BioMCP: AI-Powered Biomedical Research¶

Transform how you search and analyze biomedical data with BioMCP - a powerful tool that connects AI assistants and researchers to critical biomedical databases through natural language.

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NEW Remote BioMCP Now Available!

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🛠️ 23+ Tools Full suite of biomedical research tools

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What Can You Do with BioMCP?¶

Search Research Literature¶

Find articles about genes, variants, diseases, and drugs with automatic cancer genomics data from cBioPortal

biomcp article search --gene BRAF --disease melanoma

Discover Clinical Trials¶

Search active trials by condition, location, phase, and eligibility criteria including genetic biomarkers

biomcp trial search --condition "lung cancer" --status RECRUITING

Analyze Genetic Variants¶

Query variant databases, predict effects, and understand clinical significance

biomcp variant search --gene TP53 --significance pathogenic

AI-Powered Analysis¶

Use with Claude Desktop for conversational biomedical research with sequential thinking

# Claude automatically uses BioMCP tools
"What BRAF mutations are found in melanoma?"

5-Minute Quick Start¶

Choose Your Interface¶

Claude Desktop (Recommended)Command LinePython SDK

Best for: Conversational research, complex queries, AI-assisted analysis

Install Claude Desktop from claude.ai/desktop
Configure BioMCP: json { "mcpServers": { "biomcp": { "command": "uv", "args": [ "run", "--with", "biomcp-python", "biomcp", "run" ] } } }
Start researching: Ask Claude about any biomedical topic!

Full Claude Desktop Guide →

Best for: Direct queries, scripting, automation

Install BioMCP:

# Using uv (recommended)
uv tool install biomcp

# Or using pip
pip install biomcp-python

Run your first search:

biomcp article search \
  --gene BRAF --disease melanoma \
  --limit 5

CLI Reference →

Best for: Integration, custom applications, bulk operations

Install the package:
```
pip install biomcp-python
```

Use in your code:

from biomcp import BioMCPClient

async with BioMCPClient() as client:
    articles = await client.articles.search(
        genes=["BRAF"],
        diseases=["melanoma"]
    )

Python SDK Docs →

Key Features¶

Unified Search Across Databases¶

PubMed/PubTator3: 30M+ research articles with entity recognition
ClinicalTrials.gov: 400K+ clinical trials worldwide
MyVariant.info: Comprehensive variant annotations
cBioPortal: Automatic cancer genomics integration

Intelligent Query Processing¶

Natural language to structured queries
Automatic synonym expansion
OR logic support for flexible matching
Cross-domain relationship discovery

Built for AI Integration¶

24 specialized MCP tools
Sequential thinking for complex analysis
Streaming responses for real-time updates
Context preservation across queries

Explore All Features →

Learn by Example¶

Find Articles About a Specific Mutation¶

# Search for BRAF V600E mutations
biomcp article search --gene BRAF \
  --keyword "V600E|p.V600E|c.1799T>A"

Discover Trials Near You¶

# Find cancer trials in Boston area
biomcp trial search --condition cancer \
  --latitude 42.3601 --longitude -71.0589 \
  --distance 50

Get Gene Information¶

# Get comprehensive gene data
biomcp gene get TP53

More Examples →

Popular Workflows¶

Literature Review¶

Systematic search across papers, preprints, and clinical trials Workflow Guide →

Variant Interpretation¶

From variant ID to clinical significance and treatment implications Workflow Guide →

Trial Matching¶

Find eligible trials based on patient criteria and biomarkers Workflow Guide →

Drug Research¶

Connect drugs to targets, trials, and research literature Workflow Guide →

Advanced Features¶

NCI Integration: Enhanced cancer trial search with biomarker filtering
AlphaGenome: Predict variant effects on gene regulation
BigQuery Logging: Monitor usage and performance
HTTP Server Mode: Deploy as a service

Documentation¶

Getting Started - Installation and first steps
User Guides - Detailed usage instructions
API Reference - Technical documentation
FAQ - Quick answers to common questions

Community & Support¶

GitHub: github.com/genomoncology/biomcp
Issues: Report bugs or request features
Discussions: Ask questions and share tips

License¶

BioMCP is licensed under the MIT License. See LICENSE for details.