# Pubtator MCP Server

> Use this tool when you need to integrate biomedical text-mining capabilities into your application, providing access to multiple tools through a standardized MCP agent protocol interface. It solves problems related to entity recognition, relation extraction, and concept identification in biomedical texts. The server accepts API requests and returns annotated text outputs, making it ideal for use cases involving large-scale biomedical data analysis.

Canonical page: https://skillsregistry.net/skills/qingyuanfl-mcp-server-pubtator3  
JSON: https://api.skillsregistry.net/v1/skills/qingyuanfl-mcp-server-pubtator3

## Description

Provides an async Python server for interacting with the PubTator3 API, exposing multiple biomedical text-mining tools compatible with the MCP agent protocol.

## Trust

- **Trust score (0–1):** 0.70
- **Verification tier:** verified
- **Last scanned:** 2026-09-01

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** other
- **Updated:** 2026-09-01

## Source

- **Source listing:** [Glama](https://glama.ai/mcp/servers/vcfjc16dt0)
- **Repository:** <https://github.com/QIngyuanfl/mcp-server-pubtator3>

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "qingyuanfl-mcp-server-pubtator3"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/qingyuanfl-mcp-server-pubtator3` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/qingyuanfl-mcp-server-pubtator3/pull`

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SkillsRegistry indexes agent skills from public registries and GitHub. Skills we have analysed are scanned with Circle-IR and scored on six dimensions; each listing states its scan coverage. More: https://skillsregistry.net/llms.txt