# science.uniprot.taxonomy

Search UniProt taxonomy to find organism names, NCBI taxonomy IDs, lineages, and protein counts. Returns taxon ID, scientific name, common name, taxonomic rank, full lineage path, and the number of reviewed (Swiss-Prot) and unreviewed (TrEMBL) proteins for that organism. Use to resolve organism names to taxonomy IDs for protein_search filtering (e.g. "human" → taxon_id 9606, "mouse" → 10090, "E. coli K12" → 83333). CC BY 4.0 — Universal Protein Resource (UniProt Consortium)

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

## Facts

- Tool: `science.uniprot.taxonomy`
- 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: 3 (1 required)
- Recommended policy verdict: Allowed

## Parameters

| Parameter | Type | Required | Description |
| --- | --- | --- | --- |
| `rank` | string | no | Filter by taxonomic rank (e.g. "species" to exclude higher-level taxa) |
| `limit` | integer | no | Number of taxonomy results (1–20, default 5) |
| `query` | string | yes | Organism or taxonomic name to search — e.g. "human", "Homo sapiens", "Mus musculus", "bacteria", "fungi". Returns taxonomy ID, lineage, and protein counts |

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.taxonomy",
    "arguments": {
      "query": "<query>"
    }
  }
}
```

## Why science.uniprot.taxonomy is rated Low

Queries UniProt taxonomy database; returns reference data with no side effects or modifications.

From the tool's own definition: "Search taxonomy, find organism names, returns taxon ID, lineage, protein counts."

## Use case

AI agents call science.uniprot.taxonomy 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.taxonomy": {}
  }
}
```

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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