BioContextAI Knowledgebase
An MCP server that provides standardized access to biomedical knowledge bases and resources, enabling AI systems to retrieve verified information from sources like bioRxiv, EuropePMC, and various protein/gene databases.
What is BioContextAI Knowledgebase?
BioContextAI Knowledgebase is a Model Context Protocol (MCP) server that allows AI assistants like Claude, Cursor, and VS Code to mcp server that provides standardized access to biomedical knowledge bases and resources, enabling ai systems to retrieve verified information from sources like biorxiv, europepmc, and various protein...
An MCP server that provides standardized access to biomedical knowledge bases and resources, enabling AI systems to retrieve verified information from sources like bioRxiv, EuropePMC, and various protein/gene databases.
This server falls under the Data Science & ML category on MCPgee, the world's largest MCP server directory with 33,000+ servers.
Features
- An MCP server that provides standardized access to biomedica
Use Cases
Maintainer
Works with
Installation
Manual Installation
npx biocontextai-knowledgebase-mcpConfiguration
Configuration Details
claude_desktop_config.json
Performance
Response Metrics
Resource Usage
How to Set Up and Use BioContextAI Knowledgebase
The BioContextAI Knowledgebase MCP server provides AI systems with standardized, reliable access to more than 14 authoritative biomedical databases, covering genes, proteins, scientific literature, biological pathways, and disease-gene associations. Sources include bioRxiv/medRxiv, EuropePMC, Ensembl, the Antibody Registry, InterPro, Protein Atlas, AlphaFold DB, KEGG, Reactome, STRING, PanglaoDB, PRIDE, and OpenTargets. Researchers and bioinformaticians use this server to ground AI-generated biomedical answers in verified, citable data rather than relying on model memory.
Prerequisites
- Python 3.12 (recommended; set via UV_PYTHON environment variable)
- uv package manager installed (https://docs.astral.sh/uv/)
- An MCP-compatible client such as Claude Desktop, VS Code, Cursor, or Windsurf
- Internet access to reach external biomedical APIs (KEGG is local-use only)
Install uv package manager
uv is required to install and run the biocontext_kb package. Install it with the official installer.
curl -LsSf https://astral.sh/uv/install.sh | shAdd to Claude Desktop configuration
Edit your Claude Desktop config file to register the BioContextAI Knowledgebase MCP server. The uvx command automatically downloads and runs the latest version.
{
"mcpServers": {
"biocontext_kb": {
"command": "uvx",
"args": ["biocontext_kb@latest"],
"env": {
"UV_PYTHON": "3.12"
}
}
}
}Configure for VS Code or Cursor
For IDE integration, add the same configuration to .vscode/mcp.json or the equivalent IDE MCP config.
{
"mcpServers": {
"biocontext_kb": {
"command": "uvx",
"args": ["biocontext_kb@latest"]
}
}
}Run via Docker for isolated deployment
Clone the repository and build a Docker image if you prefer containerized deployment.
git clone https://github.com/biocontext-ai/knowledgebase-mcp.git
cd knowledgebase-mcp
docker build -t biocontext_kb:latest .
docker run -p 127.0.0.1:8000:8000 biocontext_kb:latestTest in development mode
Verify the server is working by running it in stdio development mode before connecting a client.
export MCP_ENVIRONMENT=DEVELOPMENT
uvx biocontext_kbBioContextAI Knowledgebase Examples
Client configuration
Production-ready Claude Desktop configuration using uvx with Python 3.12.
{
"mcpServers": {
"biocontext_kb": {
"command": "uvx",
"args": ["biocontext_kb@latest"],
"env": {
"UV_PYTHON": "3.12"
}
}
}
}Prompts to try
Example biomedical research queries you can ask once the server is connected.
- "Look up the Ensembl gene ID and chromosome location for BRCA2"
- "Search EuropePMC for papers about single-cell RNA sequencing of the tumor microenvironment"
- "What are the STRING interaction partners of EGFR with a score above 900?"
- "Fetch the AlphaFold confidence scores for human p53 (TP53)"
- "Which diseases does PTEN associate with in OpenTargets?"
- "List cell types that express ACE2 according to PanglaoDB"Troubleshooting BioContextAI Knowledgebase
Rate limit errors when querying external databases
The server is designed for local use. Hosting it remotely or making many rapid requests increases rate-limit exposure. Run the server on the same machine as your client and space out queries.
uvx fails to find Python 3.12
uv can install Python automatically. Run `uv python install 3.12` to ensure Python 3.12 is available, then set UV_PYTHON=3.12 in the MCP server env block.
KEGG queries return no results or licensing errors
KEGG data may only be used locally for academic purposes. Commercial use and remote hosting are prohibited under KEGG's license. Do not expose the server publicly if you need KEGG data.
Frequently Asked Questions about BioContextAI Knowledgebase
What is BioContextAI Knowledgebase?
BioContextAI Knowledgebase is a Model Context Protocol (MCP) server that mcp server that provides standardized access to biomedical knowledge bases and resources, enabling ai systems to retrieve verified information from sources like biorxiv, europepmc, and various protein/gene databases. It connects AI assistants to external tools and data sources through a standardized interface.
How do I install BioContextAI Knowledgebase?
Follow the installation instructions on the BioContextAI Knowledgebase GitHub repository. Clone the repo, install dependencies, and add the server config to your AI client.
Which AI clients work with BioContextAI Knowledgebase?
BioContextAI Knowledgebase works with all major MCP-compatible AI clients including Claude Desktop, Claude Code, Cursor, VS Code (GitHub Copilot), Windsurf, and Cline.
Is BioContextAI Knowledgebase free to use?
Yes, BioContextAI Knowledgebase is open source and available under the Apache 2.0 license. You can use it freely in both personal and commercial projects.
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