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Pubtator MCP Server

@QIngyuanfl

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作者

QIngyuanfl

Pubtator MCP Server について

概要はまだありません

Pubtator MCP Server の設定

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このサーバーの README には解析可能な MCP 設定ブロックが含まれていません。インストール手順はリポジトリをご確認ください。

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Pubtator MCP Server のツール

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この掲載には表示できるツール一覧がまだありません。サーバーにツールがないという意味ではありません。対応機能はプロジェクトのドキュメントをご確認ください。

ツールは README から自動的に抽出されます。メンテナーは ## Tools という見出しの下に記載することで、このタブに反映できます。

概要

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

よくある質問

1

What Python version is required?

Python 3.10 or higher is required.

2

Do I need an API key or authentication?

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

3

What is the maximum number of results per query?

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

4

What does the `get_paper_text` tool return?

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

5

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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