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uniprot_search_proteomes

Read-only

Searches UniProt proteomes using queries like organism ID, proteome type, or taxonomy name to retrieve matching proteome entries.

Instructions

Search UniProt proteomes. Examples: 'organism_id:9606' for human, 'proteome_type:1' for reference proteomes only, 'taxonomy_name:bacteria' for all bacterial proteomes.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYes
sizeNo
response_formatNomarkdown

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

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

Annotations already indicate readOnlyHint=true and openWorldHint=true, so the description does not need to repeat that. However, it adds no additional behavioral context (e.g., rate limits, error handling, or search limitations). The description is consistent with annotations.

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 extremely concise: a single sentence with three example queries. Every word serves a purpose, and the key information (purpose and usage examples) is front-loaded.

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

Completeness3/5

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

Given the tool has three parameters, one required, and an output schema exists, the description is adequate but minimal. It lacks details on pagination, default behavior, or how the search works. The output schema likely fills some gaps, but the description could be more comprehensive.

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 description coverage is 0%. The description provides examples for the query parameter, adding meaningful guidance on how to construct queries. However, it does not describe the 'size' or 'response_format' parameters, leaving gaps for the agent.

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 proteomes and provides concrete query examples. It distinguishes itself from siblings like uniprot_get_proteome (which retrieves a specific proteome) and uniprot_search (which likely searches entries).

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

Usage Guidelines3/5

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

While the description gives example queries, it does not explicitly state when to use this tool versus alternatives such as uniprot_get_proteome or uniprot_search. No guidance on when not to use it or prerequisite conditions.

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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