Atlas MCP

AI-powered MCP server for searching and conversing over FHIR R4 clinical documents.

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What it can do

  • Agent Query: Query the HC-AI agent with a natural language question. Uses a multi-agent workflow with query classification, hybrid search + reranking, validation, and response synthesis.
  • Agent Clear Session: Clear agent session history for a given session ID.
  • Agent Health: Check agent health status and configuration.

What data it sees

Do you need an account

No: the server works without sign-in

AI-powered MCP server for searching and conversing over FHIR R4 clinical documents. Features hybrid retrieval (BM25 + pgvector), cross-encoder reranking, LangGraph multi-agent workflow, PII masking, and multi-provider LLM support (Ollama, OpenAI, Anthropic, Bedrock). 15+ tools for agent queries, document retrieval, session management, and embeddings ingestion.

How to connect

How to connect Atlas MCP to Claude

The server address to paste into Claude settings:

https://atlas_mcp--rsanandres.run.tools

  1. Open Claude (claude.ai or the desktop app).
  2. Go to Settings → Connectors.
  3. Click Add custom connector.
  4. Paste the server address copied below into Remote MCP server URL and click Add.
  5. In a chat, click + → Connectors and switch the new connector on.

Custom connectors are available on Free, Pro, Max, Team and Enterprise plans (Free is limited to one). On Team and Enterprise an organization Owner adds the connector first under Organization settings → Connectors.

Authorization

After you click Add, a sign-in window for the service opens. Sign in with your own account and approve access. Claude never sees your password.

How to connect Atlas MCP to ChatGPT

The server address to paste into ChatGPT settings:

https://atlas_mcp--rsanandres.run.tools

  1. Open ChatGPT in a browser (chatgpt.com). A Plus, Pro, Business, Enterprise or Edu plan is required.
  2. Turn on developer mode once: Settings → Apps → Advanced settings → Developer mode.
  3. Open Settings → Connectors and click Create.
  4. Fill in the form: Name (anything), Description (one line about what the service does), MCP server URL (copy it below).
  5. Under Authentication choose OAuth if the service requires sign-in, otherwise None. Click Create.
  6. In a new chat open + → Apps/Connectors and enable the connector.

OpenAI has renamed this section before (Connectors → Apps/Plugins). If the label differs, search settings for "developer mode". On Business/Enterprise workspaces an admin must allow custom connectors first.

Authorization

On first use ChatGPT opens the service's sign-in window. Sign in and approve access.

How to connect Atlas MCP to Cursor

The server address to paste into Cursor settings:

https://atlas_mcp--rsanandres.run.tools

Fastest: click Open in Cursor below and confirm the prompt.

Manually:

  1. In Cursor open Settings → Cursor Settings → MCP and click Add new global MCP server.
  2. Paste the JSON copied below into ~/.cursor/mcp.json (per project: .cursor/mcp.json in the repo root).
  3. Save the file. The server appears in the MCP list; authorize it there if asked.

Authorization

If the service needs sign-in, an authorize button appears next to the server in the MCP list.

Server tool list (15)

Raw names from tools/list. Only developers need these.

agent_queryQuery the HC-AI agent with a natural language question. Uses a multi-agent workflow with query classification, hybrid search + reranking, validation, and response synthesis.
agent_clear_sessionClear agent session history for a given session ID.
agent_healthCheck agent health status and configuration.
rerankRerank documents by relevance to a query using cross-encoder models.
rerank_with_contextRerank documents with optional full FHIR bundle context.
batch_rerankBatch rerank multiple queries in parallel.
session_append_turnAppend a conversation turn to session history.
session_getGet session state including recent turns and summary.
session_update_summaryUpdate the session summary.
session_clearClear all session data for a session ID.
ingestIngest a clinical note for chunking and embedding into the vector database.
embeddings_healthCheck embeddings service health and configuration.
db_statsGet database connection and queue statistics.
db_queueGet ingestion queue status.
db_errorsGet error logs with optional filtering.