PubTator MCP Server

Name: PubTator MCP Server
Author: JackKuo666

@JackKuo666

关于 PubTator MCP Server

🔍 A biomedical literature annotation and relationship mining server based on PubTator3, providing convenient access through the MCP interface.

#biomedical #literature-annotation #relationship-mining

基本信息

分类

其他

许可证

MIT

运行时

python

传输方式

stdio

发布者

JackKuo666

配置

使用下面的配置,将此服务器添加到你的 MCP 客户端。

{
  "mcpServers": {
    "pubtator-mcp-server-jackkuo666": {
      "command": "npx",
      "args": [
        "-y",
        "@smithery/cli@latest",
        "install",
        "@JackKuo666/pubtator-mcp-server",
        "--client",
        "claude",
        "--config",
        "{}"
      ]
    }
  }
}

工具

未检测到工具

工具是从 README 中自动提取的。维护者可以在 ## Tools 标题下列出工具,即可填充这部分内容。

概览

What is PubTator MCP Server?

PubTator MCP Server is a biomedical literature annotation and relationship mining server based on PubTator3, providing access 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 or manually (clone repo, pip install -r requirements.txt) with Python 3.10+ and FastMCP. Run the server directly (python pubtator_server.py) or via Docker. Configure transport (TCP default, stdio available) and host/port via environment variables. Use MCP client tools (e.g., Claude Desktop, Cursor, CLine) to invoke functions such as export_publications, find_entity_id, find_related_entities, search_pubtator, and batch_export_from_search.

Key features of PubTator MCP Server

Literature Annotation Export in multiple formats (pubtator, biocxml, biocjson)
Entity ID Lookup for biological concepts via free text
Relationship Mining to discover biomedical relationships between entities
Literature Search by keywords and entity IDs
Batch Processing of annotation export from search results

Use cases of PubTator MCP Server

Automating extraction of annotated biomedical entities from PubMed articles
Querying standardized identifiers for genes, diseases, chemicals, and species
Discovering relationships like treatments, causes, or interactions between entities
Performing large-scale batch annotation export for research datasets
Integrating biomedical literature mining into AI assistant workflows

FAQ from PubTator MCP Server

What are the runtime requirements and dependencies?

Python 3.10+ and the FastMCP library are required. Docker is also supported for containerized deployment.

What transport protocols does the server support?

Both stdio and TCP transports are supported. The default is TCP on host 0.0.0.0 port 8080, configurable via MCP_TRANSPORT, MCP_HOST, and MCP_PORT environment variables.

What are the usage limitations?

API request rate limit is maximum 3 requests per second. When batch exporting, use a reasonable batch_size to avoid timeout. For relationship queries, entity IDs must start with "@" (e.g., @DISEASE_COVID-19).