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get_functional_annotation

Retrieve functional annotations for proteins from the STRING database to analyze biological roles and relationships in protein-protein interaction networks.

Instructions

Retrieve all functional annotations for proteins.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
identifiersYesProtein list
speciesNoNCBI/STRING taxon (e.g. 9606 for human)
allow_pubmedNoInclude PubMed annotations (default: false)
only_pubmedNoReturn only PubMed annotations (default: false)
Behavior2/5

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

With no annotations provided, the description carries the full burden of behavioral disclosure. It mentions retrieving annotations but doesn't specify aspects like rate limits, authentication needs, data format, or potential side effects. This is a significant gap for a tool with multiple parameters and no output schema.

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 a single, efficient sentence that directly states the tool's purpose without any wasted words. It's appropriately sized and front-loaded, making it easy for an agent to parse quickly.

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

Completeness2/5

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

Given the tool's complexity (4 parameters, no annotations, no output schema), the description is incomplete. It doesn't address behavioral traits, usage context, or output details, leaving gaps that could hinder an agent's ability to invoke the tool correctly without additional information.

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 input schema has 100% description coverage, so the schema already documents all parameters well. The description adds no additional meaning beyond the schema, such as explaining interactions between parameters (e.g., how 'allow_pubmed' and 'only_pubmed' relate). Baseline 3 is appropriate when the schema does the heavy lifting.

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

Purpose4/5

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

The description clearly states the action ('Retrieve') and resource ('functional annotations for proteins'), making the purpose understandable. However, it doesn't differentiate from sibling tools like 'get_functional_enrichment' or 'get_enrichment_figure', which might retrieve related but different data, so it falls short of a perfect score.

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

Usage Guidelines2/5

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

The description provides no guidance on when to use this tool versus alternatives like 'get_functional_enrichment' or other sibling tools. It lacks context about prerequisites or exclusions, leaving the agent to infer usage from the tool name and parameters alone.

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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