| Oracle® Health Sciences Translational Research Center User's Guide Release 3.1.0.3 E66623-05 |
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PDF · Mobi · ePub |
| Oracle® Health Sciences Translational Research Center User's Guide Release 3.1.0.3 E66623-05 |
|
|
PDF · Mobi · ePub |
This section contains the following topics:
In the current release of Oracle Health Sciences Cohort Explorer (CE), a user's account has permissions to make minimal changes for basic accessibility options, but the user cannot customize the viewing screens.
If Oracle Access Manager (OAM) is configured, the user has the following functions:
User logs into the CE application by using Single Sign-On interface which can be shared among multiple applications. For example, if the user also purchased Oracle Business Intelligence Enterprise Edition Plus (OBIEE) full license the same credentials can be used for generating OBIEE reports.
Password is created by the user and not visible to an administrator.
User is locked out after a configurable number of unsuccessful login attempts.
Login session times out after a configurable time of inactivity.
Roles are automatically setup as listed in the Roles and Permissions section.
If OAM is not configured, the identified roles must be manually set up in a Weblogic instance. For more information, refer to Create Users and Add Users to Groups in the Oracle® Fusion Middleware Oracle WebLogic Server Administration Console Online Help. In OBIEE, you may need to perform Policy Migration to see the roles. Policy Migration documentation can be found in the Oracle Health Sciences Translational Research Center Installation and Configuration Guide.
Note:
Due to the caching approach leveraged and in compliance with the licensing agreement, multiple users should not log into the system with the same user name and password at the same time. Doing so may result in inconsistent data.A user is assigned one or more of the role groups in the following list:
trc-basic-user-group
Able to view and execute OBIEE-based reports in the Dashboard page but is unable to modify individual reports.
Can access the following screens:
Dashboard: Standard Reports
Dashboard: Custom Reports
Dashboard (top level tab)
trc-bioinformatician-group
Can download files from the web interface. Files must have a link stored in ODB and can be located in the middle tier in an accessible location.
Can access the following screens:
Dashboard: Standard Reports
Dashboard: Custom Reports
Dashboard (top level tab)
Cohort Query Tab
Cohort Query Tab: Genomic Data (tab in accordion)
Query Tab: Relative Time Events: gene variant (radio button)
Cohort Viewer (top tab)
Cohort Viewer: Cohort List
Cohort Viewer: Cohort Timeline
Cohort Reports
Cohort Viewer: Genomic Data Export
Single Patient Viewer: View Record
Single Patient Viewer: View Record: Genomic Data Collected
Circular Genomic Viewer (Visquick)
Genomic Query
Genomic Query: Columns after searching for gene/variant coming from CDM (Patient Count, Specimen Anatomical Site columns)
Genomic Query - Gene/Variant Search-Result summary Export VIA GENE/VARIANT SEARCH
My Workspace: My Recent Queries
Short Cuts
My Cohort Lists
Queries or Lists shared with me
Queries or Lists shared with All
My Queries
Gene Sets
Manage Queries
Manage Gene Sets
Manage Cohort List
Jobs
trc-cohort-group
Can query any data from CDM by using any of the CE User Interfaces. This group is unable to query ODB directly.
Can export the clinical data in any supported format, and is able to view the Dashboard.
Can access the following screens:
Dashboard: Standard Reports
Dashboard: Custom Reports
Dashboard (top level tab)
Cohort Query Tab
Cohort Viewer (top tab)
Cohort Viewer: Cohort List
Cohort Viewer: Cohort Timeline
Cohort Reports (Only Clinical)
Single Patient Viewer: View Record
Circular Genomic Viewer (Visquick)
My Workspace: My Recent Queries
Short Cuts
My Cohort Lists
Queries or Lists shared with me
Queries or Lists shared with All
My Queries
Manage Queries
Manage Cohort List
trc-limited-user-group
Can only see the Query Patients page (that is the count of patients) but is unable to view other detailed data.
Can access the following screens:
Dashboard: Standard Reports
Dashboard: Custom Reports
Dashboard (top level tab)
Cohort Query Tab (Save Query button should not be accessible)
trc-omics-group
Can query and read data from ODB by using User Interfaces and components marked as licensed with ODB only.
Can export omics data in file formats readable by genome viewers. For example, VCF, SEG, RES formats for IGV.
Although unlikely, if the user has only this role as standalone, you can only view from My Workspace page the Recent Gene Sets report and Omics Explorer and Gene Sets User Interfaces. All other CE bound components of the User Interface is grayed out.
Can access the following screens:
Cohort Viewer: Genomic Data Export
Genomic Query
Short Cuts
Gene Sets
Manage Gene Sets
Jobs
trc-comics-limited-user-group
Can query data from CDM and ODB using Query Patients interface, however cannot access Patient Viewer User Interfaces except Patient Genomic Data export
Can access MyWorkspace, view queries and gene sets
Can create his own Gene Sets
Can access the following screens:
Cohort Query Tab (Save Query button should not be accessible)
Cohort Query Tab: Genomic Data (tab in accordion)
Query Tab: Relative Time Events: gene variant (radio button)
Cohort Viewer (top tab)
Cohort Viewer: Genomic Data Export
My Workspace: My Recent Queries
Short Cuts
My Queries
Gene Sets
Manage Queries
Manage Gene Sets
Jobs
trc-pi-user-group
Has specific privileges allowing access to identifiable information on patients or subjects.
Can view personally identifiable (PI) data in Cohort List page. Together with user's VPD profile, this role enables the user to have access to PI attributes from the UI
Can view personally identifiable data in Single Patient or Subject Viewer > View Record page.
When in Subject context, View Record page allows this user to see merged version of both Patient and Subject clinical data all in one page.
Can access the following screens:
Dashboard: Standard Reports
Dashboard: Custom Reports
Dashboard (top level tab)
Cohort Query Tab
Cohort Query Tab: Genomic Data (tab in accordion)
Query Tab: Relative Time Events: gene variant (radio button)
Cohort Viewer (top tab)
Cohort Viewer: Cohort List
Cohort List (PI attributes)
Cohort Viewer: Cohort Timeline
Cohort Reports
Cohort Viewer: Genomic Data Export
Single Patient Viewer: View Record
Single Patient Viewer: View Record (PI atrributes)
Single Subject Viewer: View Record (PI atrributes)
Single Subject Viewer: View Record (show patient data together)
Single Patient Viewer: View Record: Genomic Data Collected
Circular Genomic Viewer (Visquick)
Genomic Query
Genomic Query: Columns after searching for gene/variant coming from CDM (Patient Count, Specimen Anatomical Site columns)
Genomic Query - Gene/Variant Search-Result summary Export VIA GENE/VARIANT SEARCH
My Workspace: My Recent Queries
Short Cuts
My Cohort Lists
Queries or Lists shared with me
Queries or Lists shared with All
My Queries
Gene Sets
Manage Queries
Manage Gene Sets
Manage Cohort List
Jobs
trc-standard-report-group
Has access to Dashboard tab in Cohort Explorer and more specifically Standard Report subtab and all reports it contains
Can access the following screens:
Dashboard: Standard Reports
Dashboard (top level tab)
trc-custom-report-group
Has access to Dashboard tab and Custom Reports subtab in Cohort Explorer and can view all custom reports as selected by customer.
Can access the following screens:
Dashboard: Custom Reports
Dashboard (top level tab)
trc-admin-group
Has access to Navigator option Manage User Groups in Cohort Explorer
Can create new user groups etc for sharing cohort queries or lists
Can add or remove users from groups
Can manage user roles
Can access the following screens:
Manage User Group
If users only belong to the following groups, then limited functionality is available based on the assigned roles:
trc-comics-limited-user-group
trc-limited-user-group
trc-standard-report-group
trc-custom-report-group
trc-basic-user-group
Users with the specific OBIEE license bundled with TRC have the roles listed in the previously configured in OBIEE. Additionally, if full OBIEE license is purchased, the following additional roles can be granted which are specific to OBIEE:
trc-basic-user-group
Able to view and execute OBIEE-based reports in the Dashboard page but cannot modify individual reports.
trc-developer
Can modify the OBIEE Web Catalog.
To publish the report, trc-Administrator should place it in a shared directory and assign appropriate access permissions.
If only a limited OBIEE licensed is purchased, neither the trc-developer nor the trc-administrator role is available. Without these roles, users in groups 1-5 are unable to build new reports or modify the content of existing reports. With a full OBIEE license, users with the trc-developer role can build reports but the trc-administrator role is required to publish them.
Note:
For optimal display of TRC, ensure that your screen resolution is at least 1024 pixels.Cohort Explorer application can be switched to run in either Patient or Study Subject context. In patient context, all queries are directed at patient tables in Cohort Data Model schema, while in the study subject context, the UI Query Engine queries subject tables in CDM.
By default, the Cohort Explorer context is set to Patient. The context can be set in the upper right hand corner of the screen as shown in the following figure.
When user switches context, the next login session will remember the last context set and keep it until it is changed again by the end user. Switching context will clear out loaded data in most of the viewer pages, however, it will not clear out criteria in Cohort Query page. Any criteria that are applicable in either context will be kept intact and criteria that are not applicable will be disabled. For example, Encounter criteria is not supported in Subject context thus when switching into Subject context, the criteria is disabled. If user switches back to Patient context, the criteria will be enabled again. If user elects to save the query, any disabled criteria will not be saved in the query. Also, each saved query is saved along with the context it was generated against. Queries in My Workspace page are displayed based on context they were generated against so in Patient context, only Patient context saved queries should be shown, and similarly, in Subject context, My Workspace would only show Subject context queries.
For a Subject to be considered deleted and not visible for selection, a given Subject's delete flag in CDM should be set to Y. Otherwise if a Study is deleted, it will not cause any of the Subjects in this study to be deleted. Those subjects will still be visible, while the study will no longer be available for selection. To maintain data integrity, the Subject's delete flag should be set to yes alongside the deleted Study.
The landing page consists of all the options required to complete your clinical and omics tasks, and consists of 6 main tabs with multiple subtabs under each.
Manage User Groups, available under the Home tab, is a set of utility user interfaces, custom built for users of Cohort Explorer in order to enable collaboration. Any user can create user groups and assign users to those groups in order to simplify sharing. Instead of sharing queries or lists with each user individually, setting up a list of user makes it easier for end user to share multiple items with a group of individuals. Note that only the user that is the owner of a given list can modify members of a given list. However, any user can elect to utilize a given list for sharing and see members of a list, even if he or she is not the owner.
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