MCPmed Bioinformatics Web Services

Adapts the Model Context Protocol (MCP) to bioinformatics web server backends. This creates a standardized, machine-actionable layer for LLMs to interact with external biological resources, matching the 2026 standard for agentic tools.

When to Use This Skill

• "Query STRING database for protein-protein interactions via MCP"
• "Fetch dataset metadata from GEO using MCPmed"
• "Access UCSC Cell Browser data through MCP"

Core Capabilities

1. GEO Integration: Search and retrieve Gene Expression Omnibus metadata autonomously.
2. STRING DB Access: Query protein-protein interaction networks contextually.
3. UCSC Cell Browser: Programmatic access to single-cell datasets.

Workflow

1. Step 1: Start the MCPmed server to expose the bioinformatics backend tools.
2. Step 2: Connect the LLM client using MCP to query the integrated databases.

Example Usage

User: "Query the STRING database for interactions with TP53."

Agent Action:

python3 -m mcpmed.cli query string --gene TP53