OpenSpecimen allows controlling data access by assigning roles to users. The privileges can be controlled at a very granular level for each resource in the system.
OpenSpecimen provides default roles that administrators can assign to different users. To view details about default user roles, follow the below steps:
Navigate to the 'Roles' card.
Click on any of the roles to view more information.
Only Super Admins can create custom roles or edit existing roles.
Default Roles
OpenSpecimen is installed with some default roles. Below mentioned are the default roles with descriptions.
Name
Description
Name
Description
Administrator
Users can perform all operations within the assigned sites.
Coordinator
Users can perform all operations within the assigned protocols.
Principal Investigator
The user has read access to all data within the assigned protocols.
Researcher
The user has read access to non-PHI data within the assigned protocols and its catalog request.
Technician
Users can perform specimen operations without access to PHI data within the assigned protocols.
Tissue Banker
Users can perform all operations within the assigned protocols.
Clinician (v6.2)
Users can register participants and collect and ship primary specimens within assigned protocols.
(The user cannot access child specimens, containers, and other workflows.)
Consent Collector (v7.0)
Users can perform all the operations on the participant(PHI), Consent, and Query module.
Resources
The resources define the module and data entry access given to the user.
Resources
Description
Participants(DeId)
User will only be able to access and see the de identified(non PHI) data of the participant.
Participants(PHI)
Users can access all data of the participant including identified fields(PHI) like name, birth date, MRN etc.
If Participants(PHI) resource privilege is given to the user, Participants(DeId) can be skipped.
Primary Specimens
Users will have access to Primary Specimens only.
Specimens
Users will have access to specimens of all the lineage i.e. primary, derived and aliquots.
Gels
Gives access to gels module. Refer to the wiki page for more details on Gels.
Shipping and Tracking
Users will have access to ship and receive the specimens/containers within sites that use OpenSpecimen. Gives access to the Shipment module.
Refer to the wiki page for more details on Shipment
Jobs
Users will have access to the Jobs module. Refer to the wiki page for more details on Jobs.
Privileges of Users
Resource
Access To
Resource
Access To
Collection Protocols
Collection Protocols based on the configuration in the user's role tab.
Consent Response
Consents response within a Collection Protocol or Distribution Protocol. Note: Only super admins can add/edit the Consents at the global.
Distribution Protocols
Distribution Protocols based on users' sites.
Gels
Gels based on users' sites.
Jobs
Users can only see jobs created or shared with them.
Orders
Orders for the DPs they have access to.
Primary Specimens
Primary specimens for the CPs they have access to. Note: This is typically given to Clinical Coordinator staff, who are responsible for collecting the primary specimens.
Participant (PHI)
All participant data (PHI and de-identified).
Participant (DeId)
Only de-identified fields.
NOTE: Users with 'Participant (DeId)' read, create, update, delete permissions will not be able to register a new participant within the CP. They can only see the existing participants, collect new visits, and add specimens.
Path Report
Can upload and access pathology reports. It also contains additional controls for lock/unlock path reports. This can be used if path reports will be locked after manual review or de-identification.
Query
Query module.
Specimens
All specimens (primary, derivative, and aliquots) for their CPs
Storage Containers
Containers within their site. Note: Container types can be added only by super admins and institute admins.
Shipping and Tracking
Shipments within their site.
Supplies
Supplies based on their CP and site access.
Users
Users within their institute.
Visits
Visits for their CPs.
Catalogs
Users can access catalogs and their requests.
PHI Fields
The below fields marked as PHI in OpenSpecimen won't be visible to the roles with 'Participant (DeId)' privileges:
First Name
Middle Name
Last Name
Birth Date
Social Security Number
Death Date
Master Patient Index
Medical Record Number (MRN)
Surgical Pathology Number
Any custom fields marked as PHI.
Edit Default Roles
The default role listed below should not be renamed or edited. They get auto-assigned to specific users, as stated below:
Role
Auto-assigned to
Role
Auto-assigned to
Administrator
Institute Administrator, Site Coordinators
2. The rest of the default roles can be edited.
3. No role can be deleted via UI.
4. While editing a role, keeping at least one resource privilege is mandatory.
5. Editing means you can assign or unassign permissions to a user or altogether remove a resource.
Sign in as Super admin → Navigate to Roles
Click on the user you wish to edit, for example, Administrator.
Click on edit --> Go to any resource. For example Supplies
To give only read access, tick only the read permission.
If you wish not to provide import-export access, then untick the import-export permissions.
Click on the delete icon to remove the privilege.
Once provided with all required access, click the 'Update' button.
Add Coordinator or PI at CP Level
CP level PI and coordinators are not assigned any role by default.
After creating the CP, the admin has to manually assign specific roles to all the users who need to access the CP.
Provide Researcher access to edit request
Researchers can edit their request(if it's pending) if they have 'Read' access to the 'Catalog' resource.
Ensure the researcher also has access to non-PHI data displayed in the catalog.
Create Custom Role
You can create new roles to suit your local needs.
Log in as a super admin user.
Click the 'Roles' card from the home page.
Click the 'Create' button, and enter valid details.
Click the 'Resources' dropdown and select the desired resources.
Check the checkboxes of the privileges assigned to selected resources and click 'Create.'
Repeat steps 4 & 5 to add new resources.
Import / Export
If you have the 'Exp/Imp' privilege along with 'Create' or 'Update' on any resources, you can perform bulk import and export operations of those resources.
Query Resource (v6.3)
The 'query' resource allows you to access the query module.
CRUD + IE rights on the 'Query' resource is added to all the system shipped roles but the 'Researcher.' By default, the 'Researcher' role acquires only the Read and IE rights.
Users who do not have Read privilege on the 'Query' resource will not be able to view the query module in OpenSpecimen.
More details on operations associated with every privilege on query resource: Query Resource Privilege.
