PubMed

KnowledgePublisher: 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.

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. Every MCP server reuses them.

1. Add PubMed MCP server to your Resources

UI
Terraform
Pulumi
API

Open the Admin Catalog and click Add MCP.
Select the PubMed template.
Enter a DNS-label Name, such as pubmed.
Choose the Space containing your Connector, such as default.
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.

Set space_id to the ID of the Space containing your Connector.

resource "formal_resource" "pubmed" {
  name                    = "pubmed"
  technology              = "mcp"
  hostname                = "pubmed.mcp.claude.com"
  space_id                = "<SPACE_ID>"
  native_users_v3_enabled = true
  port                    = 443
  tags = {
    "mcp-endpoint" = "/mcp"
  }
}

This public server does not need formal_resource_oauth_settings.

Set spaceId to the ID of the Space containing your Connector.

import * as formal from "@formalco/pulumi";

const resource = new formal.Resource("mcp", {
  name: "pubmed",
  technology: "mcp",
  hostname: "pubmed.mcp.claude.com",
  port: 443,
  spaceId: "<SPACE_ID>",
  tags: { "mcp-endpoint": "/mcp" },
  nativeUsersV3Enabled: true,
});

Create a Resource with the MCP endpoint and its Space ID.

export FORMAL_API_KEY="<YOUR_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 @- <<JSON
  {
    "name": "pubmed",
    "hostname": "pubmed.mcp.claude.com",
    "port": 443,
    "technology": "mcp",
    "spaceId": "<SPACE_ID>",
    "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?

Nothing in the request identifies the Formal user. Formal attributes these requests only when they come through the Formal Endpoint. 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.

UI
Terraform
Pulumi
API

Go to Network Rules and create a rule named pubmed-mcp.
Paste this expression, set the rule to Active, then save:

{
  "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
  }
}

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
}

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
      }
    }
  `,
});

export FORMAL_API_KEY="<YOUR_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 only. See 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.<connector-hostname>/mcp. Find it in the Admin 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

Mask a tool's output

This policy replaces email addresses in results returned by get_article and get_full_text.

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 for the input.mcp fields and Rewrite Action for body rewrites.

5. Check the logs

Open 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.See Logs for search syntax and filters.

Troubleshooting

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. Other clients, such as a browser, reach PubMed directly unless the rule also matches them. See Network rules.

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.

Getting Started

Example Use Cases

AI Governance

Configuring Formal

Integrations

Configuration

0. Prepare your Connector

1. Add PubMed MCP server to your Resources

2. Setup Authentication

3. Route Endpoint traffic

4. Create policies

Tools

Policies examples

5. Check the logs

Troubleshooting

Next Steps

MCP Gateway

All MCP servers

​0. Prepare your Connector

​1. Add PubMed MCP server to your Resources

​2. Setup Authentication

​3. Route Endpoint traffic

​4. Create policies

​Tools

​Policies examples

​5. Check the logs

​Troubleshooting

​Next Steps

MCP Gateway

All MCP servers

0. Prepare your Connector

1. Add PubMed MCP server to your Resources

2. Setup Authentication

3. Route Endpoint traffic

4. Create policies

Tools

Policies examples

5. Check the logs

Troubleshooting

Next Steps