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Proteomes Search

proteomes_search
Read-onlyIdempotent

"Reference proteome for [organism]" / "complete protein set of [species]" — search UniProt reference proteomes (the curated representative protein set per organism). Use as a starting point for genome-scale protein analyses.

Input Schema

NameRequiredDescriptionDefault
sizeNo
queryYes

Output Schema

NameRequiredDescriptionDefault
facetsNoSearch facets
resultsNoArray of proteome entries

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.2/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true, openWorldHint=true, idempotentHint=true, and destructiveHint=false, which establish the tool's safety. The description adds that it searches for reference proteomes and provides example query patterns, supplementing the annotations without contradiction.

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 two sentences with zero wasted words. It immediately presents example patterns and states the tool's purpose. Examples are front-loaded in both description and input schema, aiding quick comprehension.

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

Completeness4/5

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

Given the rich annotations (readOnly, openWorld, idempotent) and presence of an output schema, the description is largely complete. It explains what the tool searches and its intended use, though it could mention that results are lists of proteome entries or that queries are case-insensitive.

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?

Schema coverage is 0% (no property descriptions), so the description must compensate. It gives example queries like 'homo sapiens' and 'escherichia coli' and describes expected formats (e.g., 'complete protein set of [species]'). However, the 'size' parameter is not explained, leaving a gap for agents.

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?

The description clearly states the tool searches UniProt reference proteomes, which is a specific verb-resource pair. It distinguishes from siblings like 'search' and 'taxonomy_search' by focusing on proteomes. Examples in the description and input schema reinforce the purpose.

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?

The description says 'Use as a starting point for genome-scale protein analyses,' providing clear context for when to use it. However, it does not explicitly mention when not to use it or alternatives, though sibling tools cover other search types.

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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