PubTator MCP Server

@BioMCP-Hub

About PubTator MCP Server

No overview available yet

Config

Add this server to your MCP-compatible client using the configuration below.

{
  "mcpServers": {
    "PubTator-MCP-Server": {
      "command": "npx",
      "args": [
        "-y",
        "@smithery/cli@latest",
        "install",
        "@JackKuo666/pubtator-mcp-server",
        "--client",
        "claude",
        "--config",
        "{}"
      ]
    }
  }
}

Tools

No tools detected

Fetch the live tool list by running this server in a temporary sandbox using the button above.

Overview

What is PubTator MCP Server?

It is a biomedical literature annotation and relationship mining server based on PubTator3, providing AI assistants access to PubTator3 through the Model Context Protocol (MCP). It allows AI models to programmatically search scientific literature, obtain annotation information, and analyze entity relationships.

How to use PubTator MCP Server?

Install via Smithery (npx command) or manually clone the repo and run pip install -r requirements.txt. Start the server with python pubtator_server.py. Configure transports via environment variables MCP_TRANSPORT, MCP_HOST, MCP_PORT. Use the MCP client (e.g., Claude Desktop, Cursor) to connect and call tools like export_publications, find_entity_id, find_related_entities, search_pubtator, and batch_export_from_search.

Key features of PubTator MCP Server

Export PubTator annotations in multiple formats (pubtator, biocxml, biocjson)
Look up standard identifiers for biological concepts via free text
Discover biomedical relationships (treat, cause, interact, etc.)
Search literature by keywords and entity IDs
Batch export annotations from search results

Use cases of PubTator MCP Server

Retrieve annotated publications for given PMIDs for analysis
Find the official ID of a gene, disease, or chemical from a natural language query
Identify entities related to a known biomedical concept
Search literature on a topic and export all annotations in batch
Integrate literature mining directly into AI assistant workflows

FAQ from PubTator MCP Server

What are the rate limits?

API requests are limited to a maximum of 3 requests per second.

What data formats are supported for annotation export?

Supported formats are pubtator, biocxml, and biocjson.

What transport options are available?

The server supports both stdio and TCP transport, configurable via the MCP_TRANSPORT environment variable (default is TCP).

Are there any special requirements for entity IDs in relationship queries?

Entity IDs must start with "@", for example @DISEASE_COVID-19.

What are the runtime dependencies?

Python 3.10+ and the FastMCP library are required.

Frequently asked questions

What are the rate limits?

API requests are limited to a maximum of 3 requests per second.

What data formats are supported for annotation export?

Supported formats are pubtator, biocxml, and biocjson.

What transport options are available?

The server supports both stdio and TCP transport, configurable via the `MCP_TRANSPORT` environment variable (default is TCP).

Are there any special requirements for entity IDs in relationship queries?

Entity IDs must start with "@", for example `@DISEASE_COVID-19`.

What are the runtime dependencies?

Python 3.10+ and the FastMCP library are required.

Comments

Basic information

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