Resource and Data Exchange - Health Research | UVA

Home Page

The home page is the default page for an RDE instance. It serves as a landing page with introductory content intended to inform users about the capabilities of the instance / website at a high level.

Click the instance logo on any page in an RDE instance to navigate to the home page.

Resource Explorer

Resource Explorer Search Overview

The Resource Explorer allows you to discover informational content that has been added to the Resource and Data Exchange by authenticated users.

All authenticated users are encouraged to add relevant resources using the Add Resource feature (plus icon in the upper right) and completing the simple web form. Events are a special type of resource, as they have an associated location (virtual or physical), date, and time, and can be added directly to users' calendars. Resource Owners (and Resource Explorer Administrators at their organization) control content and visibility.

Resources can be associated with multiple categories, allowing them to be discovered by users who filter or browse content by category. The Resource Explorer search allows all users to quickly find relevant content using text search, applying filters, or Browse categories.

Authenticated users will see resources curated for their institution by default with the "Audience" filter applied. Authenticated users can also "favorite" resources, making them easier to find in the future using the "My Favorites" filter, and can locate content they own by selecting the "Owned by Me" filter.

For assistance, refer to the help section of the application for documentation and to request personal consultations.

Resource Explorer Search Bar

Type in the search bar to the left to match text that appears in the title, body, or any field of a resource. You must type at least two characters. You can choose an autocomplete suggestion or press enter to search for the characters you added. Text search will look for characters at the start of words, but not in the middle of words.

Resource Explorer Search Sort

Use the "Sort by" feature to reorder your results. The default sort is "Most Favorited", which lists resources first based on the number of users who have favorited them.

When searching by string matching, results will default to sorting by "Relevance", prioritizing items where the string appears in the title of the resource or event.

Select sort by "Recently Updated" to prioritize content that was most recently added to the Resource Explorer.

Resource Explorer Search Filters

Apply filters to narrow your search results. The filter applies "AND" logic between filter sections and "OR" logic within a specific filter section.

Audience (Default Filter): If you are logged in, the Resource Explorer will default to resources curated for your organization (unless you explicitly specify another audience filter).

Owned by Me (Authenticated Users Only): Shows resources where you are listed as an owner. Add content using the "Add Resource" button at the top of the page, then easily find it later using this filter.

My Favorites (Authenticated Users Only): Displays only the resources you have added to your favorites. To add favorites, click the appropriate icon while viewing a resource, then quickly access them later using this filter.

Resource Type: Defaults to displaying informational resources and upcoming (or ongoing) events (Future Events). Past events are excluded unless you check the "Past Events" box.

Category: Select one or more categories to filter results to resources associated with any of the chosen categories. Resources can belong to multiple categories.

Visibility (Resource Explorer Administrators Only): Administrators can view all resources, including "Owners Only" or "All Users". If not listed as an owner, they will only see resources that are visible to "Owners Only" if the resource Creator Organization is same as the Resource Explorer Administrator's organization.

Resource Explorer Export to CSV

This feature is available to Resource Explorer Administrators only. They can export all resources they have access to in search, or a subset of those resources that is the result of a search.

Click "Export to CSV" to initiate the download. Only resources that are shown in the current set of results will be exported. To export all resources, be sure to remove all filters and search strings.

Add Resource Overview

Click "Add Resource" in the top right of the Resource Explorer and complete the form with the relevant information in each of the fields listed below.

Note that when you first save a resource it is only visible to you. However, you will have the option to edit Resource Details or Resource Access once you view the saved resource.

Type: Select "Resource" for informational resources. Select "Event" for any resources that have a date and time, including in person events, virtual events, and even funding opportunities. Entering funding opportunities as events allows users to filter opportunities to those that are currently open. If your event has multiple dates (for example a course with a series of dates) we suggest you add an informational resource describing the group of events and that contains links to each of the specific events. This allows each event to be added independently to users' calendars.

Title (required): Name your resource. We suggest adding "FUNDING:" to the start of the name when adding funding opportunities.

Icon (required): This icon will be displayed at the top of your resource page and on resource tiles. Select one option from a list of default icons that you feel best relates to your resource. If more than one icon applies, select your preferred icon. The text selected will be displayed when users hover on the icon.

Creator Organization (required, not editable): Your organization will appear here. If your RDE instance has multiple participating organizations, only the Resource Explorer Administrators at your organization will have special view/edit access.

Show Creator Organization Logo (required): This checkbox is selected as a default. However, you may choose to remove that selection if the resource you are adding is multi-institutional, represents an external resource, or in any other case where displaying your organization's logo is not appropriate or meaningful.

Description (required): Type or paste in your main page content. You can use the editing tools at the top of this box to do some basic formatting.

We suggest you:

mention a few key details even if linking to an external web page
include words in your description that users might use in Search Resources
highlight underutilized aspects of your resource
address any misconceptions or direct users to related resources

Categories (required): Every resource must be associated with at least one category in the Resource Explorer. It is possible to associate your resource with multiple categories. Pick the categories where you think it fits best.

Contact Name (optional): Name or description of the best contact for this resource.

Contact Email (optional): Email to use for more information about this resource.

Contact Phone (optional): Phone number to call for more information about this resource.

Website (optional): You can choose to link your resource to an external website. You might use the main description section to describe what users will find by following this link and when they should reference your online resources.

Select Cancel to discard any entries you have made in the form. Select Save to create and view the new resource. Upon clicking save, the system will notify you if any of the entries are not valid. You do not need to be fully done with the page to save and close it if the required fields have valid input.

Remember that after saving you will need to edit "Visibility of Resource Details" under Resource Access to add other owners or to make this resource visible to other users.

Upon the first save, the resource will be assigned a unique ID which you will see in the URL. Copy and paste the URL to share with other owners (or the public once you have made it visible to all users).

View Resource Overview

Resources are added by authenticated users. Resource Owners can choose to make their resource visible to all users. If you are viewing a resource, you are either listed as a Resource Owner or Resource Explorer Administrator OR the Resource Owners have made the resource visible to all users.

View Resource Details

Icon: This icon is selected by Resource Owners

Title: Each resource has a title that appears at the top.

Visit Website (optional): Resource Owners may add a link to external website.

Add to Calendar (events only): Clickable link to add the event to your calendar.

Add to (or remove from) Favorites (logged-in users only): Clickable link to add or remove the resource from your personal favorites. Logged-in users can access their favorites by applying the "My Favorites" filter in the Resource Explorer search.

Location (events only): All events will have an in person or virtual location provided.

Date and Time (events only): The start and end date and time of an event.

Description: This field contains informational content added by the Resource Owners.

Contact Name, Email, Phone (optional): Resource Owners may elect to add contact information. If no contact information is provided but you would like to know more, you can go to the Help page using the left-side navigation and request a consultation.

Creator Organization: The name of the organization associated with the original creator (Resource Owner).

Categories: A list of one or more Resource Explorer categories that the owner has associated with this resource.

Website (optional): Resource Owners may add a link to external website.

Attachments (optional): Clickable attachment link(s) to download file(s) to your computer. Attachments can include images, videos, PDFs, etc. Note that you can right-click the attachment link to obtain a URL that can be used in emails or provided as a link elsewhere. Resource Owners can add or delete attachments.

View Resource Access

Only Resource Owners can see this section of the page. If you are a Resource Owner, you may select the Edit Resource Access icon to make changes.

Resource Permissions: This is a list of Resource Owners emails. Owners can Edit Resource Details and Edit Resource Access.

Visibility of Resource Details: This section indicates whether the resource is visible only to Resource Owners (and Resource Explorer Administrators from the same organization as the Creator Organization) or to anyone on the internet.

Recommended Audience: If you select an organization, then all users logged in to that organization will see this page after selecting "Audience" filter in Search Resources. "Guest Users" applies to non-authenticated users who are accessing the Resource and Data Exchange without logging in through their organization.

Edit Resource Details Overview

Resource Owners (and Resource Explorer Administrators at the organization listed as "Creator Organization") can edit any resource field using this form. See the Add Resource help section for more instructions around the specific fields of the form.

Any edits you make to resource will be reflected in the system immediately upon successfully saving it.

To edit Resource Access (Permissions, Recommended Audiences, and Visibility), select Cancel to return to View Resource and then select the edit icon next to Resource Access.

Edit Resource Access Overview

Resource Owners (and Resource Explorer Administrators from the organization listed as "Creator Organization") can control Resource Permissions, Recommended Audiences, and Visibility. Each access type is described below.

Edit Resource Permissions

Resource creators are "Resource Owners" by default and can assign other resource owners by adding their organizational email or removing current owners.

Resource Owners (and Resource Explorer Administrators from the organization listed as "Creator Organization") can see Resource Access information and can edit both Resource Details and Resource Access.

Edit Resource Visibility

Select "All Users" when you are ready for your resource to be visible to anyone online. Otherwise, select "Owners Only". Note that Resource Explorer Administrators from the organization listed as "Creator Organization" can see and edit all resources associated with their organization, even if you have not made those resources visible to "All Users".

Edit Resource Recommended Audience

In addition to making content visible to all users in the Resource Explorer, you can curate your content for specific audiences.

Besides users from your organization, which other groups are the intended audiences? This selection helps focus users' Browse experiences.

Groups you select below will see this page after selecting the "Audience" filter in the Resource Explorer search. Select "Guest Users" to curate content for people who are not logged in through an organization.

Delete Resource

Resource Owners will see an option to "Delete Resource". If selected, the system will prompt the Resource Owner to confirm the deletion. Resource Explorer Administrators from the organization listed as "Creator Organization" also have access to this functionality.

Click "Permanently delete this resource!" if you wish to continue with deleting the resource. Otherwise, click "Cancel" to cancel the deletion process. If you have erroneously deleted a resource, immediately request a consultation using the Help section to the left of the page.

Private Data Enclave

Private Data Enclave Search Overview

The Private Data Enclave is a data management infrastructure that supports the indexing, organization, personalized permissions, and optional public visibility of components of research projects. These components include things like project details (research descriptions, contacts, funding sources, etc.), project documents, and datasets. Users can manage their data throughout the research lifecycle while generating searchable indices of their research products.

You can only see the Private Data Enclave if you are logged into the Resource and Data Exchange. You also need to meet all security requirements for this Resource and Data Exchange instance as configured by your local Private Data Enclave Administrators. This may include network or IP address requirements.

The public visibility of project details, dataset details, and dataset files are independently controlled through the application. Researchers may opt to keep all project and dataset information private to specific members of their team. You will see all projects in the Private Data Enclave where you are listed as a project owner or project collaborator.

Select "Add Project" to add a new project to the Private Data Enclave. Note that some instances are configured to restrict this feature to local system administrators.

Select "Add Dataset" from within a project to describe datasets and upload related files. Note that some information is extracted automatically and added to Dataset Details when you upload certain types of datasets. Some files undergo automated pre-processing depending on the user's selections.

As you navigate, select the help button to learn more about special features.

Request a consultation in Help by using the navigation panel to the left.

Private Data Enclave Search Bar

As a default, you will see all projects that you have access to, listed in order of most recently updated. Select "Datasets" to see all datasets you have access to, listed in order of most recently updated.

To search within your projects and datasets, select Projects or Datasets, then type the desired string to search by into the search bar.

The string search will find all projects or datasets to which you have access and that have the specified string in any of Project Details or Dataset Details. If there are multiple words in the specified string, a project or dataset is matched if its details have any one of those words.

Results are returned based on relevance to the string searched, with the following ranking order applied: keywords, title, description. You may elect to sort the search results by most recently updated.

Private Data Enclave Search Sort By

As a default, results are listed in order of most recently updated. After searching a string, the sorting method changes to order by most relevant. Use the dropdown menu under Sort By to change the sort order at any time.

Private Data Enclave Search Filters

The Private Data Enclave filters to "Projects" by default. Select "Datasets" if you wish to filter to those instead.

Private Data Enclave Export to CSV

This feature is available to Private Data Enclave Administrators only. They can export all current search results to a .csv file. The file only contains the results they have permission to see (those stored at and their local organization, and any others where they have been individually assigned permissions).

Click "Export to CSV" to initiate the download. Only projects or datasets that show in the current set of results will be exported. To export all, be sure to remove any search strings. Project and dataset lists must be exported independently by toggling the filter.

Add Private Project Overview

Complete the form with the relevant information in each of the fields listed below. You cannot save the project without completing all required fields.

Note that when you first save a project it is only visible to you, Private Data Enclave Administrators at your organization, and anyone you have added as a Principal Investigator. However, you will have the option to edit Project Details or Project Access once you view the saved project.

Title (required): Enter the full name of your project.

Project Lead / Principal Investigator Email(s) (required): Enter a list of email addresses for one or more Principal Investigators (PIs).

Note that storage totals will be calculated for PIs listed by summing the total size of dataset files associated with the project.

Note also that PIs are automatically assigned the Project Owner role.

Description (required): Type or paste in your project description.

Keywords (required): Enter a list of words or phrases that people can use to search for this project.

Website (optional): Paste link to any external web page that you would like to have associated with the project.

Storage Organization (required, not editable): The default value will be the organization associated with the project creator's login. Note that all datasets added to the project will also be saved at this organization.

Show Storage Organization Logo (required): This checkbox is selected as a default. However, you may choose to remove that selection if the project you are adding is multi-institutional, represents an external resource, or in any other instance where displaying your organization's logo on it is not appropriate or meaningful.

Partner Organizations (optional): Enter a list of partner organization names for this project.

Funding Source(s) (optional): Enter a list of funding sources for this project.

Contact Name (optional): Name or description of the best contact for this project.

Contact Email (optional): Email to use for more information about this project.

Contact Phone (optional): Phone number to call for more information about this project.

Related Resources (optional): Paste the URL(s) to the Resource Explorer page(s) in the field provided and press Enter after each entry. If any of the of the URLs are not recognized by the system, you will receive an error message when attempting to submit.

Related Resources will display as tiles in Project Details upon successful submission.

Select Cancel to discard any entries you have made in the form. Select Save to create and view the new Project. Upon clicking save, the system will notify you if any of the entries are not valid. Once all elements are valid, the system will then prompt you to confirm that no Personally Identifiable Information (PII) has been included in any of these text fields.

You will need to select Edit Project Access from the View Project page if you need to add team members or if you want to make Project Details visible in the Public Data Commons.

Upon the first save, the Project will be assigned a unique ID which you will see in the URL. You can share the URL with other people who have access to this Project in the Private Data Enclave. NOTE: If you choose to make the Project Details publicly visible, a second URL for the project's view in the Public Data Commons will be available. This URL can be discovered by right-clicking on the "View in Public Data Commons" link when viewing the project in the Private Data Enclave. Use the Public Data Commons URL when sharing the project outside of your project team.

View Private Project Overview

Only users who are listed as Project Owners or Project Collaborators (and Private Data Enclave Administrators) can view Projects in the Private Data Enclave. Some RDE instances also require users to be connected to a secure network.

View Private Project Details

Project Details include: Title, Description, Keywords, Principal Investigator, Contact Name, Contact Email, Storage Organization (institution where the Project is saved), Partner Institution(s), Funding Source(s), Website, and Related Resources.

Resources from the Resource Explorer can also be associated with a project. These fields are visible to Project Owners and Collaborators.

Project Owners can edit Project Details. Project Owners can publicly share Project Details by editing Project Details Visibility in the Project Access form. If the Project Details have been made publicly visible, users in the Private Data Commons will see a link to view the project in the Public Commons. This allows the team to quickly jump to a public view of this object.

View Private Project Access

Project Permissions lists all Project Owners and Collaborators. These permissions can be viewed by Project Owners, Project Collaborators, and Private Data Enclave Administrators from the organization listed as "Storage Organization" but can only be edited by Project Owners.

Anyone who can log in through a participating organization can be added to the Project. Note that dataset permissions are independently controlled by anyone who adds a dataset.

Visibility of Project Details: Indicates whether the project is visible in the Public Data Commons.

Visibility can be viewed by Project Owners, Project Collaborators, and Private Data Enclave Administrators from the organization listed as "Storage Organization", but they can only be edited by Project Owners. Note that the visibility of Dataset Details and Dataset Files are independently managed by Dataset Administrators.

View Private Project Documents

All Project Owners and Collaborators can download and upload Project Documents.

Click the "+ Add" button to add a new Project Document. Click the download icon next to a document to download. Only Project Owners can delete Project Documents.

Note that these documents are always only visible in the Private Data Enclave and cannot be published to the Public Data Commons. Any files that you would like to make public can be added as a Dataset with Dataset Details and Dataset File both made visible in the Public Data Commons.

Note that a Data Security Plan (DSP) must be uploaded as a project document prior to any datasets being added to the project that contain Highly Sensitive Data (HSD). This DSP will be presented to the dataset team member for review prior to download of an HSD dataset so they can ensure adherence to their plan. Note that any DSP associated with an HSD dataset cannot be deleted due to the previously described functionality.

View Private Project Associated Datasets

This section displays a list of the datasets that are associated with this project and where you are listed as a Dataset Administrator or Dataset Collaborator. If you are a Private Data Enclave System Administrator for the project's "Storage Organization" organization, you will see all associated datasets.

The listing is dependent on the permissions of the authenticated user viewing the screen, as each dataset has its own permissions controlled by Dataset Administrators. Note that dataset permissions are checked just prior to this page loading. If you are accessing a Highly Sensitive dataset, your permissions will be verified in the local IRB database and updated based on the status of the associated IRB protocol and your status on that protocol.

If you do not see a dataset you expect to see, reach out to a team member who administers the dataset or requests a consult using the Help section through left side navigation in the application.

Any Project Owner or Project Collaborator can add a new dataset to the Project by clicking the "Add" button. If you add a new dataset, you become a Dataset Administrator by default and can control Dataset Access for that dataset. No one else on the Project Team (including Project Owners and Project PIs) will see the dataset here unless you assign them Dataset Administrator or Dataset Collaborator permissions. Note that Private Data Enclave Administrators where the parent project lives will also see any dataset added.

Edit Private Project Details Overview

Project Owners can edit Project Details and Related Resources using this form. To edit Project Access (Permissions and Visibility), select Cancel to return to View Project and then select the edit icon next to Project Access.

You can add, edit, or remove values as long as the form validation criteria is met. See the Add Project help for more instructions around the specific fields of the form.

NOTE: Adding or changing the PI listed will result in the incoming PI being assigned the Project Owner role automatically. This will not revoke Project Owner permissions for the outgoing PI - that is at the discretion of the incoming PI and other Project Owners.

Upon clicking "Save", the system will notify you if any of the metadata elements are not valid. Once all elements are valid, the system will then prompt you to confirm that no Personally Identifiable Information (PII) has been included in any of these text fields. Click "Confirm" to finalize the changes and return to View Project.

Edit Private Project Access Overview

Project Owners can edit Project Access including Project Permissions and Visibility.

Edit Private Project Permissions

Project Permissions lists all Project Owners and Collaborators.

Project creators and the listed Principal Investigators are "Project Owners" by default and can add other team members by adding their organizational email (i.e. USERID@virginia.edu, USERID@carilionclinic.org, USERID@vt.edu, etc.).

If user access does not align with expected permissions, please ensure valid email addresses were used according to the formats provided in the help text.

The system will only validate for a correctly entered domain/organization, not the entire email address.

Project Owners can delete team members or change their role using the "Add", "Edit", and "Delete" buttons in the Project Permissions table. Note that dataset permissions are independently controlled by Dataset Administrators.

Edit Private Project Details Visibility

The default is "Visible only to Project team and Private Data Enclave Administrators". Select "Visible in the Public Data Commons" when you are ready for your Project Details to be visible to anyone online. The project will become discoverable in the Public Commons.

Click the "Visibility" radio button to change whether the project is visible to only the Project Team and Private Data Enclave Administrators or visible in the Public Data Commons.

Add Private Dataset Overview

Complete the form by entering the relevant Dataset Details in each of the fields listed below. You cannot save the Dataset Details without completing all required fields. Note that when you first save a dataset it is only visible to you and local Private Data Enclave Administrators. However, you will have the option to edit Dataset Details or Dataset Access once you view the saved dataset. Dataset files can also be uploaded at that time.

Dataset Type (required): Choose between Generic, DICOM, and REDCap for the dataset type. The default type is Generic.

Dataset Title (required): Enter the name of your dataset.

Description (required): Type or paste in your dataset description.

Keywords (required): Enter a list of words or phrases that people can use to search for this dataset.

Storage Organization (required, not editable): The default value will be the organization associated with the parent project. Note that this is also the organization where the dataset details and dataset files will be stored. If you want to store data at another organization, someone at that organization must create a new project and the dataset can be added there.

Show Storage Organization Logo (required): This checkbox is selected as a default. However, you may choose to remove that selection if the project you are adding is multi-institutional, represents an external resource, or in any other circumstance where displaying your organization's logo on it is not appropriate or meaningful.

HIPAA Identifiers (required): Enter patient data types captured. If the data does not come from medical records, enter N/A. Note: This value cannot be changed for DICOM dataset objects after the initial save.

IRB Number (required if you indicate the dataset contains Highly Sensitive Data): Select the IRB # under which use of this data is approved. This field will present you with a list of active IRB protocols where you are listed as a member of the study team in your local IRB database.

Associated Data Security Plan (required if you indicate the dataset contains Highly Sensitive Data): Associating a DSP with a dataset provides the team with easy access to documentation that tells them where they are allowed to store the data and who it can be transferred to. This step is required for HSD because it is essential that team members with this type of data have access to this document so they can ensure compliance.

Data Granularity (required for data derived from medical records): Select the level of granularity of the dataset using either Row Level Data, Data Aggregated to Groups of 11 or more, or Other for unique cases such as imaging files, time series, etc.

Other Sensitive Data (required): Select which types of other sensitive data are contained in this dataset, such as HIV Status, Psychiatric, Financial, Employment, Student, Consumer, Criminal, Additional Status, Sexual Health, Gender Identity, Personally Identifiable Information, Social Security Number, Controlled Unclassified Information (CUI), and Other Sensitive.

Associated Contract (optional): If the project involves data sharing with another institution, then a contract should be uploaded to the project and associated with any datasets covered by that agreement.

License (optional): Specify a license that should be associated with this dataset (i.e. Creative Commons license).

Variables Measured (optional): This list of variables tells collaborators what data elements the dataset contains.

DOI (optional): A DOI is a Digital Object Identifier. If you are indexing a dataset that already has a DOI, you can add it here. If you publish a Dataset File to the Public Commons, a DOI will be created for you and this field will auto populate.

Data Attribution (optional): This is a free text field where you can describe appropriate attribution language for any future reuse of the dataset.

Link to External Dataset File (optional): Datasets can be indexed by entering Dataset Details even when the dataset file is stored elsewhere. Paste a link to an external website or file path where the file is stored if appropriate. Note that you can save files directly in the Private Data Commons by uploading a Dataset File after saving Dataset Details.

Select Cancel to discard any entries you have made in the form. Select Save to create and view the new dataset. Upon clicking save, the system will notify you if any of the entries are not valid. Once all elements are valid, the system will then prompt you to confirm that no Personally Identifiable Information (PII) has been included in any of the text fields.

You will need to select Edit Dataset Access from the View Dataset page if you need to add access for team members or if you want to make Dataset Details visible in the Public Data Commons.

Upon saving, the dataset record will be created in your local Private Data Enclave. The new dataset will be assigned a unique ID which you will see in the URL after you save the new dataset. You can share the URL with other people who have access to this dataset in the Private Data Enclave. NOTE: If you choose to make the Dataset Details publicly visible, a second URL for the dataset's view in the Public Data Commons will be available. This URL can be discovered by right-clicking on the "View in Public Data Commons" link when viewing the dataset in the Private Data Enclave. Use the Public Data Commons URL when sharing the dataset outside of your project team.

Add Dataset DICOM Fields

If you have selected a Dataset Type of "DICOM", additional fields appear for you to populate. DICOM refers to a clinical imaging data standard: "Digital Imaging and Communications in Medicine".

Brain Imaging Data Structure (BIDS) (required, defaults to FALSE): Brain Imaging Data Structure (BIDS) refers to a file and folder structure aimed at reusability for neuroimaging research. If TRUE is selected, a script to convert the DICOM study files to BIDS structure will run at the time of DICOM study upload. Note: This value cannot be changed for DICOM dataset objects after the initial save.

Quality (required, defaults to "unknown"): This field allows users to record (and later filter on) image quality. This field can be set to "unknown" at the time of dataset creation but can still be updated later by a Dataset Administrator who performs an imaging review.

Note that upon upload, the system will read the file's metadata and automatically populate the fields listed below. You will see these fields and their values when you view the dataset after file upload.

Study Date (auto populated): Date on which the study took place

Scanner Manufacturer Name (auto populated): Manufacturer of the scanner used in scanning the subject

Scanner Model Name (auto populated): Model name of the scanner used in scanning the subject

Organ Name (auto populated): Name of the body part that is part of the study (body part for which the DICOM images have been taken)

Field of View (auto populated): Angular measurement of field of view of the organ being scanned (a numeric value)

Field Strength (auto populated): Magnetic field strength used in scanning (a numeric value)

The following additional metadata fields will also be extracted:

Acquisition Date
Angio Flag
Institution Name
Largest Image Pixel Value
Modality
MR Acquisition Type
Patient Sex
Protocol Name
Scanning Sequence
Sequence Name
Series Description
Slice Location
Slice Thickness
Software Versions

Follow the Upload File to Dataset instructions to complete DICOM file upload.

Add Dataset REDCap Fields

If you have selected a Dataset Type of "REDCap", additional fields appear for you to populate. "Research Electronic Data Capture" (REDCap) is an electronic case report form system created by Vanderbilt University and widely used by academic researchers. You can set up a Private Data Enclave dataset that is linked to a REDCap project. You can choose to automatically update a CSV file in this dataset any time the REDCap database updates. This allows you to easily share an up-to-date copy or subset of the REDCap project data with your Private Data Enclave team members.

REDCap Project URL (required): Paste the web URL of the desired REDCap Project into this field to index your project data.

Extract From REDCap (required): You can automatically export data from REDCap directly to the Private Data Enclave. Any files associated with this object will be coming directly from REDCap. The data files are automatically updated each time a permissioned user accesses the dataset.

Options:

None - No REDCap extract or data dictionary will be associated with this dataset object. If you select this option, you can elect to upload files manually.
Data Dictionary - Only the data dictionary of the Redcap project associated with the URL entered will be extracted from REDCap.
Single Report - An extract of the data will be exported from REDCap based on the REDCap Report ID entered. This will not include the data dictionary for this data file.
All Data - An extract of the data will be exported from REDCap including the data dictionary for this data file.

REDCap Project API Token (required unless "Extract from REDCap" is "None"): To find this token, open your REDCap project and select "API" under the "Applications" section of the left hand menu. Copy the token you see on the screen and paste into you see on the screen this field in the RDE. Note that the user generating the REDCap API token also needs to have "logging permissions" on the REDCap project. This allows the latest update date/time to be passed to the RDE, allowing the RDE to avoid repulling data when nothing has changed in REDCap. If you do not see "API" as an option or do not have "logging permissions", contact your REDCap administrator at RedCap@hscmail.mcc.virginia.edu for assistance.

REDCap Report ID (required if "Single Report" is selected for "Extract from REDCap"): Paste the ID of a report of a REDCap project to be used for extracting a limited set of data from the REDCap project.

The system will also read the extracted file's metadata and automatically populate the fields listed below when "Extract from REDCap" is TRUE.

If you set "Extract from REDCap" to TRUE, the following fields will be automatically updated by REDCap after you first save this form:

REDCap Project Title (auto-populated): Title of the REDCap project as listed in REDCap at the time of an auto-extract from REDCap to the Commons.

REDCap Project PI (auto-populated): Name of the REDCap project PI as listed in REDCap at the time of an auto-extract from REDCap to the Commons.

View Private Dataset Overview

Dataset Details are visible to the dataset's Dataset Administrators and Dataset Collaborators (and local Private Data Enclave Administrators). Dataset Details include the following. Please note that optional fields will only appear if populated by the Data Administrator.

Dataset Type: Can be Generic, DICOM, or REDCap.

Dataset Title: Name of your dataset.

Description: Description of the dataset.

Keywords: A list of words or phrases that people can use to search for this dataset.

Storage Organization: The organization associated with the parent project. Note that this is also the organization where the dataset details and dataset files will be stored. If you want to store data at another organization, someone at that organization must create a new project and the dataset can be added there.

HIPAA Identifiers: Patient data fields included in the dataset. If the data does not come from medical records, the value should be N/A.

IRB Number (required if the dataset contains Highly Sensitive Data): The IRB # under which use of this data is approved.

Associated Data Security Plan (required if the dataset contains Highly Sensitive Data): Associating a DSP with a dataset provides the team with easy access to documentation that tells them where they are allowed to store the data and who it can be transferred to. This step is required for HSD because it is essential that team members with this type of data have access to this document so they can ensure compliance.

Data Granularity (required for data derived from medical records): The level of granularity of the dataset using either Row Level Data, Data Aggregated to Groups of 11 or more, or Other for unique cases such as imaging files, time series, etc.

Other Sensitive Data: Select which types of other sensitive data are contained in this dataset, such as HIV Status, Psychiatric, Financial, Employment, Student, Consumer, Criminal, Additional Status, Sexual Health, Gender Identity, Personally Identifiable Information, Social Security Number, Controlled Unclassified Information (CUI), and Other Sensitive.

Associated Contract: If the project involves data sharing with another institution, then a contract should be uploaded to the project and associated with any datasets covered by that agreement.

License: i.e. Creative Commons license.

Variables Measured: This list of variables tells collaborators what data elements the dataset contains.

Link to External Dataset File: Datasets can be indexed by entering Dataset Details even when the dataset file is stored elsewhere. This field provides a link to external storage locations when appropriate.

Dataset details can be edited and/or published to the Public Data Commons by the Dataset Administrators. If the Dataset Details have been made publicly visible, users in the Private Data Commons will see a link to view the dataset in the Public Commons. This allows the team to quickly jump to a public view of this object.

Datasets that are of type REDCap or DICOM have additional fields, some of which are auto populated at the time of dataset creation or DICOM file upload.

REDCap fields include: REDCap Project URL, Extract from REDCap, REDCap Report ID, REDCap Project Title (auto-populated), and REDCap Project PI (auto-populated)

DICOM fields include: Brain Imaging Data Structure (BIDS) and Quality. Additionally, the following fields will be filled out automatically after a DICOM zip file is uploaded: Scanner Manufacturer Name, Scanner Model Name, Organ Name, Field of View, Field Strength, Angio Flag, Institution Name, Largest Image Pixel Value, Modality, MR Acquisition Type, Patient Sex, Protocol Name, Scanning Sequence, Sequence Name, Series Description, Slice Location, Slice Thickness, and Software Versions.

View Private Dataset Access

Dataset Access is visible to the Dataset Administrators and Dataset Collaborators (and local Private Data Enclave Administrators). Dataset Administrators can edit Dataset Access.

The Dataset Permissions table lists all Dataset Administrators and Dataset Collaborators.

Dataset Details Visibility indicates whether Dataset Details are visible in the Public Data Commons.

Dataset File Visibility indicates whether the most recent version of the dataset file is accessible for download in the Public Data Commons.

View Private Dataset Files

If a file has been uploaded to the dataset, current and past versions are available for download by Dataset Administrators and Collaborators (and local Private Data Enclave Administrators) using the "Download" button.

The most recently added version is the "current version".

If the dataset is marked as Highly Sensitive Data, users are presented with the associated Data Security Plan and must agree to manage the file in accordance with the plan prior to download. The download and upload features are locked for Highly Sensitive Data files when the associated research protocol does not have active status with the local IRB.

Upload Private Dataset Files

Dataset Administrators and Collaborators (and local Private Data Enclave Administrators) have the ability to upload new versions of dataset files by clicking "Add" next to Dataset File Versions.

Note that an alternative to uploading a dataset file is to link to an external dataset using the optional "Link to External Dataset File" field in the Dataset Details.

File size limits are set by your local Private Data Enclave Administrators. Upload time for large files will depend on the upload speed of your internet connection and available system resources at the time of upload. Do not navigate away from the page while the upload is in progress. The newest version will appear as the top entry in the list with an appropriate timestamp when successfully uploaded.

Note that the software may scan the file as it is uploaded to check for the presence of HIPAA identifiers like medical record number, zip, dates, email addresses, phone numbers, etc. The system will display a "HIPAA WARNING" if the Dataset Details indicate the dataset contains patient data but the HIPAA identifiers detected do not match the data sensitivity level indicated in the Dataset Details. On hover of the "HIPAA Warning" text, tooltip help will show which additional identifiers the scan think may be present in the data. An email is also sent to local Private Data Enclave Administrators so that they can audit the file if needed. Dataset Administrators cannot publish any file with an active HIPAA alert.

Note that DICOM datasets will scan the file and perform automatic extraction of certain structured details at the time of file upload (see Add Dataset help for more details).

Delete Private Dataset

Dataset Administrators will see an option to "Delete Dataset". If selected, the system will prompt the Dataset Administrator to confirm the deletion

Click "Permanently delete this dataset!" if you wish to continue with deleting the dataset. Otherwise, click "Cancel" to cancel the deletion process.

If you have erroneously deleted a dataset, immediately request a consultation using the Help section to the left of the page.

Edit Private Dataset Details Overview

Dataset Administrators can edit Dataset Details using this form.

You can add, edit, or remove values as long as the form requirements are met. See the Add Dataset help for more instructions around the specific fields of the form.

To edit Dataset Access (Permissions and Visibility), select "Cancel" to return to View Dataset and then select the edit icon next to Dataset Access.

Select "Cancel" to discard any entries you have made in the form. Upon clicking "Save", the system will notify you if any of the metadata elements are not valid.

Once all elements are valid, the system will then prompt you to confirm that no Personally Identifiable Information (PII) has been included in any of these text fields.

Click "Confirm" to finalize the changes and return to View Dataset.

Edit Private Dataset Access Overview

Dataset Administrators can edit Dataset Access including Dataset Permissions and Visibility.

Edit Private Dataset Permissions

Dataset Permissions lists all Dataset Administrators and Dataset Collaborators.

Dataset creators are "Data Administrators" by default and can use the "Add", "Edit", and "Delete" buttons in the Dataset Permissions table to give other team members Dataset Administrator or Dataset Collaborator permissions.

Give all users who have access to the primary associated project access to the current dataset by checking the box next to "Live Sync to Project Permissions" at the bottom of the "Dataset Permissions" table. "Dataset Permissions" will continue to sync any changes made to "Project Permissions" until the box is unchecked.

If the dataset is marked as Highly Sensitive Data, the list of project team members you can select will be further limited to those individuals who are listed by the IRB as active investigators on the associated IRB protocol.

Individuals from an institution that is NOT logged in at the Storage Organization can only be added as a collaborator or dataset admin IF there is also a contract uploaded to the project that covers the data sharing between institutions.

Edit Private Dataset Visibility

The default is "Visible only to Dataset Team and Private Data Enclave Administrators".

Select "Visible in the Public Data Commons" when you are ready for your Dataset Details to be visible to anyone online. The dataset will become discoverable in the Public Data Commons.

Note that the visibility of the dataset files is controlled independently so you can publish dataset details while keeping the dataset files private.

Edit Private Dataset File Visibility

The default visibility of dataset files is "Visible only to Dataset Team and Private Data Enclave Administrators".

Select "File is Visible in the Public Data Commons" when you are ready for your most recent dataset file version to be visible to anyone online AND when you are certain that your organization permits public sharing of the file. Note that the system will block you from public sharing in certain instances, but ultimately you are responsible for making the file public.

The system will only give you this option when the following conditions are met:

The dataset does not contain sensitive data:

No patient data UNLESS aggregate / non-reidentifiable patient data
No other sensitive data

The automated HIPAA scan of your dataset file must be complete
No active HIPAA alerts
Dataset Type is not REDCap
Dataset Details have been made visible in the Public Data Commons
At least one data file has been uploaded

Once you select "File is Visible in the Public Data Commons", a popup will ask you to confirm you've met the public sharing requirements. Upon confirmation, the dataset file will be uploaded to LibraData and to the Public Data Commons, and your dataset will be issued a DOI (digital object identifier) which you will see in the Dataset Details.

If you select "Visible only to Dataset Team and Private Data Enclave Administrators" the published current version of the file will be removed from the Public Data Commons and new versions are no longer sent to Libradata. However, to remove previously published versions of the file from LibraData, you must submit a request to the LibraData admin at libra@virginia.edu.

Public Data Commons

Public Data Commons Search Overview

All users have access to the Public Data Commons. This includes any Project Details, Dataset Details, and Dataset Files that research teams have elected to share out from the Private Data Enclave. Note that some Public Projects and Datasets are mirror objects in external public repositories, thus enabling the discovery of these assets via the Resource and Data Exchange Public Data Commons. If you would like to request that other external public datasets be added to this index, please submit a consult request via the Help feature.

Public Data Commons Search Bar

To search within these results, select Projects or Datasets, then type the desired string to search by into the search bar.

The string search will find all projects or datasets that have the specified string in any of Project Details or Dataset Details. If there are multiple words in the specified string, a project or dataset is considered a matched project if its details have any one of those words. Results are returned based on relevance to the string searched, with the following ranking order applied: keywords, title, description.

Public Data Commons Search Sort

To search within these results, select Projects or Datasets, then type the desired string to search by into the search bar.

Public Projects and Datasets are listed by default in order of most recently updated. The sort defaults to "Relevance" after you search a string, but you may elect to sort the string search results by most recently updated.

Public Data Commons Search Filters

The "Projects" filter is applied as a default. Select "Datasets" to change this.

Public Data Commons Export to CSV

This feature is available to Private Data Enclave Administrators only. They are able to export all current search results to a .csv file.

Only projects or datasets that show in the current set of results will be exported. To export all, be sure to remove any search strings and click "Export to CSV". Project and dataset lists must be exported independently by toggling the filter.

View Public Project Overview

Both authenticated users and guests can view the project details, associated resources and associated datasets for a project in the Public Data Commons.

View Public Project Details

Any Project Owner can make their Project Details and Related Resources visible in the Public Data Commons via the visibility settings in the Private Data Enclave. Select a project tile to view the project details.

Project Details include Title, Description, Funding Source(s), Website, Keywords, Contact Name, Contact Email, Source Organization, Partner Institution(s), Funding Source(s), Website, and Related Resources.

Resources from the Resource Explorer may also be associated with a project.

View Public Project Associated Datasets

This section displays a list of datasets associated with this project. Only a subset of datasets and some files that have been made visible in the Public Data Commons by the Dataset Administrators will appear in this public view. Select a dataset tile to view the Dataset Details.

View Public Dataset Overview

Both authenticated users and guests can view public dataset descriptions and the other elements of the dataset that have been made visible by Dataset Administrators.

View Public Dataset Details

Any Dataset Administrator can make their Dataset Details visible in the Public Data Commons via visibility settings in the Private Data Enclave. Select a dataset tile to view the Dataset Details. Dataset Details include title, description, dataset type, keywords, storage organization, HIPAA identifier(s), study IRB number, associated data security plan, data granularity, other sensitive data, associated contract, license, DOI, data attribution, link to external datasets. These fields can be edited and/or published to the Public Data Commons by the Dataset Administrators.

View Public Dataset File

If a file has been uploaded to the dataset, the Dataset Administrator may choose to keep the file private or to also share it publicly here.

If a file has been uploaded to the object and made visible to all users, the current version is available for download using the Download Dataset File button.

If a file has been uploaded to the object but not made visible to all users, you will see a message stating, "The associated dataset file has not been made visible in the Public Data Commons."

If a file has not yet been uploaded to the object, you will see a message stating, "No data files have been uploaded."

Some content and features in the Resource and Data Exchange are publicly available, while others require users to log in using their organizational credentials. For example, only logged-in users can add content and access privately permissioned content.

To log in, select your organization's logo or select "Continue as Guest" to return to the home page, noting that some features may be unavailable to you.

Once you've logged in with your organizational credentials, the session will last for 8 hours.

Five minutes before expiration, you can re-submit your active credentials by clicking the "Extend Session" prompt that will appear in the banner across the top of the page when you are within 15 minutes of an expired session.

If your organizational login has also expired (depending on the length of time determined by your organization), you may have to log in again.

Request a Consult

Email our team at rde_admin@virginia.edu to get help with using any part of this application. The email should be filled out with enough detail for the consultation team to determine which team member is best suited to assist with the issue or request. We will reply within one business day.