MINERVA configuration: Administrator’s manual

Table of contents

Administrator view

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

Login

Administrator view is accessible via the button with the lock icon in the upper left corner of the user view (see below). See also User manual - Main view).

Login view

Many projects (maps, networks) can be hosted in parallel on a single MINERVA instance (see User manual - Accessing the project). and a user having administrator rights to at least one of them can log via ADMIN link. After successful login (see below), you will have access to the administrator panel to manage your MINERVA instance.

Successful login

Comments

This panel allows you to manage comments provided by users of your maps (see Section User manual - Comments). The panel to the right (Projects) allows you to switch between different maps. Current active map will be highlighted. The field Title is a hyperlink to a given comment in the map. For the current active map, comments will be displayed in the panel to the left.

In case the comments are not loaded correctly, press Refresh button to show them.

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, and its status will be updated in the Comments panel (see below).

Removed Comment status

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

This view gives information about: - 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 User manual - chemical target. - Organism: the taxonomy id of the species, for which the map is primarily developed, e.g. 9606.

Detailed map management

The magnifying glass symbol in the last column of the map manager gives access to the management dialogue (see below).

detailed management tab 1

There are four tabs available: - General - allows to edit information about this map, including disease and species - Overlays - allows to manage overlays for this map, both general and user-provided - Data mining - obstolete, will be removed in the upcoming version of MINERVA - Users - allows to manage users’ rights to access and manage this map

Manage overlays tab

This tab allows you to edit the details about the overlays and their ownership. You see here overlays that have been: 1. uploaded with the project (see Section Add project) - Important! overlays named Pathways and compartments, Network and Empty allow for different ways of displaying the map’s content, and they don’t have any data associated with them. 2. uploaded by the users (see Section Upload user-provided overlay data) 3. uploaded by the administrators (see this section, below)

In this tab, besides Name and Description, the following columns are available: - Directory - an internal reference for storage at the MINERVA webserver - Owner - the user having the access right to a given overlay. Dropdown menu allows to choose from exisitng users. - Important! Choosing the owner to be ‘N/A’ (top of the list) makes this overlay a General overlay, publicly visible for all users - Data - action buttons allowing to download the associated dataset of a particular overlay - Update - action buttons to save any changes in the configuration of a particular overlay - Remove - action buttons to remove a particular overlay

detailed management tab 2

Manage users tab

This tab contains a table of all users of the system (including the administrators) and allows to assign them rights to this particular map. It contains the following columns of checkboxes: - Manage comments - Manage overlays - View project Ticking a checkbox in a respective column for a given user assigns this privilege to them. Each change needs to be saved with the Update privileges button.

User privileges are discussed in detail in Section User manager)

Important! Columns ‘Drug targeting advanced view’ and ‘Edit suggested connections’ are obstolete.

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

Fields of the Add project window

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

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:

HGNC
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
Uniprot:
Uniprot identifier, if present, will be used to retrieve additional information, including HGNC symbol and identifier, and Entrez Gene identifier
Entrez Gene
Entrez Gene identifier, if present, will be used to retrieve additional information, including full name, synonyms, description, HGNC symbol and identifier, and ENSEMBL identifier
ENSEMBL:
ENSEMBL identifier, if present, will be used to retrieve additional information, including symbol, full name, synonyms, HGNC symbol and identifier, and Entrez Gene identifier
ChEBI:
Uniprot identifier, if present, will be used to retrieve additional information, including synonyms, parents and children in the ChEBI ontology tree
Gene Ontology
Gene Ontology identifier, if present, will be used to retrieve additional information, including full GO definition for this identifier.
Biocompendium
Warning! this annotation service is unstable due to maintenance
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

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

Clicking on each element or interaction type (Classes) in the left panel:

top right panels
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
bottom right panels
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.

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.

Examine warnings

Warnings

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

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:

Warning type Explanation
Warnings generated by automatic annotation
[Annotator] annotation problem [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
Cannot find information for element. 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
Chemical name cannot be found in chebi: [name] 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.
Former symbols list different than default [list]. Ignoring Existing annotation of an element (list of symbols) is different than the [list] retrieved by one of the assigned annotators.
New full name different than default [full name]. Ignoring. Existing annotation of an element (full name) is different than the [full name] retrieved by one of the assigned annotators.
New symbol different than default [symbol]. Ignoring. Existing annotation of an element (symbol) is different than the [symbol] retrieved by one of the assigned annotators.
Synonyms list different than default [list]. Ignoring. Existing annotation of an element (list of synonyms) is different than the [list] retrieved by one of the assigned annotators.
Warnings generated by verification of manual annotation
contains invalid annotations:[annotation] Configuration in **Validate manual annotations** did not foresee [annotation] as allowed for this element or interaction.
misses one of the following annotations:[list]. Configuration in **Validate manual annotations** required one of [list] of annotations for this element or interaction, but none was found.
misses annotations. No annotation exists for this element or interaction.
Unknown miriam uri: [MIRIAM type] An element or interaction was annotated with [MIRIAM type] - this type of identifier is currently not handled.

User manager

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

User manager

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.

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

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

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 (bottom left) displays the table of global parameters, which can be edited set using and Save button (bottom right).

Global MINERVA configuration parameters are:

MIRIAM

The MIRIAM panel lists all MIRIAM-supported resources (http://www.ebi.ac.uk/miriam/main/mdb?section=intro) currently handled by MINERVA platform. In particular:

Source file

The source file is uploaded to establish a project on your MINERVA instance. It is a SBGN-compliant file in the .xml format. Two modes of upload can be discussed - basic and advanced. In the basic mode, a single SBGN file (.zip compressed files are also accepted) is uploaded via the Add project button (see Section Add project). This way the SBGN-compliant network is uploaded, without additional files.

Advanced upload mode assumes that a zip-compressed directory will be submitted as an input, with the following structure:

For an example, see Examples - Advanced file upload. Detailed description of each section of the source file follows below.

Images

The images subdirectory contains static image files in .png format that will be displayed after pressing the Show overview button (see User manual - Show overview). Besides the images, the directory also has to contain a text, tab-separated file named coords.txt, describing links between the images and the associated network(s). The coords.txt file is a table with the following structure:

Example of a coords.txt file:

FILE POLYGON LINK_TYPE LINK_TARGET MODEL_COORDINATES MODEL_ZOOM_LEVEL COMMENT
image.A.png 51,218 107,218 107,252 51,252 MODEL PD_151023_1.xml 7488,11986 5 A link from image.A file to a point in the display area with zoom level 5
image.B.png 15,187 73,187 73,52 15,52 IMAGE image.A.png A link from image.B file to invoke image.A
image.C.png 30,8 10,8 10,7 30,7 SEARCH reaction:c1,reaction:c2 A link from image.C to results of a search query pointing to interactions **c1** and **c2**

Overlays

The layouts subdirectory contains files with custom colorings of the uploaded content that will be accessible to all the users. The format is identical to the format of files uploaded by registered users. See Section Upload custom data - format for details on file format.

Submaps

The submaps subdirectory contains SBGN files that will be displayed in the Submaps tab in the functional area of the User view (see Section User view - Submaps). Additionally to the submap files, one additional file, a submap mapping file, can be added to the directory. This file describes connections between the submaps and the main map itself. See below for the exact structure of the submap mapping file.

Submap mapping file

Submap mapping file is a CellDesigner file, in which relations between the uploaded maps is represented graphically. Two types of components and one type of interaction is considered when parsing this file:

Remark to alias vs identifier: CellDesigner has a single species identifier for all copies of a certain element (e.g. protein) in a file. Different instances of the same element have a distinct species alias. It is the species alias that is used to link specific map elements with submaps.

A screenshot below demonstrates an exemplary submap mapping file.

SubmapsMapping



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