DMR Updates & Release Notes

1. ProFoRMS
   • Adjusted column widths on multiple tables
   • Auto-Population capabilities for Data Collection Fields at the Data Element Level:
     • New feature added that allows users with privileges to configure auto-population during data collection
     • Once the user fills out the first collection, subsequent collections will be pre-filled with the same data for the same GUIDs
     • Will minimize errors when collecting data for the subjects, especially on fields that are common across Visit Types
        
2. Subject Management/GUID
   • Enhanced the “Check if GUID exist” error message to indicate that certain letters and numbers are not part of the GUID string
      
3. Data Dictionary
   • Data Elements
     • Updated actionable button appearance on the Admin interface to reflect the correct status based on the selected Data Element
     • Moved the actionable button to the top of the table for better usability
     • Adjusted column widths on multiple tables
   • Form Structure
     • ​​​​​Added ability to search for Form Structures by Form Structure Keywords
     • Adjusted column widths on multiple tables
   • Create eForm/eForm Builder
     • Added ability to display PVs/PVDs in single column instead of the default two columns
        
4. Data Repository
   • View Studies Table
     • Added ability for users to hide and show columns based on the selected dropdown items
     • Added a new “Subjects” column which displays the unique GUID/PseudoGUID count based on the submitted data for the study
     • Updated spacing between lines on Study Details page
   • Edit Studies
     • Aligned the flag icon and column width across various tables
   • Submission Tool
     • Retired the Webstart version of the Submission Tool
     • Optimized the file loading, validation, and upload capabilities – more enhancements to come
     • Added ability to upload multiple CSVs within sub-directories
     • Enhanced Validation Report to only display the first 100 Errors/Warnings for faster validation results
     • Updated validation rule to accept milliseconds during validation
     • Updated Extra Validation Keys
   • Download Tool
     • ​​​​Retired the Webstart version of the Download Tool
     • Adjusted the display to show the selected items at the top of the table under Package Contents section
   • PDBP Biosample
     • Updated the derived data pull based on the new criteria for catalog import
        
5. Query Tool
   • ​​​​​​​Enhanced User Interface (UI) for Studies and Forms in the right panel.
     • Study Title and Form Structure names show up in bold
     • Added icons for Subjects and Count for Form Structures and Studies
   • Replaced Triplanar image rendering with VolViewer
     • VolViewer is “an image rendering tool that is commonly used in the field of medical imaging.  It allows users to view and manipulate volumetric data, such as CT or MRI scans, in a 3D space”
   • Added Data Types under the left panel (e.g., Clinical, Imaging)
   • Updated the criteria for Change in Diagnosis highlights
   • Enhanced the usability of the Data Element Search feature by shortening the table height
      
6. Accounts
   • ​​​​​​​Ability for Admin users to Cancel Permission Group requests
   • Added Download button to Account Group Lists
   • Confirmation message sent to Admins after sending reset password link
      
7. Biosample
   • ​​​​​​​Made OID button linked in Your Orders table
      
8. Public Site
   • ​​​​​​​When user hovers over menu, background page gets grayed out
   • Reduced space between bar and text of tabs
   • Added Dictionary page back to Public Site
     ​​​​​​​

1. ProFoRMS
   • Synchronized the Scheduled Visit Dates with the My Collections Date so that when the user updates the date under the Scheduled Visit Date, it gets reflected in the My Collections data table 
   • Several User Interface (UI) updates
     • Moved majority of filters to the left pane
     • Enhanced the display format for eForm listing on Create/My Visit Types page
     • Widened the fields under Assigned Roles page for better visibility
     • Cleaned up redundant attributes/fields from Subject information section that were not being used
        
2. Subject Management/GUID
   • Ability to associate a GUID/Pseudo-GUID with a Data Repository study
     • This will allow users to view and select GUIDs created by their study team under the ProFoRMS module
   • Pseudo-GUID creation now permission based (admins only feature)
      
3. Data Dictionary
   • Data Elements  - Mapping for other Biomedical Standards
     • Added Concept Name, Concept Identifier, and Terminology Source attributes at the Data Element and Permissible Value level for capturing/mapping the biomedical industry standards UMLS, LOINC, SNOMED, RxNorm
     • Updated the Data Element import template to include the new attributes for bulk import
     • Added capability to search for new attributes in the Data Element Search page
     • Updated delimiters to be pipes instead of semi colons
   • Data Elements
     • Made previously required Classification > Domain and Sub Domain optional fields
   • Form Structure
     • ​​​​Added new Data Types in Form Type list (Biosample, Other-Omics, Pre-Clinical)
     • Addition of Date Range filters on search page
   • Create eForm/eForm Builder
     • New skip rule for adding auto-populated answers
     • Ability to view calculation rules and test the eForm prior to publication
     • Addition of Audit Logs for logging changes made to Calculation Rules or Skip Rules after eForms get published
     • Update to hover over message for email trigger
     • Addition of Date Range filter search page
   • UI Updates - Data Elements and Form Structure View
     • Accordions have been updated to tabs to display the components/sections for better user experience
        
4. Data Repository
   • View Studies Table
     • Accordions have been updated to tabs to display the components/sections for better user experience
     • Fed Reporter links updated so that Grant IDs point to the correct URL
     • Added the new Data Types in the search criteria
   • Submission Tool
     • Updated Extra Validation Keys
   • Biosample Catalog
     • Updated catalog file to search and compile on additional criteria
       ​​​​​​​
5. Query Tool
   • ​​​​​​​Added subject count to the Study and Form Structure container in the right pane
   • Updated filters for Data Types (Biosample, Other Omics, Pre-Clinical)
      
6. Accounts
   • Addition of Lock and Deactivate feature for accounts that have been inactive for a long period of time
   • System email will be sent when user updates their account password
   • Updated telephone number field in biosample form to accept international phone numbers
     ​​​​​​​​​​​​​
      

1. ProFoRMS
   • Performance enhancement across various pages
   • Introduced Visit Type Group capability
     • Admins can create and manage Visit Type templates
     • Users can import the templates created by the Admins in their protocols (as needed)
   • Removed the study list section from Protocol Information page
   • eForm Display - updated a few UI elements to make user experience better (more to come in future releases)
      
2. GUID
   • Made minor UI updates by moving the filters from the top of the tables to the left navigation pane
      
3. Data Dictionary
   • Updated a few UI elements to make user experience better
   • Updated the eForm Builder page to make it consistent with the rendered version in ProFoRMS
      
4. Data Repository
   • View Studies Table
     • Adjusted column widths for “Row No, Shared Data, and Study ID”
     • Moved the filters in the left pane
     • Added an icon next to the study title if the study has supporting documentation(s)
     • Left Navigation Menu changes – reorganized items in the left menu for better user experience
   • Download Tool
     • Associated files to be excluded by default
     • Data Repository Downloads - Data Element Detail files to be included with downloaded data instead of the PV mapping file
     • Data Privacy Disclosure Agreement form to be asked once per online session for each tool
   • Submission Tool
     • Added capability for including Description and Flag to datasets during the Upload process.  This will be visible on the Dataset Submissions table under the study
     • Made significant performance improvements with uploading large package uploads
     • Made update to file extension validation rules to use exclude list instead of include list
     • Multiple files with same name & extension (from different sub-folders) to be treated as separate files
     • Made the data validation tool recognize dates which are entered in non-ISO format
   • Submission Tool API
     • Added the following new end points for the Submission Tool
       • Prevalidation – validates all the data on the csv. against the Form Structure except for the associated files.  Users DO NOT need to upload the associated files during prevalidation
       • Initialize
       • Upload Files
       • Finalize Upload
          
5. Query Tool
   • Query Tool joins will be done on GUID and Visit Type
   • Added filters for Data Types (Clinical, Genomics & Imaging)
   • Added a new ‘Add All to Cart’ button which will add all the items from the right pane to the cart
      
6. Public Site
   • Performance improvements, graph and visualization updates
      
7. Technical Upgrades
   • Upgraded Drupal from version 8 to version 9
   • Upgraded the JQuery UI Library
   • Automated properties deployments

1. Navigation and User Experience Updates
   • Updated color scheme for PDBP portal
   • Updated the Menu, Left Navigation, and Filters UI across all modules
      
2. ProFoRMS
   • Removed Visit Type and Category fields from Create Visit Type and made the Description optional
   • Increased the limit for submitting form IDs to Admin from 50 Form IDs to 1000 Form IDs to increase data correction efficiencies
      
3. Data Dictionary
   • Changed the pagination to scroll bar on Search Form Structures and eForms pages
   • Updated the tool tip for Conversion Factor legend under the eForm builder
   • Added Validation Checks for See Also field for Data Elements
      
4. Data Repository
   • Improved the filter users feature under the Grant Permissions tab
   • Added history/audit log under the Grant Permissions tab
   • Made the Study URL clickable link
   • Added a new column “Study Title” to one of the downloadable reports
   • Swapped the order of the Web Start and JavaScript tools (completed for the Download Tool and Submission Tool)
   • JavaScript version is now the primary version and Web Start version will eventually be removed
   • Made minor modifications to Manage Study Group’s display order
   • Submission Tool – Data Validation Tool now checks for duplicate rows of data and displays error messages for it
      
5. Query Tool
   • Query by GUID feature - selected GUIDs from the search field are prepopulated under the Data Element filter
   • Updated the Download to Queue message so that it is clearer for users to know where to access and download their data

1. JS version of the Submission Tool
   • Allows submission to be performed directly from the web browser
   • No software installation is required
      
2. Submission Tool Enhancement (webstart and JS version)
   • Updated date/time format to allow users to submit with milliseconds and display a warning message instead of blocking the submission with an error message
      
3. Internet Explorer is no longer supported message
   • A notification will appear at the top of a user’s browser on the public and portal sites saying that Internet Explorer (IE) version 11 is no longer supported
      
4. Query Tool Enhancements
   • Ability to search by GUIDs/Pseudo GUIDs which returns Form Structures and Studies that contain the searched GUIDs/Pseudo GUIDs
   • Addition of the associated GUID/Pseudo GUIDs column under the data table so users can view the linked GUIDs/Pseudo GUIDs
   • Ability to view Permissible Value (PV) count for the Data Elements under the filter section.  This displays the number of times the PV appears in the query that was run
   • Data under the Datasets column is linked so that users can click on the Dataset ID and see the details for it
   • The order for the Repeatable Group data is persistent in the Query Tool data table and also when it is downloaded.  Now the data stays in the same order as it was uploaded during the submission
   • Optimized the functionality for hiding columns in the data table
      
5. Data Repository Enhancements
   • Updated data tables to use the scroll bars instead of pagination
   • Renamed the Download Report to Study Access Report and added an additional report named Study Information Report
   • Cleaned up the UI and moved a few buttons and aligned the tables when creating/editing a study
   • Added the ability to Edit/Delete the data under multiple tables
   • Added new fields and additional values in the Study Type dropdown
   • Made the Study Type and Funding Sources values multi-select

1. ProFoRMS
   • Fixed the issue in Data Collection where the collection would show as "In Progress" status but had a Locked Date for it
      
2. Account Management
   • "De-activated" users will no longer receive the "Dataset Submission is complete!" email notification when there are data corrections/resubmissions for older collections

1. Notification to PIs when their study data is set to be shared
   • Per NINDS program guidelines, any study submitting data to the PDBP DMR is required to share their clinical data with all authorized PDBP DMR users after being active for greater than one year (unless otherwise agreed upon with the NINDS program team).
      
2. GUID Tool Updated to ‘Subject Management’
   • Interface updates made, main functionality of tool to remain the same
   • Data Privacy agreement and acceptance required one time at initial use of too​​l
      
3. Query Tool Enhancements
   • New tool-tips added
   • Ability for user to download query logic box information
   • Distinct separation of program defined queries from system user/shared queries
      
4. ProFoRMS Enhancements
   • Relocated legend keys for various statuses to the left above the list of eForms
   • Replaced GUID tool in ‘Add Subject’ section with a GUID table that allows a user to select a GUID they have already created in the Subject Management module, and add that GUID to their protocol
      
5. Data Repository Enhancements
   • Warning message to appear when trying to submit data to a form with retired data elements

1. PDBP MDS-UPDRS_Virtual Visit - created due to COVID-19 and the inability to collect all clinical assessments in-person:
   • https://dictionary.pdbp.ninds.nih.gov/portal/dictionary/dataStructureAction!view.action?dataStructureName=MDS_UPDRS_VirtualVisit
      
2. PDBP MoCA_Virtual Visit - created due to COVID-19 and the inability to collect all clinical assessments in-person:
   • https://dictionary.pdbp.ninds.nih.gov/portal/dictionary/dataStructureAction!view.action?dataStructureName=MoCA_VirtualVisit

1. ProFoRMS
   • Locked forms showing status of 'In Progress' with a locked date and time
      
2. Account Management
   • Cancelling a permissions group request for a user results in error during account review and approval

1. Hiding certain PII/PHI values in the system
   • In an effort to be more compliant with HIPAA policy and changing research standards, data associated with individual participant AgeYrs and VisitDate values will be converted and/or hidden in the system. 
     • AgeYrs values will be converted from absolute values to a numeric range (e.g.  65 = 60 – 69) and study participants with an age equal to or greater than 90 will be aggregated into a “90+” category. Changes will be reflected for both current and future data in the DMR.
     • VisitDate values will be hidden from the Query Tool and removed from the download package when exporting data from the DMR.
        
2. Query Tool Updates
   • New ‘Row Count’ column and column/view “freeze/lock” capability.
      
3. Transition of the Download Tool from a Java Webstart to a Javascript application *Beta Version*
   • Ability to launch the download tool functionality directly from the browser, as opposed to downloading, installing, and launching the java webstart version. New feature also accounts for usability and users/organizations that do not support deprecated Java versions and software. Note: This is a beta version of the application and the existing Java Web Start version will be available to use. It is recommended that for large dataset downloads or datasets that include multiple file attachments, you continue to use the Java Web Start version. 
      
4. Updates to the Biosample Catalog API
   • Addition of a new form data element to capture the PDBP Study ID in order to distinguish samples collected for participants enrolled in multiple studies.
   • New translation feature to convert and add STEADY-PD3 samples into the Biosample Catalog.
      
5. ProFoRMS Enhancements
   • Various data tables have been updated to display both the GUID and Subject ID for faster reference and GUID to participant association.
      
6. Replacement of the current data transfer process (Mirth) to a new, more efficient web-service. 
   • Effort makes the transfer of data from ProFoRMS to the Data Repository more efficient. Custom notifications have been added along with end-to-end transactional status updates and indicators for better oversight of data migration.
      
7. Ability for users to renew expiring accounts and/or DMR privileges directly in the DMR
   • Currently, users request a renewal of privileges by email to the PDBPOps Support email. 
     
      

1. PDBP Special Attributes – Captures genes/mutations of interest: https://dictionary.pdbp.ninds.nih.gov/portal/dictionary/dataStructureAction!view.action?dataStructureName=PDBP_Special_Attributes
    
2. NINDS Biorepository PDBP Biosample Catalog - Updated version which includes the new PDBPStudyID data element
    
3. PDBP Imaging PET – Positron Emission Tomography imaging information specific for PDBP: https://dictionary.pdbp.ninds.nih.gov/portal/dictionary/dataStructureAction!view.action?dataStructureName=PDBP_ImagingPET
    
4. Updates to the PDBP Next-Generation Sequencing Dataset (PDBP_NGS_Data_Set) and PDBP SNP Array Data Set (PDBP_SNP_Array_Data_Set) forms - inclusion of protocol file upload data elements
    

1. Public Site - Summary Graph Corrections
   • Biosample graphs display total samples available as opposed to unique GUIDs
   • LBD NPI summary chart - total participant quantity updates

1. Query Tool - Advanced Search Capabilities
   • Inclusion of boolean search and additional search operators
     • Inclusive/Exclusive
     • Exact search text criteria
     • AND, OR, NOT
   • Default full-outer join for queried data and form joins (previously set to a default left-outer join)
   • Real-time SQL script creation
   • Ability to configure returned data by: 1) Permissible Value Descriptions (PVDs) or 2) Permissible Value output code(s)
      
2. DMR Genomics DUC Workflow
   • New workflow to automate the PDBP DMR Genomics DUC renewal process. Users requesting access to PDBP Genomics data must provide an institutional signature via the Genomics DUC. Access to PDBP Genomics data is reviewed on an annual basis and requires an updated Genomics DUC.
      
3. Highlight of MDS-UPDRS Rescored Data
   • Due to inner-rater reliability issues at the Penn State site, the MDS-UPDRS Pt. III data were re-scored by the site’s expert rater for a subset of patients at their months 12-18 visits.  These new scores can be found by querying the "PDBP MDS-UPDRS_Penn State Rescored" form structure and are indicated in red font. Note that rigidity scores could not be reevaluated and are left blank here. Users can query the rescored separately or join the recored data with the existing MDS-UPDRS study data for comparison.
      
4. 64-bit Implementation of the Submission Tool
   • A new, 64-bit version of the DMR Submission Tool is available for data upload to the Data Repository. Note: Users should have the 64-bit version of Java installed prior to running this version of the tool

1. Removal of the Biorepository Subject ID
   • Field and associated data (PII/PHI) has been removed from ProFoRMS
      
2. Updated LBD Biosample Inventory Graph
   • Updates to the LBD Biosample Inventory graph on the PDBP public website. Graph and query has been modified to accurate display DNA samples, which are only collected at baseline for LBD studies

1. 21 Code of Federal Regulations (CFR) Part 11 Compliance
   • The PDBP DMR is fully certified and subsequently electronic records and electronic signatures within BRICS are considered trustworthy, reliable, and equivalent to paper records: 21CRFPart11 Certification
   • 21 CRF part 11 - eSignature: The user account creation process includes new functionality for acknowledging/signing a the new electronic signature policy
   • 21 CRF part 11 - system auditing: Improved user activity logging, capturing: 1) when a user has/is logged into the DMR; 2) how long the user is logged into the system; and 3) when the user is logged out. Access logs are available for review and download by system administrators in the Accounts Module
   • 21 CRF part 11 - ProFORMS Module updates: New "save & lock" eSignature acknowledgements, modifications to the collection audit log, mandatory write-up for change in collection/eForm, and capture of exact user name for locked forms in ProFoRMS to the Data Repository.
      
2. New Neuropathology Data Set (NACC Form Structure)
   • Addition of the NACC-Neuropathology Form Structure for brain data collection in the DMR Data Dictionary. To access the Form Structure, Click here. The Form is based on version 10 of the form. Note: This form is available for data collection in ProFoRMS. Users must submit data to this form using the Submission Tool available in the Data Repository. 
      
3. PDBP GUID Migration
   • As part of the centralized GUID solution, a collaborative effort between PDBP, NINDS, and NIA, all PDBP GUIDs (GUIDs & Pseudo-GUIDs) have been officially migrated to the centralized server. This allows for the potential of GUID sharing/visibility across PDBP, NINDS, and NIA, pending user permissions.
      
4. Query Tool - Performance Improvements
   • Improvements to the Query Tool Module include:
     • Significant performance improvements for data querying and form joins: system returns a 5-form join with approx. 1M records in ~20 seconds
     • Transition the Query Tool data-table to a Virtual Table to improve data rendering performance
     • Improvements to the Biosample Ordering process, allowing for a "select all" control for all or filtered biospecimen records
     • Replace data-table pagination with a single page view
        
5. Replacement of Mirth Web-services
   • Replacement of the older web-service (Mirth) that submitted ProFoRMS data to the Data Repository on a nightly basis to a newer, more efficient service

1. ProFoRMS Admin Privilege Removal
   • A status of "Active-Expiring Soon" caused ProFoRMS admin privileges to be removed from the Account Module
      
2. ProFoRMS - eForm retrieval issue
   • Permissions related to user access to the Data Dictionary and being able to retrieve/add eForms to a visit type
      
3. Number keypad disabled in GUID Module
   • Number pad on keyboard did not work with the GUID module. Attempting to interact with the GUID client and input participant information using the number pad was disabled

1. GUID Client Transition to JavaScript
   • Refactor of the current Java web-start client to a browser based, JavaScript application. This new feature will allow users the ability to generate GUIDs online The current Java (.jnlp file) application will be replaced, removing the need for users to download and install the GUID client each time they want to generate a GUID. The JavaScript version will load directly on the users page, allowing for faster, more efficient interactions with the GUID client. The GUID JavaScript application is supported on all browsers (Google Chrome, Firefox, Microsoft Edge, Safari, and Internet Explorer v10 and higher). All functionality from the previous webstart version is maintained
      
2. 5-Form Join Performance Improvements
   • Effort includes enhancing the speed and overall perform of returned queries for large form joins and resolving issues with large data packages being sent to the Download Tool
      
3. OpenJDK Alternative to Oracle Java
   • The inclusion of OpenJDK is intended to mitigate any potential issues regarding Oracle and Java license fees and/or support. OpenJDK will ensure that users are able to continue using BRICS webstarts (Download Tool, Submission Tool, MIPAV, etc.). For additional details on how to download and install OpenJDK, Click here.
      
4. Manage Protocol Using GUID or Subject ID
   • Allow protocol coordinators the ability to change GUID to Subject ID in Manage Protocols section in ProForms

1. Removal of Users from Account Permission Groups
   • Permission violation issue resolved for user account being removed from permissions groups
      
2. PDBP Public Site Anchors
   • Resolution of multiple URL anchors on the pdbp public site
      
3. PDBP Public Site - PubMed API
   • Refactor of the NHLBI PubMed API to automatically retrieve PDBP specific publications

1. Flag GUIDs with a Change in Diagnosis
   • This feature will highlight any/all GUIDs (records) in the Query Tool for subjects that have been identified as having a change in diagnosis. The process surveys the PDBP Change in Diagnosis form structure and highlights all GUIDs where the 'Change in Diagnosis' data element's permissible value is equal to "Yes." RDFGen has been modified to automate the highlight, removing the dependency on querying the specific PDBP Change in Diagnosis form structure and/or 'Change in Diagnosis' data element.
      
2. Query Tool 5-Form Join
   • This feature allows users the ability to join up-to five (5) form structures in the query tool. The previous configuration allowed for a maximum of three forms to be joined.
      
3. Multi-Tenant GUID Solution
   • This feature allows for the recognition and sharing of GUIDs across participating BRICS instances. Users can now 'link' GUID permissions across multiple instances and/or view 'matching' GUIDs across all instances. Pending permissions, users will be able to view the GUID along with specific meta-data including: Registered User; Registered Entity; and Date Registered. Further, this new feature has allowed for new, advanced database technologies to be incorporated (mongoDB), ensuring that the solution is scalable and secure.
      
4. Account Module Security Updates
   • In order to make the publicly available portions of BRICS more secure, additional controls are being added which include:
     • File upload limit - one file per upload type
     • File upload types - a restriction on file types (e.g. .pdf, .doc, etc.)
     • Implementation of reCAPTCHA to ensure requests are legitimate and being submitted by an actual user
        
5. jQuery Datatable Updates
   • Updating all BRICS data-tables and making them consistent across all modules. This release focused on the following modules/data-tables:
     • ProFoRMS - Reports tab (all), Collect Data tab (all), and Manage Protocol tab (all)
     • Biosample Order section (all)

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