# pubtator-link

> pubtator-link — berntpopp-pubtator-link. Use this tool when you need to annotate biomedical literature with gene, variant, disease, and chemical entity information. It solves problems of cumbersome raw data analysis by returning compact, citable passages, making it ideal for researchers and scientists. The pubtator-link tool takes biomedical literature searches as input and outputs annotated passages, providing a streamlined interface for entity annotation.

Canonical page: https://skillsregistry.net/skills/berntpopp-pubtator-link  
JSON: https://api.skillsregistry.net/v1/skills/berntpopp-pubtator-link

## Description

MCP server for NCBI PubTator3: biomedical literature search with gene, variant, disease and chemical entity annotation — returns compact, citable passages instead of raw BioC.

## Trust

- **Trust score (0–1):** 0.82
- **Verification tier:** verified
- **Last scanned:** 2026-09-28

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** container
- **Runtime environment:** vm
- **License:** MIT
- **Updated:** 2026-09-28

## Source

- **Source listing:** [GitHub](https://github.com/berntpopp/pubtator-link)

## 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": "berntpopp-pubtator-link"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/berntpopp-pubtator-link` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/berntpopp-pubtator-link/pull`

---
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