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search_proteomes

Search for proteomes by organism name or NCBI taxonomy ID. Optionally filter to reference proteomes only to get the complete protein set of a genome.

Instructions

Search UniProt proteomes (the protein set of an organism's genome).

Returns the proteome id (UPID), organism, proteome type (Reference / Non-reference / etc.), and protein/gene counts. Filter by organism_id and set reference_only=True for reference proteomes.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryNoFree-text proteome query, e.g. 'Escherichia coli' or 'Mycobacterium tuberculosis'. May be omitted if organism_id is set.
organism_idNoNCBI taxonomy id filter, e.g. 9606 for human.
reference_onlyNoOnly reference proteomes (one high-quality proteome per species group).
sizeNoMax proteomes to return (1-500).
formatNo'summary' = compact list (default); 'tsv' = table.summary

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

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

No annotations provided, so description must stand alone. Mentions it is a search (safe read operation) but does not explicitly state read-only nature or any limitations. Adequate but not thorough.

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?

Two sentences with no wasted words. First sentence defines purpose, second sentence lists key parameters and output. Front-loaded and efficient.

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 output schema exists, return values need not be explained. Covers purpose, key parameters, and output fields. Brief but complete for a search tool with good schema documentation.

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 100%, so parameters are documented. Description restates filtering options already covered in schema, adding little extra meaning beyond the schema.

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 it searches UniProt proteomes, returns specific fields (UPID, organism, type, counts), and distinguishes from sibling tools like search_uniprotkb and search_uniref.

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 guidance on filtering by organism_id and reference_only=True. Implicitly distinguishes from siblings, but lacks explicit when-not-to-use or alternative tool references.

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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