Reactome FAQs

Question 1

What is Reactome-mcp-python?

Accepted Answer

Reactome-mcp-python is a Python-based FastMCP server designed to provide a comprehensive interface for interacting with Reactome's Content and Analysis Services. It's a port of the original TypeScript proof of concept.

Question 2

Why should I use the Python version of this Reactome tool?

Accepted Answer

The Python version is ideal because Python integrates naturally into AI and bioinformatics workflows, leverages the FastMCP standard framework, and maintains alignment with the original TypeScript tool names for seamless client migration.

Question 3

What kind of Reactome functionalities does this server expose?

Accepted Answer

This server provides access to 53 MCP tools covering a wide range of functionalities including analysis, pathways, search, entities, export, interactors, and utility endpoints, along with 10 MCP resources for direct access to Reactome data.

Question 4

Can Reactome-mcp-python be integrated with other applications or clients?

Accepted Answer

Yes, it runs over stdio by default, making it ready for integration with any MCP-compatible client. Specific configurations are provided for popular environments like Claude Desktop and Claude Code.

Question 5

What are the requirements to run Reactome-mcp-python?

Accepted Answer

To run Reactome-mcp-python, you need Python 3.11 or higher and the `fastmcp` 3.x library. Installation can be done easily via `uv` or `pip`.

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