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 n...
This record as markdown: /tools/io-github-whiteknightonhorse-apibase/science.uniprot.taxonomy.md
What science.uniprot.taxonomy does on Apibase
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.
| Parameter | Type | Required | Description |
|---|---|---|---|
rank | string | — | Filter by taxonomic rank (e.g. "species" to exclude higher-level taxa) |
limit | integer | — | 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.
Why science.uniprot.taxonomy is rated Low
Queries UniProt taxonomy database; returns reference data with no side effects or modifications.
From the tool's definition Search taxonomy, find organism names, returns taxon ID, lineage, protein counts.
Attacks that exploit this kind of access
The rule that runs science.uniprot.taxonomy safely
PolicyLayer is an MCP gateway: it sits between your AI agents and Apibase, and checks every tool call against a rule you set before the call runs. Nothing changes on the server itself. For science.uniprot.taxonomy, this is the rule to start with:
science.uniprot.taxonomy is read-only, so it stays allowed. Everything else on the server is denied unless you say otherwise.
The button opens the PolicyLayer dashboard: create your workspace, connect Apibase, apply this rule, and every science.uniprot.taxonomy call is checked against it from then on.
Questions about 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). It is categorised as a Read tool in the Apibase MCP Server, which means it retrieves data without modifying state.
science.uniprot.taxonomy accepts 3 parameters: rank, limit, query. Required: query. The full parameter table on this page comes from the server's own tool schema.
Register the Apibase MCP server in PolicyLayer and add a rule for science.uniprot.taxonomy: allow, deny, rate-limit, or require approval. Point your MCP client at the PolicyLayer proxy URL and the rule is enforced on every call, before it reaches Apibase. Nothing to install.
science.uniprot.taxonomy is a Read tool with low risk. Read-only tools are generally safe to allow by default.
Yes. Add a rate_limit block to the science.uniprot.taxonomy rule in your PolicyLayer policy. For example, setting max: 10 and window: 60 limits the tool to 10 calls per minute. Rate limits are tracked per agent session and reset automatically.
Set action: deny in the PolicyLayer policy for science.uniprot.taxonomy. The AI agent will receive a policy violation error and cannot call the tool. You can also include a reason field to explain why the tool is blocked.
science.uniprot.taxonomy is provided by the Apibase MCP server (apibase-mcp-client). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.
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