Copilot Agent to assist with query of the All of Us dataset hosted by NIH.

• https://www.researchallofus.org/research-project-directory/
• https://www.researchallofus.org/publication-directory/

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• Steve Carroll - Microsoft
• Intial version: 2026-07-10

Assumptions:

The deployment code assumes:

• Active Azure Subscription
• Access to the AzureCLI
• Permissions to a subscription that may create a resource group and required objects.

Deployment steps

Azure Function

Deployment Variables

The following varaiables are defined in the top of the deploy_azure_infrastructure.txt file. They represent the following configurations:

Variable	Default Value	Purpose
$rg	"rg-allofus-demo01"	Resource group name
$loc	"eastus"	Deployment Region
$sfx	"aou1234"	Suffix to apply to resources
$storageAcctName	"staallofus$sfx"	Resource name of storage account (includes suffix)
$functionSvcName	"func-allofus-$sfx"	Resource name of Azure Function (includes suffix)
$vnetName	"vnet-allofus"	Resource name of vNet
$vnetAddressSpace	"192.168.0.0/24"	CIDR of vNet
$funcSubnetName	"pe-functions"	Subnet name used for Azure Function
$funcSubnetAddrSpace	"192.168.0.0/25"	Subnet CIDR for Azure Function
$peSubnetStorage	"pe-storage"	Subnet name used for storage acct. private endpoints
$peSubnetStorageAddrSpace	"192.168.0.128/25"	Subnet CIDR for storage acct.

Infrastructure Deployment Process

The code used to deploy the infrastructure can be found in /deployment/deploy_azure_infrastructure.txt

Deployment will perform the following:

• Create a new resource group
• Create a new vNet
  • Create two separate subnets (Azure Functions + Private Endpoints)
• Create a storage account
  • Standard LRS
• Create Azure Function App
  • Uses newly created storage account
  • Flex Consumption
  • Python Version 3.12
  • Uses Azure Functions subnet
  • Creates System Assigned Managed Identity
• Assign the Function's System Assigned Managed Identity to
  • Storage Blob Data Contributor
  • Storage Queue Data Contributor
  • Storage Table Data Contributor
• Creates Private DNS Zones
  • privatelink.blob.core.windows.net
  • privatelink.queue.core.windows.net
  • privatelink.table.core.windows.net
• Creates the following private endpoints and associates record to correct DNS zone.
  • blob
  • queue
  • table
• Update Azure Function to use system assigned managed identity to access storage account
• Enable CORS to allow testing from https://portal.azure.com and https://ms.portal.azure.com

Function Code Deployment

Use the same window that the infrastructure deployment completed in.

Note: Code build / deploy takes ~5 minutes

cd /code
func azure functionapp publish $functionSvcName --build remote

When successfully deployed user will see the deployed functions and the URL associated to each.

Testing

Testing scrips can be found in /deployment/testing_azure_functions.txt

Testing Variables

The following parameters are defined in the /deployment/testing_azure_functions.txt file

Variable	Default Value	Purpose
$rg	"rg-allofus-demo01"	Deployment resource group name
$sfx	"aou1234"	Suffix defined in deployment steps
$app	"func-allofus-$sfx"	Not needed unless changed in deployment
$uri	"https://$app.azurewebsites.net/api"	Not needed unless operating in other than commericial Azure subscription

Testing functions

• Health - evaluates response from the Health endpoint and returns number of records in cache
• Refresh - causes the cache to become invalidated and forces a refresh
• Search - Executes a basic query and displays results

Custom Connector (AKA Copilot Studio Tools)

1. Open the /custom_connector/openapi-swagger.yaml file.

2. Replace the values found in: host: .azurewebsites.net with the correct URL deployed in prior section.

3. Naviate to https://copilotstudio.microsoft.com

4. Naviate to Tools -> New Tool -> Custom Connector

   This will launch the Power Apps Custom Connector screen

5. New Custom Connector -> Import an OpenAPI file Provide the connector name and the /custom_connector/openapi-swagger.yaml file

   NOTE: This file must have the correct URL specified in before importing.

   • Optional: After importing the openapi-swagger.yaml file, configure the connector icon available in /custom_connector/icons

6. Click Update connector to save the custom connector.

7. Click Test and create a new connection. The API key can be found in the Azure Function under Functions > App keys > default

8. Select "childhood asthama" as the query, "both" for directory, 8 for top then click "Test operation"

Expect a Status 200 response with a body response with identified articiles.

Copilot Studio Agent

Note: After editing each section, be sure to click Save

1. Naviate to https://copilotstudio.microsoft.com

2. In the Agents page > Create blank agent

3. Name your agent: "All of Us - Research Finder" (this will be the displayed name in the UI)

   Note: Associate to a custom solution in this screen by selecting "Agent settings (Optional)"

4. Description:

   Given a description of a research idea, finds similar existing work in the NIH All of Us publication and research-project directories and returns the most likely matches with clickable source links.

5. Select your agent's model:

   GPT5 Chat

6. Instructions:

   You are the All of Us Similar Research Finder. Your job is to help a user discover existing NIH All of Us work that is similar to a research idea, topic, method, or question they describe. You have one tool: searchDirectories, which searches publications and research projects and returns the most similar records with a source link for each.
   
   How to behave:
   - When the user describes what they are studying or looking for, call searchDirectories. Pass their description (lightly cleaned into keywords) as 'query'. Do not answer from your own knowledge — always search first.
   - Choose 'directory':
       - If the user asks about published papers, use 'directory="publication"'.
       - If they ask about active/ongoing projects in the Researcher Workbench, use 'directory="project"'.
       - If they don't specify, use 'directory="both"'. You may briefly ask whether they'd like to narrow to publications or projects, but never block on it.
   - Return the most likely matches (default 5–8). For EACH match, present:
   - The title as a clickable markdown link to its source: 'Title'.
   - A tag showing whether it's a Publication or Project.
   - One line of context from the snippet, plus helpful metadata when present (date/journal for publications; access tier for projects; institutions).
   - Order results from most to least similar (the tool returns them ranked).
   - Ground every statement in the returned records. Never invent titles, authors, findings, or links. Only show links returned by the tool.
   - If the tool returns no results, say so plainly and invite the user to rephrase or broaden their description. Do not fabricate matches.
   - Be concise and neutral. When useful, note that inclusion in these directories does not imply NIH endorsement, and that this covers public directory data only.
   
   Scope: only help find and summarize All of Us research surfaced by the tool. For anything outside that, briefly say it's out of scope and point to https://www.researchallofus.org.
   
   Example answer shape:
   > Here are the closest matches to your idea in the project directory:
   > 1. Air pollution sensitivity and asthma incidence — Project ·
   >    Controlled Tier · studies PM2.5 exposure and asthma onset.
   > 2. … — Project · …

7. Suggested prompts:

   Title	Prompt
   Child Asthma Air Studies	I want to study how air pollution exposure affects asthma in children — what similar work exists?
   Diabetes Disparities Papers	Find publications similar to a project on diabetes disparities in underrepresented groups.
   Maternal Health Projects	Are there active projects on maternal mental health and pregnancy complications?
   Cardiovascular Genetics	Show me research related to genetic risk factors for cardiovascular disease.

8. Navigate to Tools from the top menu bar

9. Select + Add a tool

10. In the Add a tool dialog search for the custom connector name created in the prior section (NIH All of Us Directory Search)

11. When found, click "Add and Configure"

12. Under Inputs click "+ Add input"

    • Add in both directory and top

13. When configured click "Save"

14. Naviate to Channels

    • Ensure the Microsoft 365 and Microsoft Teams channels are configured.

The All of Us agent is now configured. You may publish the agent and test prompt completions.

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Known Issues