> ## Documentation Index > Fetch the complete documentation index at: https://docs.formal.ai/llms.txt > Use this file to discover all available pages before exploring further. # PubMed > Search biomedical literature, retrieve abstracts, and access available full text. Knowledge Publisher: Anthropic Route PubMed MCP traffic through Formal to control and log what AI agents do in PubMed: * **Block** tools you don't want agents to call, such as `search_pubmed`. * **Mask** sensitive data in tool results, such as emails in `get_article` responses. * **Log** every tool call with the user, the MCP client and its parameters. Cloud agents Laptop / VM Endpoint [https://pubmed.mcp.claude.com/mcp](https://pubmed.mcp.claude.com/mcp) Connector ![](https://docs.formal.ai/static/brands/pubmed.svg) ## 0. Prepare your Connector The Connector needs an MCP listener and a hostname with wildcard DNS and TLS. Set them up once by following [Deploy the Connector](https://docs.formal.ai/docs/guides/core-concepts/connectors/mcp-gateway.md#deploy-the-connector). Every MCP server reuses them. ## 1. Add PubMed MCP server to your Resources > [tab] UI > > 1. Open the [Admin Catalog](https://app.formal.ai/catalog) and click **Add MCP**. > 2. Select the **PubMed** template. > 3. Enter a DNS-label **Name**, such as `pubmed`. > 4. Choose the **Space** containing your Connector, such as `default`. > 5. Configure upstream authentication as described below, then save. > > If no Connector is in the selected Space, the **Configuration** tab shows **MCP clients can't connect directly yet**. > The reason reads: `No Connector is in this server's Space.` > > Adding PubMed to the Admin Catalog > [tab] Terraform > > Set `space_id` to the ID of the Space containing your Connector. > > ```hcl theme={"languages":{"custom":["/languages/cel.json","/languages/rego.json"]}} > resource "formal_resource" "pubmed" { > name = "pubmed" > technology = "mcp" > hostname = "pubmed.mcp.claude.com" > space_id = "" > native_users_v3_enabled = true > port = 443 > tags = { > "mcp-endpoint" = "/mcp" > } > } > ``` > > This public server does not need `formal_resource_oauth_settings`. > [tab] Pulumi > > Set `spaceId` to the ID of the Space containing your Connector. > > ```ts theme={"languages":{"custom":["/languages/cel.json","/languages/rego.json"]}} > import * as formal from "@formalco/pulumi"; > > const resource = new formal.Resource("mcp", { > name: "pubmed", > technology: "mcp", > hostname: "pubmed.mcp.claude.com", > port: 443, > spaceId: "", > tags: { "mcp-endpoint": "/mcp" }, > nativeUsersV3Enabled: true, > }); > > ``` > [tab] API > > Create a Resource with the MCP endpoint and its Space ID. > > ```bash theme={"languages":{"custom":["/languages/cel.json","/languages/rego.json"]}} > export FORMAL_API_KEY="" > RESOURCE_RESPONSE=$(curl --fail --silent --show-error \ > --request POST \ > https://api.formal.ai/core.v1.ResourceService/CreateResource \ > --header "x-api-key: ${FORMAL_API_KEY}" \ > --header "Content-Type: application/json" \ > --data-binary @- < { > "name": "pubmed", > "hostname": "pubmed.mcp.claude.com", > "port": 443, > "technology": "mcp", > "spaceId": "", > "tags": [ > { > "key": "mcp-endpoint", > "value": "/mcp" > } > ] > } > JSON > ) > > ``` ## 2. Setup Authentication PubMed is a public server and needs no credential. Choose **Pass Through**. ![Pass Through selected under How does Formal authenticate to this resource?](https://mintcdn.com/formal/R-3CwVgs8IU6liji/assets/images/mcp-servers/auth-pass-through.png?fit=max\&auto=format\&n=R-3CwVgs8IU6liji\&q=85\&s=c14ae61de2dba8b567626cba03aae2cf) Nothing in the request identifies the Formal user. Formal attributes these requests only when they come through the [Formal Endpoint](https://docs.formal.ai/docs/guides/core-concepts/connectors/mcp-gateway.md#identity-headers). Pass-through servers have no Connector address, so cloud agents can't use them. ## 3. Route Endpoint traffic Auth is managed at the Connector level when you use Linked Accounts or Shared Credentials, so the Endpoint needs to forward the MCP traffic to it. Laptops and VMs with the Formal Endpoint keep using `https://pubmed.mcp.claude.com/mcp`, and a network rule sends that traffic to the Connector. > [tab] UI > > 1. Go to [Network Rules](https://app.formal.ai/network-rules) and create a rule named `pubmed-mcp`. > 2. Paste this expression, set the rule to **Active**, then save: > > ```javascript theme={"languages":{"custom":["/languages/cel.json","/languages/rego.json"]}} > { > "condition": { > "pre_tcp": process.is_agent, > // Every MCP server added to Formal: process.is_agent && resource.technology == "mcp" > "pre_tls": process.is_agent && hostname == "pubmed.mcp.claude.com", > "post_tls": true > }, > "outputs": { > "forward_to_connector": true > } > } > ``` > [tab] Terraform > > ```hcl theme={"languages":{"custom":["/languages/cel.json","/languages/rego.json"]}} > resource "formal_network_rule" "pubmed_mcp" { > name = "pubmed-mcp" > description = "Forward PubMed MCP traffic from agents to the Connector" > status = "active" > > # Every MCP server added to Formal: set pre_tls to process.is_agent && resource.technology == "mcp" > cel_expression = <<-EOT > { > "condition": { > "pre_tcp": process.is_agent, > "pre_tls": process.is_agent && hostname == "pubmed.mcp.claude.com", > "post_tls": true > }, > "outputs": { > "forward_to_connector": true > } > } > EOT > } > ``` > [tab] Pulumi > > ```ts theme={"languages":{"custom":["/languages/cel.json","/languages/rego.json"]}} > import * as formal from "@formalco/pulumi"; > > new formal.NetworkRule("pubmedMcp", { > name: "pubmed-mcp", > description: "Forward PubMed MCP traffic from agents to the Connector", > status: "active", > // Every MCP server added to Formal: set pre_tls to process.is_agent && resource.technology == "mcp" > celExpression: ` > { > "condition": { > "pre_tcp": process.is_agent, > "pre_tls": process.is_agent && hostname == "pubmed.mcp.claude.com", > "post_tls": true > }, > "outputs": { > "forward_to_connector": true > } > } > `, > }); > ``` > [tab] API > > ```bash theme={"languages":{"custom":["/languages/cel.json","/languages/rego.json"]}} > export FORMAL_API_KEY="" > # Every MCP server added to Formal: set pre_tls to process.is_agent && resource.technology == "mcp" > CEL_EXPRESSION=$(cat <<'CEL' > { > "condition": { > "pre_tcp": process.is_agent, > "pre_tls": process.is_agent && hostname == "pubmed.mcp.claude.com", > "post_tls": true > }, > "outputs": { > "forward_to_connector": true > } > } > CEL > ) > jq -n --arg cel "${CEL_EXPRESSION}" '{ > name: "pubmed-mcp", > description: "Forward PubMed MCP traffic from agents to the Connector", > status: "active", > celExpression: $cel > }' | curl --fail --silent --show-error \ > --request POST \ > https://api.formal.ai/core.v1.DesktopService/CreateDesktopRoutingRule \ > --header "x-api-key: ${FORMAL_API_KEY}" \ > --header "Content-Type: application/json" \ > --data-binary @- > ``` The rule matches [known agents](https://docs.formal.ai/docs/guides/network-rules.md#known-agent-identities) only. See [Identity headers](https://docs.formal.ai/docs/guides/core-concepts/connectors/mcp-gateway.md#identity-headers). Cloud agents such as Claude, ChatGPT and Cursor Cloud Agents don't run the Endpoint. Point them at this server's Connector address, `https://pubmed./mcp`. Find it in the [Admin Catalog](https://app.formal.ai/catalog): open PubMed, then copy **Connector address** on the **Configuration** tab. ## 4. Create policies ### Tools The Admin Catalog lists these tools for PubMed: | Tool | Description | | - | - | | `search_pubmed` | Search biomedical literature in PubMed. | | `get_article` | Retrieve article metadata and abstract. | | `get_full_text` | Retrieve available PubMed Central full text. | | `find_related_articles` | Find articles related to a PubMed record. | | `search_by_author` | Search publications by author. | ### Policies examples > [tab] Mask a tool's output > > This policy replaces email addresses in results returned by `get_article` and `get_full_text`. > > ```rego theme={"languages":{"custom":["/languages/cel.json","/languages/rego.json"]}} > package formal.v2 > > import future.keywords.if > import future.keywords.in > > email_pattern := `[A-Za-z0-9._%+-]+@[A-Za-z0-9.-]+\.[A-Za-z]{2,}` > > response := { > "action": "rewrite", > "body": regex.replace(input.http.body, email_pattern, "[REDACTED-EMAIL]"), > "reason": "Mask emails in PubMed results", > } if { > input.resource.name == "pubmed" > input.mcp.tool_name in {"get_article", "get_full_text"} > regex.match(email_pattern, input.http.body) > } > ``` See [MCP resources](https://docs.formal.ai/docs/guides/policies/evaluation.md#mcp-resources) for the `input.mcp` fields and [Rewrite Action](https://docs.formal.ai/docs/guides/policies/enforcement.md#rewrite-action) for body rewrites. ## 5. Check the logs Open [Logs](https://app.formal.ai/logs) and search for `resource.name:pubmed`. Each PubMed tool call is one `request` log with the user, the MCP client and the tool. Open a log to see its tool parameters and the policies it triggered. A masked search shows the rewrite policy. PubMed tool calls in Logs, including a masked response and a blocked write See [Logs](https://docs.formal.ai/docs/guides/observability/logs.md) for search syntax and filters. ## Troubleshooting > [accordion] Laptop traffic doesn't appear in Logs > > **Cause:** The Endpoint isn't running, or the network rule doesn't match the client. > > **Fix:** Check the Endpoint is connected. The rule above only matches [known agents](https://docs.formal.ai/docs/guides/network-rules.md#known-agent-identities). Other clients, such as a browser, reach PubMed directly unless the rule also matches them. See [Network rules](https://docs.formal.ai/docs/guides/network-rules.md). > [accordion] MCP clients can't connect directly yet > > **Cause:** The **Configuration** tab lists the reason, most often `No Connector is in this server's Space.` > > **Fix:** Edit the server and choose the Space containing its Connector. ## Next Steps > [card] [MCP Gateway](https://docs.formal.ai/docs/guides/core-concepts/connectors/mcp-gateway.md) > > Configure Connector routing and downstream access > [card] [All MCP servers](https://docs.formal.ai/docs/guides/core-concepts/connectors/mcp-servers/index.md) > > Browse every MCP server template This documentation is built and hosted on [Mintlify](https://mintlify.com), a developer documentation platform.