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get_functional_enrichment

Perform GO and pathway enrichment analysis on protein sets to identify overrepresented biological functions and processes.

Instructions

Perform GO / pathway enrichment on a protein set.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
identifiersYesProtein list
speciesNoNCBI/STRING taxon (e.g. 9606 for human)
background_identifiersNoBackground proteome for enrichment analysis
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 the type of analysis ('GO/pathway enrichment') but lacks details on computational requirements, rate limits, output format, or error handling. This is inadequate for a tool with potential complexity.

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 with no wasted words. It's appropriately sized and front-loaded, clearly stating the core functionality without unnecessary elaboration.

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 complexity of enrichment analysis, no annotations, and no output schema, the description is insufficient. It doesn't cover behavioral aspects, usage context, or result interpretation, leaving significant gaps for an AI agent to understand the tool fully.

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 schema description coverage is 100%, so the schema already documents all three parameters well. The description adds no additional meaning beyond what's in the schema (e.g., it doesn't explain what 'GO/pathway enrichment' entails or how parameters interact), resulting in the baseline score.

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 ('perform') and the resource ('GO/pathway enrichment on a protein set'), making the purpose understandable. However, it doesn't differentiate from sibling tools like 'get_ppi_enrichment' or 'get_enrichment_figure' that might perform similar enrichment analyses, so it doesn't reach the highest 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_ppi_enrichment' or 'get_enrichment_figure', nor does it mention prerequisites or exclusions. It only states what the tool does, not when it's appropriate.

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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