TRAPI MCP

A FastMCP-based tool for writing prompts using Translator Reasoner API (TRAPI) queries. This package enables easy integration of biomedical knowledge graph queries into your LLM workflows.

Installation

You can install the package from source:

pip install -e .

Or using uv (recommended):

uv install trapi-mcp

Python API

from trapi_mcp.tools import trapi, trapi_status, trapi_results

# Submit a TRAPI query
response = trapi(
    subject="MONDO:0005148",  # Alzheimer's disease
    object_="CHEBI:6801",     # Acetylcholine
    predicate="biolink:affects"
)

# Get the query ID
pk = response["pk"]

# Check status
status_response = trapi_status(pk)
print(f"Query status: {status_response.get('status')}")

# When status is "Done", get results
if status_response.get("status") == "Done":
    results = trapi_results(pk)
    # Process results

Developer Guide

Setup Development Environment

1. Clone the repository:

git clone https://github.com/your-username/trapi-mcp.git
cd trapi-mcp

2. Install development dependencies:

uv install

Architecture

The package consists of several key components:

• api_utilities.py: Low-level functions for interacting with Translator API services - e.g., how to make API calls
• tools.py: High-level functions for building and executing TRAPI queries. Currently, NameResolver, NodeNormalizer, and ARS query endpoints are all callable as MCP servers from this repository.
• main.py: FastMCP integration and CLI setup

Integration with Goose (Example)

Goose is a framework for building LLM applications. Here's how to integrate TRAPI MCP with Goose:

install goose:

https://block.github.io/goose/docs/getting-started/installation/

Set an LLM Provider

https://block.github.io/goose/docs/getting-started/installation/#set-llm-provider

Add TRAPI MCP as an extenstion

https://block.github.io/goose/docs/getting-started/using-extensions#adding-extensions

• Under "Advanced Settings"
  • "Add custom extension"
  • Name the extension "TRAPI MCP"
  • For "Command", add "uvx trapi-mcp"
  • "Save Changes"
  • Turn "on" the extension for your session.
  • Ask questions of goose like:

  • What is the relationship between Alzheimer's disease and acetylcholine?
    

  • How many disesaes is ABCA1 related to?
    

  • What treats diabetes mellitus?