# UniProt

> Use this tool when you need to access curated protein data from UniProtKB, a primary protein sequence database, to retrieve protein entries, sequences, or perform ID mapping and searches. It solves problems in bioinformatics workflows, protein research, and database integration projects by providing a reliable interface to UniProtKB data. The tool accepts various inputs, including database identifiers and search queries, and returns structured responses, making it ideal for AI agents and applications requiring high-quality protein data.

Canonical page: https://skillsregistry.net/skills/josefdc-uniprot  
JSON: https://api.skillsregistry.net/v1/skills/josefdc-uniprot

## Description

A UniProt MCP server built by Jose Duarte that provides read-only access to the UniProtKB protein database through five core tools: fetch_entry for complete protein entries, get_sequence for protein sequences, search_uniprot for filtered searches, map_ids for converting between 200+ database identifier types, and fetch_entry_flatfile for historical entry versions. The implementation features retry logic with exponential backoff, progress reporting for long-running ID mapping jobs, both stdio and HTTP transports with CORS support, and structured Pydantic models for type-safe responses. Useful for bioinformatics workflows, protein research, database integration projects, and AI agents that need reliable access to curated protein data from one of the world's primary protein sequence databases.

## Trust

- **Trust score (0–1):** 0.85
- **Verification tier:** verified
- **Last scanned:** 2026-09-28

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** database
- **Updated:** 2026-09-28

## Source

- **Source listing:** [PulseMCP](https://www.pulsemcp.com/servers/josefdc-uniprot)
- **Repository:** <https://github.com/josefdc/uniprot-mcp>

## 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": "josefdc-uniprot"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/josefdc-uniprot` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/josefdc-uniprot/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