Clinical Evidence MCP

Search medical literature, trial registrations, drug labels, and adverse-event reports from any compatible MCP client.

Clinical Evidence MCP is a source-first Model Context Protocol server. It queries official public APIs at request time and returns structured records with stable identifiers, direct source URLs, and retrieval timestamps.

Hosted endpoint: https://clinical-evidence-mcp.danielk.am/mcp

A bearer token is required. Tokens are issued by the operator, bound to one email account, and never accepted in URLs.

Tools

Tool	Source	Result
literature_search	NCBI PubMed and Europe PMC	Deduplicated citations and abstracts when available
literature_article_get	Europe PMC	One record by PMID, PMCID, or DOI
clinical_trials_search	ClinicalTrials.gov	Trial registrations matching terms and filters
clinical_trial_get	ClinicalTrials.gov	One study by NCT identifier
drug_label_search	openFDA	Current label records matching a drug name
drug_adverse_event_summary	openFDA FAERS	Reported reaction counts with safety warnings

The server also exposes clinical-evidence://sources, a resource describing upstream datasets and their limits.

An optional private source can add four allowlisted research tools: syndicated_source_status, syndicated_research_ask, syndicated_article_get, and syndicated_article_wait. When its private browser proxy is configured, two more tools start and finish an interactive sign-in. This integration is disabled by default. Creating a syndicated research question creates one record in that private upstream account, and the MCP annotation states this side effect.

Connect LibreChat

Add this to librechat.yaml:

mcpServers:
  clinical-evidence:
    type: streamable-http
    url: https://clinical-evidence-mcp.danielk.am/mcp
    requiresOAuth: false
    startup: false
    initTimeout: 15000
    timeout: 180000
    serverInstructions: true
    headers:
      Authorization: 'Bearer {{CLINICAL_EVIDENCE_TOKEN}}'
    customUserVars:
      CLINICAL_EVIDENCE_TOKEN:
        title: Clinical Evidence token
        description: Enter the personal token issued for your email account.
        sensitive: true

Restart LibreChat, save the token under MCP Settings, then reinitialise the connector. Each LibreChat user can have a separate token. See LibreChat's MCP documentation for UI and YAML setup.

Connect Claude

Claude's static request-header support for custom connectors has staged availability. If Request headers is available for your account:

1. Open Settings, then Connectors, and add a custom connector.
2. Enter https://clinical-evidence-mcp.danielk.am/mcp.
3. Add the request header Authorization with the full value Bearer cemcp_....

If Request headers is absent, use LibreChat or another bearer-header client. Per-user Claude sign-in requires an OAuth 2.1 authorization service, which is outside this release.

Run locally

Requirements: Node.js 22 or later.

npm ci
npm run build
cp .env.example .env
DATA_DIR=./data npm run cli -- token create --email clinician@example.com --label local
DATA_DIR=./data npm start

The token creation command prints the secret once. Store it in a password manager.

Test an initialisation request from a terminal:

curl -sS http://127.0.0.1:3946/mcp \
  -H 'Authorization: Bearer cemcp_REPLACE_ME' \
  -H 'Accept: application/json, text/event-stream' \
  -H 'Content-Type: application/json' \
  --data '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2025-11-25","capabilities":{},"clientInfo":{"name":"curl","version":"1"}}}'

Manage tokens from the terminal

npm run cli -- token create --email clinician@example.com --label librechat
npm run cli -- token list
npm run cli -- token revoke tok_REPLACE_ME

With Docker Compose, prefix those commands with:

docker compose exec clinical-evidence-mcp node dist/cli.js

The registry stores SHA-256 token digests, immutable account IDs, normalised email addresses, labels, and revocation timestamps in /data/tokens.json. Raw secrets are not stored. Protect /data, backups, and terminal output as sensitive operator data.

Deploy

The included Compose file expects:

1. A Traefik proxy on an external Docker network named coolify.
2. DNS for clinical-evidence-mcp.danielk.am pointing at the host.
3. A server-only .env file in /srv/clinical-evidence-mcp.

The deployment helper copies the working tree to dk-sin1, builds the pinned container, and checks the public health endpoint:

scripts/deploy-dk-sin1.sh

No host port is published. Traefik terminates HTTPS and forwards traffic over the Docker network.

Optional private source bridge

The public server contains a vendor-neutral bridge contract. Configure every SYNDICATED_SOURCE_* variable together to enable it for specific account IDs.

The private bridge must:

• remain on an internal Docker network with no host port or Traefik route;
• accept a separate bearer secret;
• return privacy-reduced JSON from /v1/auth-status, /v1/ask, /v1/article/:id, and /v1/article/:id/wait;
• avoid exposing history, account data, raw payloads, cookies, browser profiles, or patient identifiers;
• label question creation as a remote side effect.

Interactive private-source sign-in

Set SYNDICATED_SOURCE_LOGIN_PROXY_URL to the private bridge's internal noVNC URL, normally http://clinical-evidence-openevidence:6080. The bridge and port stay on clinical-evidence-private; the existing public service proxies only a currently authorised login session.

syndicated_source_login_start first closes any old browser session, starts one temporary browser, and returns MCP URL elicitation. The public URL carries a 32-byte nonce in its fragment, so the secret is not sent in the HTTP request or recorded by Traefik. The browser exchanges it once for a random HttpOnly; Secure; SameSite=Strict cookie. HTTP assets and the WebSocket require that cookie. The raw nonce lives for two minutes; the full browser session lives for at most 15 minutes.

Clients implementing MCP URL elicitation open the page from error code -32042. Clients that do not support it can call the same tool with delivery=link. Credentials are entered only in Chromium and never pass through MCP. After sign-in, call syndicated_source_login_finish to revoke browser access, stop Chromium, flush the private profile, and verify authentication.

Vendor terms and API permission still apply. Private deployment does not override them.

Configuration

Variable	Default	Purpose
HOST	127.0.0.1	Bind address
PORT	3946	Internal HTTP port
DATA_DIR	./data	Token registry directory
MCP_PUBLIC_URL	local URL	Public origin, HTTPS required outside loopback
MCP_ALLOWED_ORIGINS	https://claude.ai	Comma-separated browser Origin allowlist
REQUESTS_PER_MINUTE	60	Per-account request limit
UPSTREAM_TIMEOUT_MS	20000	Public provider request timeout
NCBI_EMAIL	unset	Optional NCBI client contact
NCBI_API_KEY	unset	Optional NCBI API key
SYNDICATED_SOURCE_NAME	unset	Private provider label
SYNDICATED_SOURCE_URL	unset	Internal bridge URL
SYNDICATED_SOURCE_TOKEN	unset	Bridge bearer secret
SYNDICATED_SOURCE_ALLOWED_ACCOUNT_IDS	unset	Comma-separated MCP account allowlist
SYNDICATED_SOURCE_TIMEOUT_MS	200000	Private provider request timeout
SYNDICATED_SOURCE_LOGIN_PROXY_URL	unset	Internal noVNC URL enabling temporary account-gated sign-in

Safety and data limits

Do not submit names, contact details, medical record numbers, dates of birth, or other patient identifiers. The input check catches common identifier patterns, but it is not a substitute for deidentification at the source.

This service does not diagnose, prescribe, provide emergency advice, or replace clinical judgement. Source records can be incomplete, delayed, corrected, or withdrawn.

ClinicalTrials.gov records are submitted by sponsors and investigators. Registration does not mean a study has been evaluated or approved by the U.S. government.

FAERS reports are voluntary and incomplete. Counts do not establish causation, incidence, prevalence, or comparative risk. openFDA notes that its FAERS dataset is updated quarterly and may lag by three months or more.

Publication abstracts can remain subject to publisher or author copyright. This server fetches them on demand and does not build a persistent publication corpus.

Upstream documentation

1. NCBI E-utilities
2. Europe PMC REST API
3. ClinicalTrials.gov API
4. openFDA drug labels
5. openFDA drug adverse events
6. MCP Streamable HTTP transport

Verify

npm run verify
npm run smoke:providers
npm audit --omit=dev
docker compose --env-file .env.example config --quiet
git diff --check

Licence

MIT