AIBase
EN
Explore
Pubtator MCP Server Rgj
P

Pubtator MCP Server Rgj

The PubTator MCP Server is a biomedical literature annotation and relationship mining server based on PubTator3. It provides AI models with the functions of programmatically accessing scientific literature, obtaining annotation information, and analyzing entity relationships through the MCP protocol.
Research and dataDeveloper tools#Literature annotation#Entity query#Relationship mining#Batch processing.Python
2 points
9.7K
Open Site

Overview

Installation

Content Details

Alternatives

What is the PubTator MCP Server?

The PubTator MCP Server is a medical information query tool based on the PubTator annotation system. It supports retrieving information on diseases, genes, chemical drugs, etc. through entity recognition and relationship mining.

How to use the PubTator MCP Server?

Users can obtain the required information by entering natural language questions or using query statements in a specific format. It supports multiple output formats, including PubTator, BioCXML, and BioCJSON.

Application scenarios

This system is widely used in fields such as medical research, drug development, and disease analysis, helping researchers quickly obtain relevant literature information and entity relationship networks.
Find COVID - 19 related literature
Search for papers on COVID - 19 and return the BioCJSON format data of the top 5 results.
Find drugs for treating COVID - 19
Discover chemical drugs used for treating COVID - 19.
Find compounds that interact with the BRCA1 gene
Identify chemical substances that interact with the BRCA1 gene.
What types of biomedical entities are supported?
What is the function of the @ symbol?
Can the full text of papers be obtained?
What are the differences between PubTator, BioCXML, and BioCJSON?
PubTator official website
The official website of the PubTator project, providing detailed documentation and interface information.
BioC standard specification
Detailed description and technical specifications of the BioC format.
API interface documentation
The API interfaces provided by the PubTator MCP Server and their usage methods.

Installation

Copy the following command to your Client for configuration
{
  "mcpServers": {
    "pubtator": {
      "command": "python",
      "args": ["-m", "pubtator-mcp-server"]
      }
  }
}

{
  "mcpServers": {
    "pubtator": {
      "command": "C:\\Users\\YOUR\\PATH\\miniconda3\\envs\\mcp_server\\python.exe",
      "args": [
        "D:\\code\\YOUR\\PATH\\PubTator-MCP-Server\\pubtator_server.py"
      ],
      "env": {},
      "disabled": false,
      "autoApprove": []
    }
  }
}

{
  "mcpServers": {
    "pubtator": {
      "command": "bash",
      "args": [
        "-c",
        "source /home/YOUR/PATH/mcp-server-pubtator/.venv/bin/activate && python /home/YOUR/PATH/pubtator_server.py"
      ],
      "env": {
        "MCP_TRANSPORT": "stdio"
      },
      "disabled": false,
      "autoApprove": []
    }
  }
}

{
  "mcpServers": {
    "pubtator": {
      "command": "bash",
      "args": [
        "-c",
        "source /home/YOUR/PATH/mcp-server-pubtator/.venv/bin/activate && python /home/YOUR/PATH/pubtator_server.py"
      ],
      "env": {
        "MCP_TRANSPORT": "tcp",
        "MCP_HOST": "127.0.0.1",
        "MCP_PORT": "8888"
      },
      "disabled": false,
      "autoApprove": []
    }
  }
}
Note: Your key is sensitive information, do not share it with anyone.

Alternatives

R
Rsdoctor
Rsdoctor is a build analysis tool specifically designed for the Rspack ecosystem, fully compatible with webpack. It provides visual build analysis, multi - dimensional performance diagnosis, and intelligent optimization suggestions to help developers improve build efficiency and engineering quality.
TypeScript
8.7K
5 points
N
Next Devtools MCP
The Next.js development tools MCP server provides Next.js development tools and utilities for AI programming assistants such as Claude and Cursor, including runtime diagnostics, development automation, and document access functions.
TypeScript
9.3K
5 points
T
Testkube
Testkube is a test orchestration and execution framework for cloud-native applications, providing a unified platform to define, run, and analyze tests. It supports existing testing tools and Kubernetes infrastructure.
Go
6.2K
5 points
M
MCP Windbg
An MCP server that integrates AI models with WinDbg/CDB for analyzing Windows crash dump files and remote debugging, supporting natural language interaction to execute debugging commands.
Python
9.5K
5 points
R
Runno
Runno is a collection of JavaScript toolkits for securely running code in multiple programming languages in environments such as browsers and Node.js. It achieves sandboxed execution through WebAssembly and WASI, supports languages such as Python, Ruby, JavaScript, SQLite, C/C++, and provides integration methods such as web components and MCP servers.
TypeScript
7.5K
5 points
P
Praisonai
PraisonAI is a production-ready multi-AI agent framework with self-reflection capabilities, designed to create AI agents to automate the solution of various problems from simple tasks to complex challenges. It simplifies the construction and management of multi-agent LLM systems by integrating PraisonAI agents, AG2, and CrewAI into a low-code solution, emphasizing simplicity, customization, and effective human-machine collaboration.
Python
6.1K
5 points
N
Netdata
Netdata is an open-source real-time infrastructure monitoring platform that provides second-level metric collection, visualization, machine learning-driven anomaly detection, and automated alerts. It can achieve full-stack monitoring without complex configuration.
Go
9.6K
5 points
M
MCP Server
The Mapbox MCP Server is a model context protocol server implemented in Node.js, providing AI applications with access to Mapbox geospatial APIs, including functions such as geocoding, point - of - interest search, route planning, isochrone analysis, and static map generation.
TypeScript
6.7K
4 points
G
Gitlab MCP Server
Certified
The GitLab MCP server is a project based on the Model Context Protocol that provides a comprehensive toolset for interacting with GitLab accounts, including code review, merge request management, CI/CD configuration, and other functions.
TypeScript
21.6K
4.3 points
M
Markdownify MCP
Markdownify is a multi-functional file conversion service that supports converting multiple formats such as PDFs, images, audio, and web page content into Markdown format.
TypeScript
31.1K
5 points
D
Duckduckgo MCP Server
Certified
The DuckDuckGo Search MCP Server provides web search and content scraping services for LLMs such as Claude.
Python
61.9K
4.3 points
N
Notion Api MCP
Certified
A Python-based MCP Server that provides advanced to-do list management and content organization functions through the Notion API, enabling seamless integration between AI models and Notion.
Python
18.9K
4.5 points
F
Figma Context MCP
Framelink Figma MCP Server is a server that provides access to Figma design data for AI programming tools (such as Cursor). By simplifying the Figma API response, it helps AI more accurately achieve one - click conversion from design to code.
TypeScript
58.4K
4.5 points
U
Unity
Certified
UnityMCP is a Unity editor plugin that implements the Model Context Protocol (MCP), providing seamless integration between Unity and AI assistants, including real - time state monitoring, remote command execution, and log functions.
C#
28.0K
5 points
G
Gmail MCP Server
A Gmail automatic authentication MCP server designed for Claude Desktop, supporting Gmail management through natural language interaction, including complete functions such as sending emails, label management, and batch operations.
TypeScript
18.8K
4.5 points
M
Minimax MCP Server
The MiniMax Model Context Protocol (MCP) is an official server that supports interaction with powerful text-to-speech, video/image generation APIs, and is suitable for various client tools such as Claude Desktop and Cursor.
Python
42.2K
4.8 points
AIBase
Zhiqi Future, Your AI Solution Think Tank
English简体中文繁體中文にほんご
© 2026AIBase