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uniprot-mcp

uniprot-mcp

by fzlzjerry
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Remote

get_taxonomy

Resolve an organism name or NCBI taxon ID to retrieve taxonomy details, including taxon ID, scientific and common names, rank, and lineage.

Instructions

Resolve a taxonomy name or id.

Pass a numeric taxon id to fetch that record, or a name to search. Returns the taxon id, scientific/common names, rank, and lineage — letting you turn an organism name into the organism_id used by search_uniprotkb.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "query_or_id": "<query_or_id>"
    },
    "name": "get_taxonomy"
  }
}

Input Schema

NameRequiredDescriptionDefault
query_or_idYesAn organism name ('Homo sapiens', 'human', 'E. coli') or a numeric NCBI taxon id ('9606').

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A4.1/5.0
Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Since no annotations are provided, the description carries the full burden. It discloses the return fields (taxon ID, names, rank, lineage) and the dual input behavior. However, it doesn't mention read-only nature, rate limits, authentication, or any potential side effects. For a simple lookup, this is adequate but not exhaustive.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is three sentences, front-loaded with the main purpose, and contains no fluff. Every sentence adds value: purpose, input behavior, output/use case. It is highly efficient.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the simplicity of the tool (one parameter, no nested objects), the description fully covers what the tool does, how to use it, and what it returns. The presence of an output schema further reduces the need to describe return values. The description is complete for agent decision-making.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The single parameter 'query_or_id' is fully described in the input schema (100% coverage). The description adds the concept of 'fetch' vs 'search' but does not significantly expand beyond the schema's own description. Thus it meets the baseline of adding some context but not much extra value.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

Clearly states the tool resolves a taxonomy name or ID, and explains it can accept either a numeric taxon ID or a name. It specifies what is returned (taxon ID, names, rank, lineage) and differentiates from sibling tools like search_uniprotkb by noting that it provides the organism_id needed for that search.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Provides an explicit use case: converting an organism name into an organism_id for search_uniprotkb. While it doesn't explicitly state when not to use it, the description effectively implies the tool is for taxonomy resolution before other searches. Sibling tools are listed but not directly compared, so some guidance is implicit.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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