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The Emedgene platform utilizes the Okta Identity Management solution to control user access. This improves user management, enhances access and authentication security, and allows organizations to implement single sign-on for their users.
The Top navigation panel of the platform serves as a guide to the platform. It contains:
Dashboard, Cases and Add new case buttons lead to the corresponding pages
Case search bar
Settings dropdown menu activated by clicking on the user name or profile picture
Help dropdown menu activated by clicking on the question mark icon
Emedgene Applications menu activated by clicking on the app launcher icon on the left
As of version 2.26:
The Dashboard provides a glance at key performance indicators for an organization and depicts an overview of the user activity on the Emedgene platform.
This page is divided into two panels and contains the following subsections:
Emedgene Knowledge Base panel reveals the total amount of known polymorphisms, pathogenic variants, and gene-disease connections considered during analysis. It also indicates the number of scholarly publications processed by Emedgene's novel textual recognition platform, backed by natural-language processing and artificial intelligence.
Diagnostic Yield panel presents the proportion of "solved" cases out of the total number of the organization's cases of the same type.
Status Diagram panel displays the total number of the organization's submitted cases as well as the numbers of cases under each status.
Stale Cases panel highlights the cases that are stuck at one of the intermediate stages of the analysis, and are not finalized.
Network Activities: The right panel displays a timeline of activities performed by multiple users within the organization. This log includes activity like creating a case, verifying a Preset, changing a Case status, generating a report, etc.
The Emedgene platform is divided into two applications:
Analyze - genomic analysis workbench,
Curate - the knowledge management system.
Go to the nine-dot app launcher icon located on the left of the Top navigation panel and select Curate from the dropdown menu.
Go to the nine-dot app launcher icon located on the Curate navigation panel and select Analyze from the dropdown menu.
Click on the question mark icon of the Top navigation panel to open the Help dropdown menu.
From there, you can access:
Help Center. Feeling curious? Dive right in.
What's New. Check out the release notes to be on top of our latest and greatest features!
Click on the user initials or profile picture at the rightmost corner of the Top navigation panel to open the Settings dropdown menu. From there, you can enter:
Add or edit your professional credentials, profile picture, contact information and organization's details, and review and permissions granted to you.
, custom , , create, edit and delete , set how long until a case becomes "stale", and assign user groups.
Note: Organization settings are accessible only for users having a Manager role.
Add, activate and inactivate users and manage .
networks, for each network, and networks.
for your organization, , and (the latter - only for ILMN cloud users).
Next to the user's initials or profile picture is a question mark Help icon. Clicking on this icon expands a dropdown menu with the following options:
Support Chat: reach out to our Customer Support team anytime without leaving the page;
What's New: check out the new features, enhancements, or any other updates related to the platform.
Caution: Please be aware that when performing a task, such as uploading a new sample, clicking on the buttons in the Top navigation panel may terminate the progress. However, for the most part, changes and annotations made on the analysis pages are auto-saved.
Help Center: Access the user manual and learn how to leverage powerful features to serve your patients or advance your research;
Emedgene users are defined by roles. Roles are managed in Settings > User Management. Access to the User Management tab is restricted to those with the appropriate permission.
The available roles for Emedgene are described below:
| User Role | Description | Component / Flow | User Level |
|---|---|---|---|
If you are not seeing part of the roles from the user management interface, please be in touch with our support.
Acmg Tags
Allows to see ACMG Tags
Analyze > Variant page
All
Acmg Tags Edit
Allows to edit ACMG classification
Analyze > Variant page
Analyst, Director, Manager
Add New Test
Allows to manually create a case or (32.0+) upload a batch of cases via .csv
Analyze > Add a new case
Analyst, Director, Manager
Apidocs
Allows to see API documentation
Analyze
IT team
Auto Analysis
Allows to see the AI Shortlist analysis results
Analyze > Variant page
All
Candidate Compound With
Allows to combine two compound variants by gene name on the candidate page
Analyze > Case page
Analyst, Director, Manager
Change Finalized Test Status
Allows to unlock a finalized case
Analyze > Case page
Director, Manager
Check Preset
Allows to implement Presets from a list
Analyze > Case page
Analyst, Director, Manager
Comment
Allows to send a comment
Analyze > Case page
Analyst, Director, Manager
Comment Delete
Allows to delete a comment
Analyze > Case page
Manager
Create Report
Allows to generate report template
Analyze > Clinical report
Director, Manager
Create Variant
Allows to create an additional variant
Analyze > Case page
Director, Manager
Developer
Allows to see developer settings (Webhook)
Analyze
IT team
Download
Allows to download files
Analyze > Case page
Analyst, Director, Manager
Due Date
Allows to edit due date
Analyze > Case page
Analyst, Director, Manager
Edit Test
Allows to edit test's info
Analyze > Case page
Analyst, Director, Manager
Evidence
Allows to see evidence page
Analyze > Variant page
All
Evidence Edit
Allows to edit evidence page
Analyze > Variant page
Analyst, Director, Manager
Evidence Generate
Allows to generate initial evidence
Analyze > Variant page
Analyst, Director, Manager
Evidence Pathogenicity Edit
Allows to edit evidence pathogenicity
Analyze > Variant page
Analyst, Director, Manager
Evidence Text Edit
Allows to edit evidence text (Variant interpretation)
Analyze > Variant page
Analyst, Director, Manager
Gene Lists Read Only
Allows to show the gene list
Analyze
All
Gnomad Genome
Allows to see GnomAD genome data annotation
Analyze > Variant page
All
KMS
Allows to access Emedgene Curate
Curate
All
KMS Create Gene
Allows user to create a new gene in KMS
Curate
Manager
KMS Create Variant
Allows to create new variant in KMS
Curate
Manager
KMS Export
Allows user to export from varpage to the KMS
Curate
All
KMS Import Network Variant
Allows user to import variants from Network to Curate
Curate
Manager
KMS Update Disease ID
Allows to update disease ID of the variant in KMS
Curate
Manager
KMS Update Gene Interpretation
Allows user to update gene interpretation in KMS
Curate
Manager
KMS Update Gene Transcript Ref Sequence
Allows user to update a gene selected transcript in KMS
Curate
Manager
KMS Update Gene Note
Allows user to update gene note in KMS
Curate
Manager
KMS Update Interpretation
Allows to update interpretation of the variant in KMS
Curate
Manager
KMS Update Note
Allows to update variant note in KMS
Curate
Manager
KMS Update Pathogenicity
Allows to update pathogenicity of the variant in KMS
Curate
Manager
KMS Update Transcript
Allows to update transcript of the variant in KMS
Curate
Manager
Load Bam IGV
Allows to synchronize external IGV viewer with the platform
Analyze > Case page
All
Manage Case Default Page (34.0+)
Allows to set a default page upon entering a case
Analyze > Settings
Manager
Manage Case Identifier (33.0+)
Allows to set a custom case identifier
Analyze > Settings
Manager
Manage Column Order (34.0+)
Allows to customize the default order of Variant table columns.
Analyze > Settings
Manager
Manager Edit Variant Tags
Allows user to manage variant tags
Analyze > Settings
Director, Manager
Manage Gene List
Allows to create, edit gene lists
Analyze > Settings
Manager
Manage Gene List Visibility
Allows to manage gene list visibility
Analyze > Settings
Manager
Manage Kit Bed (30.0+)
Allows user to manage kits and bed uploads
Analyze > Settings
Manager
Manage Labels
Allows to manage labels
Analyze > Settings
Manager
Manage Platform Version (33.0+)
Allows to set a platform version
Analyze > Settings
Manager
Manage S3 Credentials (32.0+)
Allows to create access key and secret key; deactivate, activate and delete access key.
Analyze > Settings
Manager
Manager Support Access (31.0+)
Enable/disable support access to the organization
Analyze > Settings
Manager
Manage Test Presets
Allows to create Presets from gene lists, filter
Analyze > Settings
Analyst, Director, Manager
Manage URL Pattern (33.0+)
Allows to set a platform version
Analyze > Settings
Manager
Manager
Organizational admin (manager) role
Analyze
Manager
Multiple Storage
Allows to change the organization URL pattern
Analyze > Settings
Manager
Network
Allows to see available networks, request to join networks, leave networks, approve or reject invitations to join networks, edit existing networks of organization
Analyze > Settings
Manager
Network Create
Allows to create a new network
Analyze > Settings
Manager
Network Manage (32.0+)
Allows to create a network and define its sharing policy; leave networks
Analyze > Settings
Manager
Phenomatcher
Allows to filter by phenotypic match
Analyze > Case page
All
Preset Create (34.0+)
Allows to create Presets from active filters
Analyze > Case page;
Analyze > Settings
Analyst, Director, Manager
Preset Group Create (34.0+)
Allows to create and edit Preset groups
Analyze > Settings
Analyst, Director, Manager
Preset Group Default (34.0+)
Allows to set a default Preset group
Analyze > Settings
Manager
Preset Group Download (34.0+)
Allows to download a legacy (V1) Preset group JSON file
Analyze > Settings
Manager
Preset Group Hide (34.0+)
Allows to hide a Preset group from the Preset groups list offered at case creation
Analyze > Settings
Analyst, Director, Manager
Preset Group Revert (34.0+)
Allows to revert migration of a legacy Preset group
Analyze > Settings
Manager
Preset Delete (34.0+)
Allows to delete a non-locked Preset
Analyze > Settings
Analyst, Director, Manager
Preset Lock (34.0+)
Allows to lock and unlock editing the Preset
Analyze > Settings
Manager
Preset Manage (34.0+)
Allows to view and edit a Preset in JSON format
Analyze > Settings
Manager
Re Upload Tab
Allows to re-upload files
Analyze > Case page
Analyst, Director, Manager
Render Template
Allows to create a variant interpretation paragraph on the fly
Analyze > Clinical report
Analyst, Director, Manager
Report
Allows to export a report as a PDF
Analyze > Clinical report
Director, Manager
Report Preview
Allows to preview report
Analyze > Clinical report
All
Sanger Edit
Allows to edit Sanger sequencing information
Analyze > Variant page
Analyst, Director, Manager
Storage Provider
Allows to manage storage providers
Analyze > Settings
Manager, IT team
Tag Variant
Allows to tag a variant
Analyze > Variant page
Analyst, Director, Manager
Test Status
Allows to change test status
Analyze > Case page
Analyst, Director, Manager
Test Status Move to Trash
Allows to assign a Move to trash Case status
Analyze > Case page
Manager
Test Status to Finalized
Allows to change case status to finalized
Analyze > Case page
Director, Manager
Transcript Edit
Allows to change the default transcript for variants
Analyze > Variant page
Analyst, Director, Manager
Unknown Phenomatch
Allows to use Unknown Phenomatch variant filter
Analyze > Case page
All
Upload
Allows to upload files to be associated to a case
Analyze > Add a new case
Analyst, Director, Manager
User
Regular user role
Analyze
All
User Management
Allows to manage users
Analyze > Settings
Manager
User Read (30.0+)
Allows users access to organization data
Analyze
All
User Rerun Case
Allows to rerun cases
Analyze > Edit case info
Analyst, Director, Manager
Versions Tab
Allows seeing the versions tab
Analyze > Case page
All