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Pubtator MCP Server
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Pubtator MCP Server

PubTator MCP Server is a biomedical literature annotation and relationship mining server based on PubTator3, providing convenient literature retrieval, annotation information acquisition, and entity relationship analysis functions for AI assistants through the MCP interface.
Research and dataDeveloper tools#Literature annotation#Biomedicine#Relationship mining#MCP interface.Python
2.5 points
17

What is PubTator MCP Server?

PubTator MCP Server is an AI assistant tool based on PubTator3, used for searching scientific literature, obtaining annotation information, and analyzing relationships between entities. It provides convenient access through the Model Context Protocol (MCP) interface.

How to use PubTator MCP Server?

Users can start using it by installing the MCP client and configuring the server. It supports integration with multiple programming languages and tools, such as Claude, Cursor, Windsurf, etc.

Application scenarios

Suitable for researchers or developers who need to quickly retrieve biomedical literature and analyze entity relationships.

Main functions

Literature annotation exportSupports exporting literature annotation results in multiple formats (e.g., PubTator, BioC XML, JSON).
Entity ID queryQueries the standard identifiers of biological concepts through free text.
Relationship miningDiscovers relationships between entities in the biomedical field.
Literature searchSupports retrieving literature by keywords and entity IDs.
Batch processingSupports batch exporting annotation information from search results.

Advantages and limitations

Advantages
Powerful biomedical literature annotation ability
Supports multiple data formats and batch processing
Easy to integrate into existing systems
Limitations
There is a limit on the API request rate (maximum 3 requests per second).
Pay attention to performance optimization when exporting in large batches.
Specific format of entity IDs is required for relationship queries.

How to use

Install the MCP client
Run the installation command in the terminal, for example, use Smithery CLI.
Start the server
Run the Python script locally or start the server using a Docker container.
Configure the client
Configure the client connection parameters according to requirements, such as the host address and port number.

Usage examples

Example 1: Literature annotation exportExport the literature annotation information about SARS-CoV-2.
Example 2: Entity relationship miningFind the chemical substances related to 'COVID-19'.

Frequently Asked Questions

How to solve the API request timeout problem?
What format should the entity ID start with?
How to batch export the annotation information of multiple pieces of literature?

Related resources

Official documentation
Project source code and detailed documentation.
Smithery CLI
A tool for quickly installing and configuring the MCP server.
Docker Hub
Pre-built Docker image.
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": []
    }
  }
}
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