The interactome as data.

Typed, directed, mechanistic protein interactions, with their pathway placement and their source papers, served as JSON. The API is public, keyless, and rate limited. ATXN3 is fully mapped today.

Quickstart

There is no account and no key. Every endpoint is a GET request returning JSON.

Read the graph over HTTP

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

Add it to an MCP client

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

The config above works in Claude Desktop or any MCP client. uvx fetches and runs the server, so there is nothing to install first.

Interactive API reference → MCP server on GitHub

What an interaction carries

Every interaction in the graph is returned with five properties. All of them are filterable.

Kind

What one protein does to the other, from a controlled vocabulary.

activates inhibits binds regulates

Type and direction

Direct or indirect, and upstream, downstream, or bidirectional.

Mechanism

How the interaction happens in molecular terms, with kinetics where the literature reports them.

Evidence

The papers behind each claim, as PubMed identifiers, with the assay and system that produced the result.

Pathway placement

The biological processes the interaction belongs to, at every level of the ontology.

Call /api/interaction-types for the live vocabulary with meanings and counts.

Endpoints

Base URL https://www.propaths.net

Endpoint	Returns
/api/search?q=	A protein by symbol, alias, or name. q=SCA3 resolves to ATXN3.
/api/protein/{symbol}	The full protein record: metadata, interactions, and pathways.
/api/interaction/{id}	One interaction with its full mechanism and evidence.
/api/edge/{a}/{b}	The interaction or interactions between two proteins.
/api/protein/{symbol}/interactions	Filtered and sorted rows. Takes kind, type, pathway, min_evidence, sort, and limit.
/api/interaction-types	The controlled vocabulary with counts.
/api/pathway/{id}	A pathway node with its lineage and member interactions.
/api/pathways/tree	The full pathway scaffold.
/api/highlights	The best evidenced interactions.
/api/protein/{symbol}/network?format=	Network export as tsv, sif, or graphml, for Cytoscape and networkx.

Every parameter and response schema is documented in the interactive API reference.

The MCP server

propaths-mcp exposes the same reads as read-only tools over the Model Context Protocol. It is a thin client over this API, so tool output is the API's JSON unchanged. It also ships MCP resources and prompts, so an agent can orient itself without being told the schema.

Tools it exposes

search_proteins get_protein get_interaction get_interaction_between list_interactions list_interaction_types get_pathway get_pathway_tree get_highlights export_network describe_schema

Or install it directly

pip install propaths-mcp
propaths-mcp

Access and limits

The API is public, keyless, read only, and rate limited per client. Nothing in it writes to the graph.

For higher rate limits, enrichment access, a hosted MCP server, or a protein mapped for your lab, get in touch.

See what the endpoints return.

The demo reads from this same graph. Every interaction you open there is one API call away.

Explore the Demo → How the graph is built