A collection of Model Context Protocol (MCP) servers for biomedical research, providing AI assistants with access to various biomedical databases and resources.
The Model Context Protocol (MCP) allows AI assistants like Claude to access external tools and data sources. These servers extend Claude's capabilities by providing access to specific biomedical databases.
This repository contains the following MCP servers:
Access the PubMed database of biomedical literature.
Access preprints from bioRxiv and medRxiv repositories.
Access information about clinical trials.
Access drug information from DrugBank.
Access drug target information from Open Targets.
Install dependencies for all servers:
pip install -r requirements.txt
For specific servers, additional setup may be required:
EMAIL
constant in pubmed_mcp.py
with your email address (required by NCBI)API_KEY
constant in drugbank_mcp.py
Run a server:
python pubmed_mcp.py # Replace with the server you want to run
To use these servers with Claude for Desktop:
Make sure you have the latest version of Claude for Desktop installed.
Edit your Claude for Desktop configuration file located at:
~/Library/Application Support/Claude/claude_desktop_config.json
%AppData%\Claude\claude_desktop_config.json
Add server configurations:
{
"mcpServers": {
"pubmed-mcp": {
"command": "python",
"args": [
"/ABSOLUTE/PATH/TO/pubmed_mcp.py"
]
},
"biorxiv-mcp": {
"command": "python",
"args": [
"/ABSOLUTE/PATH/TO/bioarxiv_mcp.py"
]
},
"clinicaltrials-mcp": {
"command": "python",
"args": [
"/ABSOLUTE/PATH/TO/clinicaltrialsgov_mcp.py"
]
},
"drugbank-mcp": {
"command": "python",
"args": [
"/ABSOLUTE/PATH/TO/drugbank_mcp.py"
]
},
"opentargets-mcp": {
"command": "python",
"args": [
"/ABSOLUTE/PATH/TO/opentargets_mcp.py"
]
}
}
}
Replace /ABSOLUTE/PATH/TO/
with the absolute path to each script on your system.
Restart Claude for Desktop.
If you encounter issues:
~/Library/Logs/Claude/mcp*.log
%APPDATA%\Claude\logs\mcp*.log
{ "mcpServers": { "mcps": { "command": "python", "args": [ "/ABSOLUTE/PATH/TO/pubmed_mcp.py" ] } } }
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