propaths-mcp

# propaths-mcp An [MCP](https://modelcontextprotocol.io) 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://www.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. ```json { "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: ```bash curl https://www.propaths.net/api/protein/ATXN3 curl 'https://www.propaths.net/api/search?q=SCA3' ``` ## Tools | Tool | What it does | |------|--------------| | `search_proteins(q, limit=20)` | Find a protein by symbol, alias, or name (start here) | | `get_protein(symbol)` | Compact interactome overview (the main entry point) | | `get_interaction(interaction_id, query=None)` | One interaction's full mechanism + evidence | | `get_interaction_between(a, b)` | The interaction(s) between two proteins, in one call | | `list_interactions(symbol, kind=, type=, pathway=, min_evidence=, sort=, limit=)` | Filtered/sorted headline rows | | `list_interaction_types()` | The controlled vocabulary (edge kinds, types, directions) + counts | | `get_pathway(pathway_id)` | A pathway node with its lineage and member interactions | | `get_pathway_tree()` | The full pathway scaffold (resolves pathway ids to names) | | `get_highlights()` | The best-evidenced interactions | | `export_netw…