuration tab, allowing edition of basic information about the project.
Using “Remove” button you can permanently delete the current active project.

![General tab](images/image03.png){:width="800px"}

<b>Layouts** tab allows you to examine and manage layouts (custom colorings of elements and interactions) in the current
project (see below). Layouts accessible for all users are marked as N/A in the “Owner” column. Below, you can examine
layouts generated by other users. If you have appropriate privileges (see <b>Section 3.4 User manager**), you can remove
generated layouts by pressing a respective button in the “Remove” column.
<div class="alert alert-danger">Removed layouts cannot be restored.</div>

![Layout tab](images/image15.png){:width="800px"}

<b>Data mining** tab allows you to examine and manage data mining files uploaded for the project (see below).
Using buttons in the “Data” column you can download respective datasets.

![Data mining tab](images/image05.png){:width="800px"}

<b>Users** tab provides a project-level overview of access and management rights of users registered on the platform
(see below). First two columns (“Drug targeting advanced view” and “Edit suggested connections”) concern functionalities
under development, they are currently not supported.
Remaining columns (“Manage comments”, “Manage layouts” and “View project”) correspond to respective user privileges are
discussed in detail in <b>Section 3.4 User manager**).

![User tab](images/image00.png){:width="800px"}

### 3.3.3. Examine warnings

![Warnings](images/image02.png){:width="800px"}

Clicking on the “exclamation mark” icon (if present) next to the project status description (see above, 3) will display
the list of warnings raised during the generation of this project (see below).

![Warnings list](images/image10.png){:width="800px"}


The list can also be downloaded as a tab-delimited text file. Types and identifiers of the elements and interactions are
listed in the left column (“No”), while the nature of an error is provided in the right column.
The table below lists possible errors and their explanations:




<table class="table table-striped">
<tr>
    <th>Warning type</th>
    <th>Explanation</th>
</tr>
<tr> <td colspan="2" class="info">Warnings generated by automatic annotation</td></tr>
<tr>
    <td>[Annotator] annotation problem</td>
    <td>[Annotator] (e.g. HGNC) could not retrieve correct information for this element or interaction. The probable reason is wrong manual annotation, or name, of this element or interaction</td>
</tr>
<tr>
    <td>Cannot find information for element.</td>
    <td>None of the assigned annotators were able to retrieve information for this element or interaction. The probable reason is wrong manual annotation, or name, of this element or interaction</td>
</tr>
<tr>
    <td>Chemical name cannot be found in chebi: [name]</td>
    <td>ChEBI annotator could not annotate the element or interaction correctly by name, as [name] is not a ChEBI-recognized name. The annotation by manually provided identifier may still be successful.</td>
</tr>
<tr>
    <td>Former symbols list different than default [list]. Ignoring</td>
    <td>Existing annotation of an element (list of symbols) is different than the [list] retrieved by one of the assigned annotators.</td>
</tr>
<tr>
    <td>New full name different than default [full name]. Ignoring.</td>
    <td>Existing annotation of an element (full name) is different than the [full name] retrieved by one of the assigned annotators.</td>
</tr>
<tr>
    <td>New symbol different than default [symbol]. Ignoring.</td>
    <td>Existing annotation of an element (symbol) is different than the [symbol] retrieved by one of the assigned annotators.</td>
</tr>
<tr>
    <td>Synonyms list different than default [list]. Ignoring.</td>
    <td>Existing annotation of an element (list of synonyms) is different than the [list] retrieved by one of the assigned annotators.</td>
</tr>
<tr> <td colspan="2" class="info">Warnings generated by verification of manual annotation</td></tr>
<tr>
    <td>contains invalid annotations:[annotation]</td>
    <td>Configuration in “Validate manual annotations” did not foresee [annotation] as allowed for this element or interaction.</td>
</tr>
<tr>
    <td>misses one of the following annotations:[list].</td>
    <td>Configuration in “Validate manual annotations” required one of [list] of annotations for this element or interaction, but none was found.</td>
</tr>
<tr>
    <td>misses annotations.</td>
    <td>No annotation exists for this element or interaction. </td>
</tr>
<tr>
    <td>Unknown miriam uri: [MIRIAM type]</td>
    <td>An element or interaction was annotated with [MIRIAM type] - this type of identifier is currently not handled.</td>
</tr>

</table>


## 3.4. User manager
This panel allows you to manage users registered for a given instance of MINERVA platform (see below).

![User manager](images/image20.png){:width="800px"}

Registered users have access to additional functionalities besides accessing the visual content generated by the platform.
Clicking on the “New user” button (above, 1) invokes the window allowing to set login, password and personal details of
a new user. The window allows to set privileges of the new user. For a detailed explanation, see below.

![User detail](images/image27.png){:width="800px"}

Clicking on the magnifying glass icon (“User manager” figure above, 2) invokes a panel, allowing to configure privileges
of a respective user. The panel is identical to the “New user“ window, with the exception of Id and login, which are
assigned and not editable. The panel is shown in the figure below.

![User detail2](images/image08.png){:width="800px"}

The “User detail” window allows to configure the following parameters for a given registered user:

* <b>Password** of the user
* <b>Name**, <b>Surname** and <b>Email** details.
* <b>Global privileges** concern all projects on your MINERVA instance
    * <b>Add project** checkbox, if checked, grants the user access right to the “Add project” button and permits the user to
    add new projects.
    * <b>Custom layouts** field defines how many layouts can be created by a given user across all projects they have access
    to on your instance of MINERVA platform
    * <b>Manage configuration** checkbox, if checked, grants the user access right to access “Configuration” tab and permits
    them to manage the global configuration of your instance of MINERVA platform.
    * <b>Map management** checkbox, if checked, grants the user right to access “Map manager” tab and manage existing projects
    * <b>User management** checkbox, if checked, grants the user right to access the “User manager” tab and permits the user
    to manage users on your instance of MINERVA platform.
* <b>Project-specific privileges** concern only the project, for which they are configured
    * <b>Manage comments** checkbox, if checked, grants the user right to the “Comments” tab, and allows them to manage
    comments for this specific project
    * <b>Manage layouts** checkbox, if checked, grants the user right to manage layouts of all users for this specific project
    * <b>View project** checkbox, if checked, grants the user right to view this specific project
    * <b>Drug targeting advanced view** and <b>Edit suggested connections** are functionalities under development and are not
    supported at the moment
* <b>Remove** button removes this registered user from your instance of MINERVA platform


## 3.5. Service status

“Service status” tab lists all external services and databases cross-linked by MINERVA platform. The left column contains
service name hyperlinked to the original website. The right column contains the status of the service. Clicking on
“Service status” tab invokes a checkup of the services and an update of their status. The checkup may also be invoked
by the “Refresh” button at the bottom of the window. The figure below illustrates the “Service status” tab.

![Service status](images/image11.png){:width="800px"}


## 3.6. Configuration
“Configuration” tab provides a summary of the current version of your MINERVA instance. Moreover, it allows privileged
users to configure global parameters of the MINERVA instance. Clicking “Refresh” button (see below, 1) displays the table
of global parameters, which can be edited set using and “Save” button (see below, 2).

![Configuration 1](images/image29.png){:width="800px"}

![Configuration 2](images/image06.png){:width="800px"}

The list of global MINERVA configuration parameters is displayed in figure above. These are:
* <b>E-mail address** : e-mail address used for sending notifications about the activity of your MINERVA instance
- project uploads, comments, etc.
* <b>E-mail server login**, <b>E-mail server password**, <b>IMAP server** and <b>SMTP server**:
configuration of your mail server for notification sending.
* <b>Default project id**: the project that will be displayed by default under the root address of the platform (your.url/MapViewer/)
* <b>Logo icon**: the filename of your logo icon, displayed in the bottom-right corner of the visualized content.
* <b>Logo link**(after click): the website to which you will be redirected after clicking on the logo
* <b>Max distance for clicking on element (px)**: the content visualized by MINERVA platform is interactive, and
clicked elements or interactions are recognized by the vicinity of the click event. This parameter controls, how close
to an element or interaction, in pixels, you need to click to select them.
* <b>Email used for requesting an account**: the “Login” tab in the user interface features a “Request for an account”
button; clicking the button will auto-generate an message to the e-mail, or list of e-mails separated by a semicolon, provided
in this field
* <b>Max number of results in search box**: it may happen that a “Search” query returns a large amount of results.
This parameter allows to tune the performance of your MINERVA instance by setting the cap for the number of displayed results.
* <b>Google Analytics** tracking ID used for statistics: MINERVA platform offers integration with Google Analytics to
track user activity of your MINERVA instance by providing an appropriate Google Analytics ID in this field.
* <b>Logo description**: the popup text that will be displayed upon mouseover on your logo.

## 3.7. MIRIAM

The “MIRIAM” panel lists all MIRIAM-supported resources
([http://www.ebi.ac.uk/miriam/main/mdb?section=intro]("https://www.google.com/url?q=http://www.ebi.ac.uk/miriam/main/mdb?section%3Dintro&amp;sa=D&amp;usg=AFQjCNHMlAnK0CQlVQA8mLNmnOMeCX57PA))
currently handled by MINERVA platform as shown in the figure below.
In particular:

* <b>Annotation type**: column lists the names of the resources, hyperlinked to the original website
* <b>Miriam identifier**: column lists corresponding MIRIAM identifiers, hyperlinked to their definition in the MIRIAM registry
* <b>Valid for elements**: column provides information, for which records this identifier is configured as “valid”
(see <b>Section 3.3.1.3 Configure automatic verification**)
* <b>Valid uri** column provides information on the correct format of corresponding MIRIAM identifier

![MIRIAM](images/image28.png){:width="800px"}


# 4. User view

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

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

![Main](images/image04.png){:width="800px"}

Main components of this view are

* <b>Display area (1)**: where the contents of the projects are visualized
* <b>Functional area (2)**: allowing for advanced interaction with explored content
* <b>Information bar (3)**: containing additional overlay functions
* <b>Project name(4)**
* <b>Admin/Export bar (5)**: allowing administrator login and advanced export of the contents

### 4.1.1. Accessing the project
Your instance of MINERVA platform can host many projects, which are uploaded via the administrator view
(see <b>Section 3.3.1 Add project). They are accessed by a provided, dedicated web address.


### 4.1.2. 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.
For more details see <b>Section 4.1.3 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 <b>Section 4.2.3 Layouts**).

### 4.1.3. Annotating, selecting and downloading the display area
Right-click in the display area invokes a contextual menu with two options - (see below).

![Annotating](images/image25.png){:width="800px"}

#### 4.1.3.1. 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](images/image13.png){:width="800px"}

“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 <b>Section 4.3.2 Comments**).

![Pinning](images/image16.png){:width="800px"}

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 <b>Section 3.2 Comments**).

#### 4.1.3.2. 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](images/image18.png){:width="800px"}

* <b>Export as model** 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.
* <b>Export as image** produces a rectangular image containing the selection. Export to vector graphics is supported,
allowing to modify and enhance the downloaded image.

### 4.1.4. Content curation
MINERVA framework handles SBGN-compliant format, produced either by CellDesigner ([http://www.celldesigner.org](https://www.google.com/url?q=http://www.celldesigner.org&amp;sa=D&amp;usg=AFQjCNGP8Z97rb6NBjGK4iCG0VamVYBGXg))
) or SGBN editors, like SBGN-ED ([https://immersive-analytics.infotech.monash.edu/vanted/addons/sbgn-ed](https://www.google.com/url?q=https://immersive-analytics.infotech.monash.edu/vanted/addons/sbgn-ed/&amp;sa=D&amp;usg=AFQjCNGKO_7rzfjlKgY0bF4SD6sY-uHS-Q)).
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:

* <b>Processing of existing annotations**: annotations to elements or interactions embedded within CellDesigner file
(MIRIAM &gt; Add relation) are automatically parsed and processed. They can be used to extensively annotate elements
(see <b>Section 3.3.1.2 Configure automatic annotation**).
and they can be verified by MINERVA platform against a set of predefined content-governing rules (see <b>Section 3.3.1.3
Configure automatic verification**).
* <b>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.
* <b>Cross-platform SBGN translation**: CellDesigner files can be uploaded to be displayed in pure SBGN notation
(see <b>3.3.1.1 Fields of the “ADD PROJECT” window**), and SBGN-displayed content can be downloaded as

## 4.2. 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.

### 4.2.1. Search
“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](images/image01.png){:width="800px"}

The panel is used in the following way:

* **Search** field: Type your search query here, separating multiple elements with comma “,”. Search will look for
similar names and synonyms of elements in the map. To search for an identifier of an interaction, you need to add “reaction:”
prefix to the searched identifier. The “search” bubbles indicate hits in the display area. They have different colors for
multiple search items and are clickable, showing information as in the left panel.
* **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 **Section 3.6 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 constructed as follows:

    your.wbrver.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.wbrver.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.wbrver.address/?id=”project id”&amp;search=”search query”


### 4.2.2. 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.

* **Find targets** field: type your search query here, separating multiple drug names with comma “,”. DrugBank and ChEMBL
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.

### 4.2.3. 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).

* **View** column contains buttons (“magnifying glass” icon) allowing to switch to a corresponding layout.
Mouseover over the button displays a short description of the dataset, if provided on upload
* **Data** column contains buttons, where applicable, allowing to download the dataset used to generate the layout.

![Layouts](images/image14.png){:width="800px"}

In the figure above:

* **General layouts** are layouts accessible for every user viewing the content
* **Custom layouts** are user-provided layouts, this menu becomes available upon login (see below).

![Layouts](images/image09.png){:width="800px"}

Custom layouts part contains the following elements (above):
* **List** of uploaded layouts containing
    * **View**  column with buttons enabling switching between custom layouts
    * **Data** column with buttons allowing the user to download the dataset used to generate the layout. The users have access only to their respective datasets.
    * **Edit** column with buttons allowing the user to provide description to the uploaded datasets
* **Adding** section with “Name” field to annotate and “+Choose” button to upload your custom dataset.

#### 4.2.3.1. Upload custom data - format

**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 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:

* **Version** `# VERSION=xyz` - a version of this custom layout
* **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 columns:

* **Name**, **Value** - same as in basic layout
* **Compartment** - name of a compartment in which coloring should take place
* **Chebi** - ChEBI identifiers of elements to be colored
* **Entrez genes** - 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** - Unprot 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.

#### 4.2.3.2. Upload custom data - 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:
* The number of available layouts is configured in the Admin view (see **Section 3.4. User manager**)

* The number of available layouts 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 layouts will be
reduced with each uploaded layout.

![Upload](images/image21.png){:width="800px"}

### 4.2.4. 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 **Section 3.6. 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 4.2.3. Layouts**).

### 4.2.5. 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 **Appendix 6.1 Source file** to learn how to upload the submaps together with the main file.

The “Submaps” tab displays the tab with the “Name” column, and the column with the buttons displaying 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 layouts.
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](images/image31.png){:width="800px"}

![Submaps2](images/image12.png){:width="800px"}


## 4.3. 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.

### 4.3.1. 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:

* 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 **Appendix 6.1 Source file**.

### 4.3.2. 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 4.1.3.1 Add comment**).

### 4.3.3. Legend

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

## 4.4. Export

# 5. Disclaimer

# 6. Appendix

## 6.1. Source file