Biomart MCP
by jzinno
Biomart MCP is a server that interfaces with Biomart using the Model Context Protocol (MCP). It standardizes how applications provide context to LLMs, leveraging the MCP python-sdk and pybiomart package.
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What is Biomart MCP?
Biomart MCP is a Model Context Protocol (MCP) server designed to provide an interface between Large Language Models (LLMs) and Biomart, a comprehensive resource for biological data. It leverages the MCP protocol to standardize how applications provide context to LLMs, enabling more informed and accurate responses from these models when dealing with biological data.
How to use Biomart MCP?
The server can be installed and run locally using tools like uv. It can be integrated with applications like Claude Desktop and Cursor by configuring the MCP server settings. The README provides detailed installation instructions and example configurations for different environments.
Key features of Biomart MCP
Mart and Dataset Discovery
Attribute and Filter Exploration
Data Retrieval
ID Translation
Use cases of Biomart MCP
Exploring Biomart database structure
Finding specific attributes and filters for datasets
Querying Biomart for biological data using specific attributes and filters
Converting between different biological identifiers (e.g., gene symbols to Ensembl IDs)
FAQ from Biomart MCP
What is Model Context Protocol (MCP)?
What is Model Context Protocol (MCP)?
MCP is an open protocol that standardizes how applications provide context to LLMs.
What is Biomart?
What is Biomart?
Biomart is a comprehensive resource for biological data, providing access to various databases and tools for data retrieval and analysis.
How do I install Biomart MCP?
How do I install Biomart MCP?
Follow the installation instructions in the README, which include cloning the repository and setting up the environment.
How do I integrate Biomart MCP with Claude Desktop?
How do I integrate Biomart MCP with Claude Desktop?
Use the uv run command with the appropriate MCP flags, as shown in the README.
How do I contribute to Biomart MCP?
How do I contribute to Biomart MCP?
Pull requests are welcome! Be mindful of compatibility with MCP clients and context window limitations.