propaths-mcp

An MCP server that exposes the ProPaths verified protein-interactome as read-only tools for AI agents. It is a thin client over the public ProPaths API (https://propaths.net), so every tool returns exactly the API's JSON. No account, no API key.

ProPaths reads a protein's primary literature and returns a verified graph of typed, directed, mechanistic interactions plus a pathway ontology. One protein (ATXN3) is fully mapped today.

Quickstart (Claude Desktop / any MCP client)

Add this to your MCP client config. uvx fetches and runs the server; nothing to clone or install.

{
  "mcpServers": {
    "propaths": {
      "command": "uvx",
      "args": ["propaths-mcp"]
    }
  }
}

Then ask, e.g., "search ProPaths for SCA3 and summarize its strongest mechanistic interaction." The agent will call search_proteins then get_protein, and drill in with get_interaction.

Prefer the raw API? It is public and keyless:

curl https://propaths.net/api/protein/ATXN3
curl 'https://propaths.net/api/search?q=SCA3'

Tools

Also exposed as MCP resources (propaths://schema, propaths://interaction-types, propaths://pathways/tree, and the propaths://protein/{symbol} template) and prompts (profile-protein, strongest-evidence, explain-pathway).

All tools are read-only and idempotent.

Configuration

Run without uvx

pip install propaths-mcp
propaths-mcp            # runs the stdio server
# or: python -m propaths_mcp

Before it is published, you can run straight from the repo:

uvx --from git+https://github.com/Tahsin-Kazi/propaths-mcp propaths-mcp

Notes

• Read-only and public; reads are rate-limited per client. Write/enrichment access and a hosted MCP are gated. Get in touch.
• Errors are graceful: a missing protein returns {"error": "...", "status": 404}; an unreachable API raises with a hint.

Docs: https://propaths.net/quick-start · License: MIT