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Pubtator MCP Server

@QIngyuanfl

Repository

Basic information

Category

Other

Transports

stdio

Author

QIngyuanfl

About Pubtator MCP Server

No overview available yet

Pubtator MCP Server config

No standard config provided

This server doesn't expose a parseable MCP config block in its README. See the repository for install instructions.

Repository

Pubtator MCP Server tools

Tool list not available yet

This listing does not currently have a tool list to display. This does not mean the server has no tools; check its documentation for supported capabilities.

We auto-extract tools from the README. The maintainer can list them under a ## Tools heading to populate this section.

Overview

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

Frequently asked questions

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.

Comments

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