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Table of contents
- MAIN VIEW
- Basic exploration tools
- Content curation
- FUNCTIONAL AREA
- Search tab
- Overlays tab
- Info tab
- INFORMATION BAR
User view refers to the visualization and functionalities accessed by users of the content hosted by your MINERVA instance.
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You can also see the summary of this page in the MINERVA Quick Reference Guide.
The main view of the MINERVA platform is summarized in the figure below.
Main components of this view are:
(1) Display area where the contents of the projects are visualized.
(2) Functional area allowing for advanced interaction with explored content.
(3) Information bar containing additional overlay functions.
(4) Plugins / Admin login allowing administrator on login and user on upload own plugin.
Note: To login as a user go to Overlays or Info tab.
(2) Functional area allowing for advanced interaction with explored content.
(3) Information bar containing additional overlay functions.
(4) Plugins / Admin login allowing administrator on login and user on upload own plugin.
Note: To login as a user go to Overlays or Info tab.
Accessing the project
Your instance of MINERVA platform can host many projects, which are uploaded via the administrator view(check Administrator’s manual - Add project). The projects 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 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.
Basic exploration tools
Right-click in the display area invokes a contextual menu (see below), which allows to annotate, select and download displayed area and visualize proteins’ structure.
Add comment
This functionality allows to annotate 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.
The field Pinned controls, whether the comment will be visible in the map.
After sending, if the Pinned box was ticked, the comment bubble becomes visible in the display area (see below left). Note that the checkbox Comments located in Information bar must be ticked to make comments visible at all.
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. Note: the end point of the polygon you draw must be the same as the start point. Right click on the selected area allows on remove the selection or download it in various formats, either as a map or an image (see below).
- 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, 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.
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).
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:
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 Administrator’s manual - Configure automatic annotation) and they can be verified by MINERVA platform against a set of predefined content-governing rules (see Administrator’s 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 in CellDesigner by:
- clicking Edit > Add layer
- enabling Layer toolbox by checking View > Change toolbar visible > Layer
- drawing TextArea objects using a corresponding button
Custom semantic zooming (CSZ) allows user to define the semantic zoom levels for any element or compartment. A particular (CSZ) levels are defined in the CellDesigner file, in the field NOTE > Edit Notes of specific element/compartment. To describe CSZ, input in that field the below terms and specify the zoom level value (0, 1, 2…):- SemanticZoomLevelVisibility: zoom_level is used to set up the visibility level for the element or the compartment (e.g. SemanticZoomLevelVisibility: 2 - meaning that on zoom level 2 the element would be displayed on the map)
- TransparencyZoomLevelVisibility: zoom_level to set up the transparency of the compartment (e.g. TransparencyZoomLevelVisibility: 1 - meaning that on zoom level 1 the content of that particular compartment would be revealed of the masking)
The CSZ can be set up for any project during its upload to MINERVA, see: Administrator’s manual - Add new project. - Cross-platform SBGN translation: CellDesigner files can be uploaded to be displayed in pure SBGN notation(see Administrator’s 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.
See here the list of CellDesigner types matching SBOTerms.
For explanation on modifying SBML file, see Example 02 - SBML file modifications.
Functional area (the panel to the left from the display area) displays additional information about selected elements andinteractions, 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: element’s compartment and full name, symbols, annotations and their source (automatic or manual by curator), see below:
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).
The reaction results are supported with information about reaction kinetics. It is available after clicking on chosen reaction in the display area.
The 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 happened to be blank (no number), it would mean that aggregated search results exceed 100.
Moreover, 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 (e.g. 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.
Moreover, 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 (e.g. 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.
- Perfect match tick box: If this box is ticked, terms with an exact match to the query will be returned. In the case oflarge networks or broad queries the search results may be capped to ensure the performance of the system. The limit ofdisplaying search results can be configured via the Admin view (see Administrator’s manual - Configuration).
Direct link to the elements in the display area is possible, as the search query can be provided within the web address ofthe displayed project. An address has to be manually constructed, directly into web browser, as below:
is a link executing the search for a given search query in the default project of your MINERVA instance. For example, an address
will directly point to an interaction with id xyz123. Referring to a given project on your MINERVA instance requiresadditionally to pass the project identifier in the address, as shown below. Identifiers of projects are accessible using the Admin view.
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 willbe 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 willbe 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 willbe 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 the viewing mode and display default multiple overlays:
- Viewing mode is changed by clicking on the magnifying glass icon, allows 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.
- Viewing mode is changed by clicking on the magnifying glass icon, allows to switch between:
- Data column contains buttons, where applicable, allowing to download the dataset used to generate the overlay.
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. Moreover, the popup contains information about Interacting drugs, chemicals and MicroRNA with selected element, available after ticking check box Show all.
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. Moreover, the popup contains information about Interacting drugs, chemicals and MicroRNA with selected element, available after ticking check box Show all.
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)
User-provided overlays table contains overlays uploaded by users. Available overlays can be reordered by name or number. Hover over any of them display short description, if one was provided on upload.
There are two types of overlays the user can provide: generic and genetic variant. Generic overlay displays a coloring of the map data set of indicated molecules (e.g. differentially expressed genes), genetic variant overlay displays a coloring for the genes where the variants are present. It also enables the genome browser popup, displaying the position of a variant in the sequence of the corresponding gene. To upload and correctly display the genomics information your instance must contain reference genomes, uploaded by admin. Also, the Organism type (e.g. 9606) must be provided for the project, and reference genomes uploaded on MINERVA instance must include its type.
The list of user-provided overlays contains columns (image above):
- No number of the overlay
- Name of the overlay
- View column with boxes 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 edit the description to the uploaded datasets
- Add overlay button invoking the dialog window with the following components
- Name field for the new overlay
- Description of the dataset
- Type - field depends on the header of uploaded file - TYPE field. This happens because genetic variant overlays need to have a specific header field. Please, refer to Upload user-provided overlay data for more details.
- 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). If providing generic overlay, choose from TYPE dropdown list GENERIC; if providing genetic variant overlay choose GENETIC_VARIANT. Check how to create a list of elements in Upload user-provided overlay data.
- Google Maps API terms of use checkbox
- Upload button to generate the user-define
The user-provided overlays are displayed identically as default general overlays. The genomics variant overlays additionally contain the genome browser in the popup window, see below image:
The genome browser allows to view the position of a variant in the sequence of the corresponding gene. In Gene variants section (see 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:
- Reference genome - contains reference genomes uploaded into the instance by admin (e.g. hg19, hg38)
- Scale - the scope of base pairs displayed, changed by +/- buttons
- Location - indicates current position in genome
- Genes ref - display the reference genes locus provided to the instance by admin, see more in Administrator’s manual - Add new genomes
- User-provided overlay - display the variants from uploaded file
Upload user-provided overlay data
For examples of basic and advanced data upload, see Example 03 - Custom data upload by registered users. The description of the formats 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 networkand for the matching ones will assign them colors: blue for negative values, red for positive values, with the saturationproportional 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 - the header and the 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 blankfields in ReactionIdentifier and LineWidth for elements, and leaving blank fields in Name for interactions.
Genetic variant format
It is a particular type of advanced format, it contains the header and the body, see below:
- Type -
#TYPE=GENETIC_VARIANT
- Genome type -
#GENOME_TYPE=UCSC
- type of reference genome being used (e.g. UCSC) - Genome version -
#GENOME_VERSION=xyz
- version of reference genome being used (e.g. hg19)
The body is a table with a following set of allowed columns:
- Position - the location of the variant in the genome
- Original_DNA - the reference DNA
- Alternative_DNA - the variant of the DNA
- Name of the gene with the variant
- Contig number of the chromosome
- Allele_frequency - relative frequency of this variant; it will be visualized by the height of the bar in the genome browser popup. See genetic variant overlay in Example 03.
Important note about adding overlay
The overlay can be uploaded by pressing Upload or by pasting data into List of elements field. In case user uploads file, it must contain the header and the body. After choosing file, the dropdown list TYPE switches automatically between GENERIC/GENETIC_VARIANT as Minerva recognizes file’s header.
If using filed List of elements, the header and the body must be provided in the list too. If providing generic overlay, choose from TYPE dropdown list GENERIC; if providing genetic variant overlay choose GENETIC_VARIANT. See more in Example 03 - Custom data upload by registered users.
Procedure
After choosing the dataset to upload, pressing Upload button will invoke a comment and upload the overlay file. 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.
After choosing the dataset to upload, pressing Upload button will invoke a comment and upload the overlay file. 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 Administrator’s manual - Users.
- The number of available overlays is common for all projects hosted on your MINERVA instance. If a user is registeredin a number of projects and uploads custom datasets in all of them, the global number of available custom overlays will bereduced with each uploaded overlay.
Submaps tab
The Submaps tab summarizes all the submap networks uploaded together and linked to the main network of this projecthosted by your MINERVA instance. See Administrator’s 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 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.
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:
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
Export
The Export page contains three tabs (Elements, Network and Graphics), allowing to download the hosted content in different formats.
- Elements tab allows to narrow down and download the list of elements in the hosted networks and export them to text file. Available filters include:
- Type - filters the exported elements by the SBGN-compliant type (e.g. Protein, RNA)
- Column - filters the contents of exported file by selecting particular columns. Available filters, among others, include:
- Id - identifier in the MINERVA system
- Name - name of the element
- Model - identifier of the (sub)network containing this element
- Type - SBGN type of element
- Complex - complex element containing this element
- Compartment - the smallest compartment/pathway containing the element
- Element external id - corresponding source file e.g. CellDesigner ID
- Annotations - filters the annotations of elements in the downloaded file; by default all annotation types are considered. Green highlighted fields are non empty annotation sources
- Included/excluded compartment/pathways - filters the elements by compartments/pathways they are in; by default all compartments are considered as “included”, none as “excluded”
- Network 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:
- Type - filters the nodes of exported interactions by the SBGN-compliant type
- Column - filters the contents of exported file by selecting, which column should be included. Available filters, among others, include:
- Elements - contain information about reactants, products and reaction modifiers
- Element external id - reaction identifier corresponding source file e.g. CellDesigner ID
- Model - identifier of the (sub)network containing this element
- Type - type of reaction (e.g. state transition, transport)
- Annotations - filters the annotations of elements and interactions in the downloaded file; by default all annotation types are considered. Green highlighted fields are non empty annotation sources
- Included/excluded compartment/pathways - filters the elements by compartments they are in; by default all compartments are considered as “included”, none as “excluded”
- Graphics tab allows to download graphics of the (Sub)map in one of the Format: PNG image, PDF and SVG image
User data
It allows a registered user to type in their login and password or request for an account from the administrators of this MINERVA instance.Platform administrators can register new users (see Administrator’s manual - General 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 is the topmost part of the user view, containing the Show overview button, Comment and Legend checkboxesand Clear button. The Clear button clears all search results currently shown in the display area. The remaining functionalitiesare detailed below.
Show overview
This button invokes a static image associated with the displayed content. It may be a graphics facilitating the understandingof the underlying network, or any other visual cue that the content curator decided to present. The initial image displayed with theShow 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 Administrator’s manual - Source file.
If this checkbox is checked, the comments provided by users with Pinned option set to Yes will become visible in thedisplay area (see also Section Add comment).
Legend
If this checkbox is checked, the legend describing element and interaction types will be displayed.
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.
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
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:
Afterwards, a plugin panel becomes available on the right (see image below). To close that panel, go to plugin icon and click Unload button.
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.
Please find below the list of available plugins. Click at the plugin name to find more information about it.
Name of the plugin | Address URL and the short description of the plugin |
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. | |
GSEA | https://minerva-dev.lcsb.uni.lu/plugins/gsea/plugin.js |
Calculate the enrichment of the elements from the selected overlay in the pathway. | |
Variants information | https://minerva-dev.lcsb.uni.lu/plugins/variationinfo/plugin.js |
Provide the information about the genes variations available in the public resources in the context of a particular disease. |
The options available in the top left corner of the map. The padlock shape icon allows the administrator to login or request an account. To login as user go to Overlays or Info tab.
You are in administrator's manual » v13.0 ||
Table of contents
- Administrator view
- PROJECTS
- Add project
- Edit project
- GENOMES
- PROJECTS
Administrator view refers to the set of functionalities for web-based management of the content and configuration of a MINERVA instance.
Login
Administrator view is accessible via the button with the lock icon in the upper left corner of the main view (see below).
Many projects (maps, networks) can be hosted in parallel on a single MINERVA instance. The users access the projects via direct hyperlinks. To manage these projects, the user with administrator’s rights to at least one of the projects can log as an administrator via lock icon. After successful login, you will have an access to the administrator panel to manage a MINERVA instance (see below).
PROJECTS
This panel allows you to (1) add new projects (2) examine messages generated during the upload of the projects (3) edit and (4) remove them.
Add project
The Add project button invokes a menu allowing you to upload your project and start its generation in the MINERVA platform.
File formats
Files uploaded to create a project on a MINERVA instance can be:
- CellDesigner files (see CellDesigner website)
- SBML files, importantly
- elements (species) and reactions should be defined by SBOTerms, to match the CellDesigner style (see the list of CellDesigner types matching SBOTerms). If not, all elements will be shown as small molecules and all reactions as state transitions. Find more in example 02 - SBML file modifications.
- layout package is supported
- MIRIAM annotations in the
<annotation>
node are supported
- SBGN files
Single files of these types are uploaded via the Add project button. Advanced project structure can also be uploaded as a compressed file, as described in the Advanced format.
Fields of the Add project window
- Upload file - Choose File invokes a file upload dialog. Available options and configurations of the source file are discussed in section Source file.
- File format - choose a format of an uploading file: CellDesigner, SBGN or SBML.
Note: Adding CellDesigner file or SBGN-format file automatically changes file format in the window. For an SBML file, the file format must be changed manually. - Map canvas type - choose Google Maps API or OpenLayers to display the map, if you choose Google Maps API you have to agree on Google Maps API Terms by ticking the checkbox.
- 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 main view; your official name of the project.
- Project Disease - the disease associated with the project, the code has to be a valid MeSH identifier, e.g.D010300. This is needed for chemical target search, see section chemical target.
- Organism - the taxonomy id of the species, for which the map is primarily developed, e.g. 9606. This is needed to display genetic variants overlays.
- Version - a text field displayed next to the name of your project in the User panel.
- Notify email - e-mail address that should be used for project-related notifications.
- 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 section Configure automatic annotation).
- Verify manual 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 section Configure automatic verification).
- Cache data - if this checkbox is checked, all hyperlinks in the project resolved by MIRIAM repository (e.g. cross-links to external bioinformatics databases) are resolved and cached.
- Auto margin - if this checkbox is checked, the map will be drawn with equal amount of empty spaces around it.
- Display as SBGN - if this checkbox is checked, the uploaded model will be displayed in SBGN format, instead of the default CellDesigner format.
- Semantic zooming contains multiple overlays - tick the checkbox to display each semantic zoom level as a separate overlay in the General Overlays panel in the map. Find out more about semantic zoom here. This mode is primarily for testing purposes and we advise it should be unchecked by default.
Configure automatic annotation
The Advanced button, next to the Annotate model automatically checkbox under Add project button, invokes a dedicated configuration window (see below).
Clicking on each element type from the tree in the left panel, an annotator can be assigned in the right panel that will attempt to automatically retrieve information from external bioinformatics databases for each relevant element and annotate them.
Copy from button in the right panel copies annotators set from other objects we choose (see above image: GenericProtein will get the same annotators as Gene already has set).
Important note: Settings for lower hierarchy levels are overridden by settings for upper hierarchy levels. For instance, if no Ensembl annotation is selected for GenericProtein, but Protein selects Ensembl, GenericProtein will be automatically annotated with Ensembl as well.
Copy from button in the right panel copies annotators set from other objects we choose (see above image: GenericProtein will get the same annotators as Gene already has set).
Important note: Settings for lower hierarchy levels are overridden by settings for upper hierarchy levels. For instance, if no Ensembl annotation is selected for GenericProtein, but Protein selects Ensembl, GenericProtein will be automatically annotated with Ensembl as well.
There are a number annotators available, working either by name, or by annotation of an element.
By annotation refers to the MIRIAM identifiers in the
<annotation>
section of SBML and CellDesigner formats.These annotators use specific identifiers, mentioned below, to retrieve additional information for elements.For instance, by UniProt annotation means that the annotator needs a valid UniProt identifier in the
<annotation>
section.Note: SBGN files can be automatically annotated only by name as they have no
<annotation>
section.- BRENDA
- - By annotation: BRENDA, UniProt.
- - Retrieves all BRENDA codes for enzymatic activity of the element.
- ChEBI
- - By annotation: ChEBI or by name (ChEBI).
- - retrieves full name and synonyms in the ChEBI ontology.
- ENSEMBL
- - by annotation: ENSEMBL.
- - Retrieves symbol, full name, HGNC Symbol and identifier, Entrez Gene identifier.
- Entrez Gene
- - By annotation: Entrez Gene.
- - Retrieves full name, symbol, synonyms, description, HGNC identifier and ENSEMBL identifier.
- Gene Ontology
- - By annotation: Gene Ontology.
- - Retrieves full GO definition for this identifier.
- HGNC
- - By annotation: HGNC and by name (HGNC symbol).
- - Retrieves full name, symbol, synonyms and UniProt identifier, RefSeq identifier, ENSEMBL identifier, Entrez Gene identifier.
- Protein Data Bank
- - By annotation: PDB, UniProt, HGNC, HGNC symbol and by name (HGNC symbol).
- - Retrieves all relevant PDB structure identifiers. If HGNC symbol or identifier are used, it will also run the HGNC annotator.
- STRING
- - By annotation: STRING, UniProt.
- - Retrieves all relevant STRING identifiers. If UniProt identifier is used, it will also run the UniProt annotator.
- UniProt
- - by annotation: UniProt.
- - Retrieves HGNC symbol and Enzyme Nomenclature identifier.
- Biocompendium
- Warning! this annotation service is unstable due to maintenance
- by name, retrieves full name, symbols, description and identifiers:RefSeq, ENSEMBL, Entrez Gene identifier, HGNC symbol, KEGG, Reactome, PubMed and others
Configure automatic verification
The Advanced button, next to the Verify manual annotations checkbox under Add project button, invokes a dedicated configuration window (see below).
Clicking on each element or interaction type in the tree in the left panel, then:
- - top right panels
- A list of MIRIAM identifiers which are configured as valid. Elements or interactions in the uploaded model annotated with any identifier other than the valid list will raise a warning.
- - bottom right panels
- A list of MIRIAM identifiers which are configured as mandatory. If checkbox One of these miriam should be required is checked, elements or interactions in the uploaded model annotated without at least one identifier from mandatory list will raise a warning.
Save button: project generation
Clicking Save in the Add project window will start generation of the project.The status of the project in the Projects tab will update during the process. Also, you can use the Refresh button. 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 when the project upload advances, 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 mouse over itwill display the reason for failure. You will receive an email message with the brief description of the error.
To find out more, check example 1 - CellDesigner file upload and annotation.
Project status
Clicking on the exclamation mark icon (if present) next to the project status description, will displaythe list of warnings raised during the generation of this project (see below).
The list can also be downloaded as a tab-delimited text file. Types and identifiers of the elements and interactions arelisted on the left side of column Content, while the nature of an error is provided on the right.Take a look at the list of possible errors and their explanations.
Edit project
This panel allows you to configure and manage the project. Functionalities are grouped in the following tabs (see below for an illustration):
- General edit information about this project: canvas type, name, version, disease and organism type or notify email address
- Overlays add or configure overlays for this map, both general and user-provided
- Maps configure visuals for the main map and submaps
- Users manage users’ access rights to this map
- Comments manage user-provided comments for this map
Overlays
This tab allows you to add new overlays and edit properties and ownership of existing overlays. You see here overlays that have been:
- uploaded with the project, if it contains overlays already (see sections Add project and Source file)
Important! Overlays named Pathways and compartments, Network and Empty allow for different ways of displaying the map’s content, and they have no data associated with them. - uploaded by the users (see section Upload user-provided overlay data)
- uploaded by the administrators by Add overlay button in top left corner
Minerva 4 User Manual Transmission
In this tab, besides Name and Description, the following columns are available:
- Public - this checkbox makes the overlay available to any user
- Default - this checkbox sets the default view of the map
- Owner - the user having the access right to a given overlay. Dropdown menu allows to choose from existing users
Important!
Choosing the owner to be ‘N/A’ (top of the list) and checking the Public checkbox makes this overlay a General overlay, accessible for all users - Data - action buttons to download the associated dataset
- Update - action buttons to save any changes in the configuration of the corresponding overlay
- Remove - action buttons to remove the corresponding overlay
Maps
This tab lists all available maps (the main map and submaps) in the project, and allows to change default displaying options of the maps, see below.
The following columns are available:
- Default center x and y sets the default center point of the (sub)map
- Default zoom level set the default zoom level for this (sub)map
- Update to save the changes
Users (of this map)
This tab lists all users of a MINERVA instance and allows to configure their access rights to this particular map.It contains the following columns of checkboxes:
- Manage comments
- Manage overlays
- View project
- Update button, to save changesTicking a checkbox in a respective column for a given user assigns the corresponding privilege to them. Each change needs to be saved with the Update privileges button.
General users privileges are discussed in detail in the following section USERS.
This panel allows you to manage comments provided by users to the particular map (see section User manual - Comments).
The field Title is a hyperlink to a given comment in the map. In the following columns there are author of the comment, his email and the content. Pinned informs if the comment’s icon is visible on the map.
Users logged in as administrators have a possibility to delete a comment by pressing press the Remove button. The removed comment will no longer be visible among the pinned comments on the map, and its status will be updated in the Removed panel with comment in the brackets (see image below).
Users logged in as administrators have a possibility to delete a comment by pressing press the Remove button. The removed comment will no longer be visible among the pinned comments on the map, and its status will be updated in the Removed panel with comment in the brackets (see image below).
USERS
Registered users can be allowed to upload data overlays to maps hosted on a MINERVA instance, and to manage it.This panel allows you to Add (1) users, Configure LDAP authentication (2) and Edit (3) their privileges, or Remove(4) them. See image below:
Clicking on the Add user button invokes the window (see below) allowing to set login, password and personal details of a new user.
The panel to Edit allows to modify user data except the login field. Remove button removes this registered user from a MINERVA instance.
The panel to Edit allows to modify user data except the login field. Remove button removes this registered user from a MINERVA instance.
The two next tabs in the window allow to configure the access rights and privileges of the user.
- Global privileges concern all projects on a MINERVA instance.
- Add project if checked, permits the user to add new projects (Add project button becomes visible).
- Custom overlays field defines how many overlays can be created by a given user across all projects.
- Manage configuration if checked, grants the access right to Configuration tab and permits to configure the parameters of MINERVA platform.
- Manage genomes if checked, grants the right to access Genomes tab and manage a reference genomes for MINERVA.
- Map management if checked, grants the right to access Map manager tab and manage existing projects.
- User management if checked, grants the right to access the User manager tab and to manage users.
- Project-specific privileges concern only the project, for which they are configured
- Top row: Default privilege for a new project checkboxes - set up default privileges assigned to this user for any new project.
- The list of available projects on a MINERVA instance, contains four columns:
- ProjectId name of the project.
- Manage comments if checked, grants access to the comments tab in Edit project and allows them to manage comments for this project.
- Manage overlays if checked, grants the right to manage overlays of all users for this project.
- View project if checked, grants the right to open the URL of this project, and makes it visible in the PROJECTS tab.Important for non-administrators, only this box should be selected.
Important unchecking this box for the user anonymous makes this map inaccessible without login. Only registered users with proper privileges will be able to open the URL of this map.
CONFIGURATION
Configuration tab allows privileged users to configure global parameters of a MINERVA instance. Particular categories of configuration items are grouped in separate tabs (see image below).
Global MINERVA configuration category are:
- Email notification details
- E-mail address - e-mail address used for sending notifications about the activity of a MINERVA instance - project uploads, comments, etc.
- Email settings for requesting an account - the Info and Overlay tabs in the user interface allow to a Request for an account action, which will auto-compose an email with the message defined in Email content used for requesting an account to addressed to the e-mail, or e-mails (separated by a semicolon) provided in the field Email used for requesting an account.
- E-mail server login, E-mail server password, IMAP server, SMTP port and SMTP server - configuration of your mail server for notification sending
- Server configuration
- Issue tracker - a tool to submit MINERVA issues.
- Default project Id - the project that will be displayed by default under the root address of the platform (your.url/MapViewer/)
- Domain allowed to connect via x-frame technology - the address of a website allowed to embed a MINERVA instance via x-frame technology
- Google Analytics tracking ID used for statistics - provide here a valid Google Analytics ID to track user activity of a MINERVA instance
- Max session inactivity time (in seconds) set the time after inactive session is expired
- Path to store big files - location in the directory structure of a MINERVA instance to store big files
- Legend and logo
- Legend 1-4 image file - path in the directory structure of a MINERVA instance for displayed legend images
- Logo description - the popup text that will be displayed upon mouse over your logo
- Logo icon - the filename of your logo icon, displayed in the bottom-left corner of the main view; path in the directory or URL
- Logo link (after click) - the website to which you will be redirected after clicking on the logo
- Show reaction type when browsing map checkbox
- URL of platform Terms of Use file
- User manual file - location in the directory structure of a MINERVA instance for the user manual file
- Point and click
- Max distance for clicking on element (px) - the content visualized by MINERVA 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
- Max number of results - sets the max number of search results, (similar elements are grouped into a single search result)
- Max number of map zoom levels - sets the max size (of canvas) of the map, that can be uploaded to MINERVA.
- Overlays
- Opacity used when drawing data overlays (value between 0.0-1.0)
- Overlay color for negative/positive values - sets the colors should be used for positive and negative values in basic overlays. Values close to zero have the lowest color saturation, values close to -1/1 have the highest color saturation
- Overlay color for value=0
- Overlay color when no values are defined - sets the color to use for coloring list of elements overlays
- see section User manual - Upload user-provided overlay data
- Default user privilegesSets default user privileges to manage comments, overlays and view projects for any project on a MINERVA instance.
- Search panel optionsDefines which search results in the left panel will be expandable via plus/minus icon.
- LDAP configuration
- LDAP address - address of the machine where LDAP server is located
- LDAP port - port on which LDAP is listening (by default it’s 389, for SSL connections usually it’s 636)
- LDAP uses SSL - check to use SSL for LDAP connection
- LDAP bind DN - Distinguished Name of the user account that should be used for LDAP connection (this user should be able to search/list accounts on LDAP server)
- LDAP password - password for the LDAP bind DN
- LDAP base DN - definition of the point from where a server will search for users
- LDAP filter objectClass - this parameter allows to filter by objectClass type of LDAP entry; * value skips the filtering
- LDAP first name attribute - which attribute in LDAP directory corresponds to “First name” of the user
- LDAP last name attribute - which attribute in LDAP directory corresponds to “Last name” of the user
- LDAP email attribute - which attribute in LDAP directory corresponds to the user email address
- LDAP filter - when there are many accounts in LDAP administrators create groups of users that have access to specific systems, this filter allows to define LDAP filter that will limit set of accounts that can access minerva, empty string disable filtering
- LDAP login (user id)
GENOMES
In this section an administrator can set up a reference genome for displaying genetic variant overlays and a genome browser in the map. Currently, MINERVA supports human genomes data from UCSC Genomics Institute. Available fields (see also image below):
- Type informs about type of data, currently MINERVA supports UCSC format
- Organism identifier of the organism of the added reference genome (e.g. 9606)
- Version version of the added reference genome (e.g. hg19)
- Progress of the upload
- Source - url address of the genome data; sets up automatically after selecting Version, or user can paste own url addressNote: the file must be in .2bit format
- Edit/Remove buttons allows to edit the gene mapping and remove the genome from the instance
Important note:
The Taxonomy id (e.g. 9606) for Organism must be provided for the project, and reference genomes uploaded on a MINERVA instance must include its type. If Organism for the project is missing, the genome browser is not displayed in the overlay’s popup window.
The Taxonomy id (e.g. 9606) for Organism must be provided for the project, and reference genomes uploaded on a MINERVA instance must include its type. If Organism for the project is missing, the genome browser is not displayed in the overlay’s popup window.
Add new genomes
In top left corner choose ADD GENOME button; the window pops up, as shown below:
The window contains two tabs:
- DETAILS - select new genome parameters as described above
- GENE MAPPING - information about the gene loci in the genome, which are visualized on the blue axis in the genome browser. In the dialog window, provide the name of the data set and its url address. The name will be displayed in the genome browser (here: gene ref), see User manual - Overlays. The data must be provided in .bb format file. More details how to create .bb file.
Minerva Instructions
PLUGINS
Minerva Instructions For Use
The plugin tab allows the administrator to add a public plugin to a MINERVA instance. These plugins will be displayed if in the Plugins menu in the map.
The Plugin tab is shown on the image below, it contains:
The Plugin tab is shown on the image below, it contains:
Minerva 4 User Manual Download
- Name of the plugin
- Version of the plugin
- URL of the plugin
- Remove the plugin from a MINERVA instance
Minerva 4 User Manual Pdf
To add a new plugin, click Add plugin button, and paste the plugin url into the URL field and click Validate (see image below). The name and version fields are usually filled automatically from the plugin content. Click Save to add the plugin to a MINERVA instance.
Note: The administrator cannot add the same plugin twice to the MINERVA in the Administrator panel (the notification is displayed). But a user can upload an already exiting plugin via Plugins menu in the user’s view of a map.