Which integrations are available for this server?

Provides tools to search and fetch articles from the PubMed biomedical literature database.

How do I use PubMed Custom Connector MCP Server?

1. Click on "Install Server". 2. Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state. 3. In the chat, type @ followed by the MCP server name and your instructions, e.g., "@PubMed Custom Connector MCP Server find recent trials on CRISPR for sickle cell disease" That's it! The server will respond to your query, and you can continue using it as needed. Here is a step-by-step guide with screenshots.

PubMed Custom Connector MCP Server

by madsd

Overview Schema Related Servers Score Discussions

Python

Hybrid

PubMed custom federated connector for Microsoft 365 Copilot

A Model Context Protocol (MCP) server that brings the public PubMed biomedical literature database into Microsoft 365 Copilot as a custom federated connector.

Users can ask Copilot natural-language questions ("find recent trials on CRISPR for sickle cell disease") and Copilot calls this server in real time to search and read PubMed articles.

What's in the box

Path	Purpose
`src/server.py`	MCP server exposing the read-only `search` and `fetch` tools
`src/pubmed.py`	Async client for the NCBI E-utilities API (with rate-limit handling)
`src/auth.py`	Microsoft Entra ID bearer-token validation (ASGI middleware)
`src/config.py`	Environment-driven configuration
`src/main.py`	ASGI entrypoint (Uvicorn)
`Dockerfile`	Container image
`azure.yaml`, `infra/`	`azd` + Bicep for Azure Container Apps
`scripts/smoke_test.py`	End-to-end MCP client test
`docs/tenant-setup-guide.md`	Step-by-step tenant configuration + validation guide

Related MCP server: PubMed MCP Server

Architecture

Microsoft 365 Copilot
   │  (1) user prompt
   ▼
Copilot orchestrator ──(2) bearer token from Microsoft enterprise token store──┐
   │                                                                            │
   │  (3) MCP search / fetch over HTTPS                                         │
   ▼                                                                            │
Azure Container Apps  ──(4) validate Entra JWT (issuer, audience, client app)──┘
   │
   │  (5) NCBI E-utilities (esearch / esummary / efetch)
   ▼
PubMed (public)

MCP tools

search(query, max_results) → { "results": [ { id, title, url, snippet } ] } where id is the PubMed PMID.
fetch(id) → { id, title, text, url, metadata } where text is the article abstract and metadata includes journal, authors, publication date, and DOI.

Both tools are read-only.

Quick start (local)

python -m venv .venv
.\.venv\Scripts\Activate.ps1
pip install -r requirements.txt

# Run without auth for local testing
$env:AUTH_REQUIRED = "false"
$env:NCBI_EMAIL    = "you@example.com"   # recommended by NCBI
python -m src.main

# In another terminal: end-to-end test
python scripts\smoke_test.py

Then point MCP Inspector at http://localhost:8000/mcp (transport: Streamable HTTP) to explore the tools interactively:

npx @modelcontextprotocol/inspector

Configuration

All configuration is via environment variables (see .env.example):

Variable	Required	Description
`AUTH_REQUIRED`	no (default `true`)	Enforce Entra bearer-token validation.
`ENTRA_TENANT_ID`	when auth on	Your Microsoft Entra tenant ID.
`ENTRA_AUDIENCE`	when auth on	Accepted token audience = the Application ID URI from the Teams Developer Portal SSO registration. Comma-separated list allowed.
`ENTRA_ALLOWED_CLIENT_IDS`	no	Allowed calling client app IDs. Defaults to the Microsoft enterprise token store `ab3be6b7-f5df-413d-ac2d-abf1e3fd9c0b`.
`NCBI_API_KEY`	no	NCBI API key for higher PubMed rate limits (10/sec vs 3/sec).
`NCBI_EMAIL`	no	Contact email reported to NCBI (recommended).
`MCP_PATH`	no (default `/mcp`)	Path of the MCP streamable-HTTP endpoint.
`ALLOWED_HOSTS`	no (default `*`)	Hosts allowed by the MCP transport-security (DNS-rebinding) check. `*` disables the check (recommended behind Azure ingress, where Entra auth still applies). Set explicit hostnames to enable strict checking.
`ALLOWED_ORIGINS`	no (default `*`)	Origins allowed by the DNS-rebinding check.
`PORT`	no (default `8000`)	Listen port.

Deploy to Azure

azd auth login
azd env new pubmed-connector
azd env set AUTH_REQUIRED false   # first deploy: get the URL, then lock down
azd up

Full deployment, Entra SSO setup, M365 admin center registration, and validation steps are in docs/tenant-setup-guide.md.

Security notes

The connector exposes only public PubMed data, but the transport is still authenticated: every /mcp request must carry a valid Entra token whose audience matches your Application ID URI and whose calling app is the Microsoft enterprise token store.
/health is intentionally unauthenticated for container liveness probes.
The server is read-only and performs no writes to any system.

This server cannot be installed

license - not found

quality - not tested

maintenance

How are these scores calculated?

Maintenance

–Maintainers

–Response time

–Release cycle

–Releases (12mo)

Commit activity

Resources

GitHub Repository

Need Help?

Related Servers

Unclaimed servers have limited discoverability.

Looking for Admin?

If you are the server author, to access and configure the admin panel.

Latest Blog Posts

Lightport: Open-Sourcing Glama's AI Gateway
By punkpeye on April 27, 2026.
open source
OpenAI
Tool Definition Quality Score (TDQS)
By punkpeye on April 3, 2026.
mcp
The Hackers Who Tracked My Sleep Cycle
By punkpeye on March 26, 2026.
security

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/madsd/m365-custom-connector'

If you have feedback or need assistance with the MCP directory API, please join our Discord server