# science.uniprot.search

Search the UniProt protein sequence database for proteins by name, gene, or organism. UniProt is the world's leading repository for protein sequences and functional annotations, covering 250M+ sequences from Swiss-Prot (reviewed) and TrEMBL (unreviewed). Returns accession, protein name, organism, gene names, sequence length, review status, and annotation score. Supports field-specific queries (gene:TP53, organism:9606) and free-text search. Use reviewed:true to restrict to Swiss-Prot's manually curated, high-quality entries. CC BY 4.0 — Universal Protein Resource (UniProt Consortium)

Agent View of the PolicyLayer registry record for `science.uniprot.search`. HTML page: https://policylayer.com/tools/io-github-whiteknightonhorse-apibase/science.uniprot.search

## Facts

- Tool: `science.uniprot.search`
- Server: Apibase (`apibase-mcp-client`) — https://policylayer.com/tools/io-github-whiteknightonhorse-apibase.md
- Install: `npx -y apibase-mcp-client`
- Homepage: https://github.com/whiteknightonhorse/APIbase
- Risk category: Read (Low risk)
- Registry record: grade F, identity unverified
- Server auth posture: open
- Server rate-limited: no
- Parameters: 5 (1 required)
- Recommended policy verdict: Allowed

## Parameters

| Parameter | Type | Required | Description |
| --- | --- | --- | --- |
| `gene` | string | no | Gene name filter (exact or partial). E.g. "TP53", "EGFR", "BRAC1". Combined with query using AND logic |
| `limit` | integer | no | Number of results to return (1–25, default 5) |
| `query` | string | yes | Protein or gene search term — e.g. "insulin", "hemoglobin", "BRCA1". Supports UniProt query syntax: field:value pairs (e.g. "protein_name:kinase") |
| `reviewed` | boolean | no | If true, restrict to Swiss-Prot (manually reviewed) entries only. Swiss-Prot has higher quality annotations than TrEMBL (unreviewed) |
| `organism_id` | integer | no | NCBI taxonomy ID to filter by organism. Common IDs: 9606 (human), 10090 (mouse), 10116 (rat), 7227 (fruit fly), 6239 (C. elegans), 3702 (A. thaliana) |

Parameters from the server's own tool schema.

## Example call (MCP tools/call, JSON-RPC 2.0)

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "science.uniprot.search",
    "arguments": {
      "query": "<query>"
    }
  }
}
```

## Why science.uniprot.search is rated Low

Tool retrieves protein sequence data from a public database without modifying, deleting, or executing code.

From the tool's own definition: "Search the UniProt protein sequence database for proteins by name, gene, or organism."

## Use case

AI agents call science.uniprot.search to retrieve information from Apibase without modifying anything. It is typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.

## Recommended policy (PolicyLayer)

Verdict: **Allowed**. Enforced by the PolicyLayer MCP gateway (https://policylayer.com/mcp-gateway) before a call reaches Apibase:

```json
{
  "version": "1",
  "default": "deny",
  "tools": {
    "science.uniprot.search": {}
  }
}
```

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## For agents

This record is a snapshot. Live verdicts and the full registry:

- Check every server in your MCP config at once: `npx -y policylayer stack`
- Vet a server before you add it: install the mcp-precheck skill — `npx skills add https://policylayer.com` (skill text: https://policylayer.com/skill.md)
- Query the registry over MCP: endpoint `https://api.policylayer.com/mcp` — tools `check_mcp_server`, `check_mcp_stack`, `check_tool`, `search_registry`, `get_change_events`

---

Source: the PolicyLayer MCP registry — one continuously verified record per MCP server. Full record: https://policylayer.com/registry?q=io-github-whiteknightonhorse-apibase · API: https://policylayer.com/registry/api · Policy library: https://policylayer.com/policies/io-github-whiteknightonhorse-apibase