Pubtator MCP Server

@QIngyuanfl

代码仓库

基本信息

分类

其他

传输方式

stdio

作者

QIngyuanfl

关于 Pubtator MCP Server

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Pubtator MCP Server 配置

暂无标准配置

该服务器的 README 中没有可解析的 MCP 配置块，请前往代码仓库查看安装说明。

代码仓库

Pubtator MCP Server 工具

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当前收录暂时没有可展示的工具列表，不代表服务没有工具。请查阅项目文档了解支持的能力。

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?

An async Python server that integrates with the PubTator3 API to provide biomedical text‑mining tools via the MCP agent protocol. It supports entity lookup, literature search, and article text extraction for researchers and developers.

How to use Pubtator MCP Server?

Install with pip install mcp-server-pubtator3, then run mcp-server-pubtator3. The server exposes four MCP tools (find_entity, search_pubtator, get_paper_text, find_related_entities) that can be called from any MCP‑compatible platform.

Key features of Pubtator MCP Server

Entity autocomplete for genes, diseases, chemicals, and variants
Literature search by keywords, IDs, or entity relations
Article retrieval from PubMed/PMC in plain text
Find entities related to a given identifier with filters
Async, non‑blocking operation via aiohttp

Use cases of Pubtator MCP Server

Identify biomedical concept identifiers from free‑text queries
Search for articles about a specific gene‑disease interaction
Extract full‑text content from PubMed or PMC articles
Discover related entities (e.g., chemicals associated with a disease)
Integrate biomedical knowledge into agent‑based analysis pipelines

常见问题

What Python version is required?

Python 3.10 or higher is required.

Do I need an API key or authentication?

No authentication is mentioned; the server directly queries the public PubTator3 API.

What is the maximum number of results per query?

Each tool’s `limit` parameter has a default of 10 and a maximum of 50.

What does the `get_paper_text` tool return?

It returns the plain text content of the article if available.

How do I access the available tools?

The tools are listed in the `list_tools` endpoint and can be invoked over the MCP protocol.

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