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Pubtator MCP Server Rgj
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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
11

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 literatureSearch for papers on COVID - 19 and return the BioCJSON format data of the top 5 results.
Find drugs for treating COVID - 19Discover chemical drugs used for treating COVID - 19.
Find compounds that interact with the BRCA1 geneIdentify 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.
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