Biomcp

BioMCP is an open - source biomedical AI toolkit that provides professional biomedical knowledge support for AI systems by connecting to authoritative data sources.

Research and data Developer tools #Biomedical AI #Clinical Trials #Genetic Variations #Literature Retrieval .Python

rating : 3 points

downloads : 10.0K

update time : 2025-04-29

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What is BioMCP?

BioMCP is an open - source tool that connects AI systems to authoritative biomedical databases such as PubMed, ClinicalTrials.gov, and MyVariant.info through the Model Context Protocol (MCP), helping users quickly obtain accurate biomedical information.

How to use BioMCP?

BioMCP can be operated through simple command - line operations. Users can easily search for literature, clinical trials, and genetic variation information.

Applicable Scenarios

BioMCP is suitable for researchers, doctors, and students who need to quickly retrieve biomedical information. For example, finding relevant research on specific gene mutations or searching for clinical trials related to diseases.

Main Features

PubMed and PubTator3 Support

Query PubMed and PubTator3 through natural language to obtain biomedical literature and their detailed information.

ClinicalTrials.gov Integration

Search for and obtain comprehensive information about clinical trials, including trial locations, results, and references.

MyVariant.info Support

Query and obtain comprehensive annotation information about genetic variations.

Advantages

Provide authoritative and real - time updated biomedical data

Support multiple natural language query methods

Easy to integrate into existing AI systems

Limitations

Require a certain network environment support

May take longer to respond to complex queries

How to Use

Install BioMCP

First, ensure that Python or the uv tool is installed in your environment.

Start the Server

Run the following command to start the BioMCP server.

Execute Queries

Use predefined commands to perform data queries.

Usage Examples

Case 1: Find Literature Related to Gene Mutations

Users want to know the research progress of specific gene mutations (such as BRAF) in melanoma.

Case 2: Search for Clinical Trials

Users want to find specific information about Phase III clinical trials for lung cancer.

Frequently Asked Questions

How to install BioMCP?

Does BioMCP support multi - language queries?

Related Resources

BioMCP Official Website

Visit the official website for more detailed information.

GitHub Code Repository

View the source code and contribute to the project.

YouTube Tutorial Video

Watch the video to learn how to use BioMCP.

🚀 Biomedical Model Context Protocol (BioMCP)

BioMCP is an open - source toolkit (under the MIT License) designed to endow AI assistants and agents with professional biomedical knowledge. Built on the Model Context Protocol (MCP), it enables AI systems to connect to authoritative biomedical data sources, thus answering questions about clinical trials, scientific literature, and genomic variations accurately and comprehensively.

🚀 Quick Start

For Claude Desktop Users

Install and configure the BioMCP plugin.
Run the example command directly:
```
biomcp --example prompt
```
View the detailed output and result analysis.

General Installation Steps

Download the BioMCP package:
```
pip install biomcp
```
Follow the step - by - step guide in the documentation for setup.
Run the example code to get familiar with the basic usage of the tool.

✨ Features

Although large language models have extensive knowledge bases, they often lack specific information in specialized fields or cannot access the latest resources. BioMCP excels in bridging this gap:

Structured Access: Connect to authoritative biomedical data sources to ensure accurate and up - to - date information.
Natural Language Queries: Support information retrieval through natural language questions, facilitating user interaction.
Cross - platform Compatibility: Compatible with various AI systems and tools, enhancing integration and scalability.

🧪 Testing and Validation

Use the MCP Inspector tool to comprehensively test your BioMCP setup and ensure the system is running properly. Follow these steps:

Download and install the MCP Inspector.
Configure the Inspector to connect to your BioMCP instance.
Run comprehensive checks and generate reports.

🏢 Enterprise Edition: OncoMCP

OncoMCP is an extended version of BioMCP, specifically designed for the healthcare industry:

HIPAA - compliant Deployment: Ensure data transmission and storage comply with strict privacy regulations.
Real - time Trial Matching: Quickly identify suitable clinical trials for patients to participate in.
Advanced Rule Processing: Support complex medical logic judgment and decision - making assistance.

For more information, visit the GenomOncology website.

📖 MCP Registry

📚 Documentation

For detailed information about BioMCP, visit https://biomcp.org.

💻 Usage Examples

Want to see BioMCP in action?

Check out the companion code repository: 👉 [biomcp - examples](https://github.com/genomoncology/biomcp - examples)

It contains real prompts, AI - generated research briefs, and evaluation runs of different models. Feel free to contribute your examples by forking the repository and submitting a PR.