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Network Enrichment

network_enrichment
Read-onlyIdempotent

Identify enriched Reactome pathways and STRING network hubs from a gene set to reveal biological mechanisms and protein interactions.

Instructions

Summarize recurrent Reactome pathways and STRING network hubs across a gene set.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
gene_listYesInput genes for enrichment analysis.
min_string_scoreNoMinimum STRING confidence score. Default 700.
max_resultsNoMaximum pathways and hubs to return. Default 10.
Behavior2/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false, idempotentHint=true, and openWorldHint=true, which adequately inform about safety and idempotency. The description adds no additional behavioral insights (e.g., rate limits, data freshness). It repeats the purpose but does not expand beyond annotation coverage.

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 sentence that is concise and front-loaded, clearly communicating the tool's purpose without extraneous words.

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?

The tool has a simple interface with 3 parameters and no output schema. The description covers the core function but omits what the output looks like (e.g., list of pathways with scores, network nodes). The input example partially compensates. Overall, it is adequate but could mention return format for completeness.

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 100% as all three parameters have descriptions in the input schema. The tool description does not add any extra meaning or nuances beyond what is already in the schema, so the baseline score of 3 is appropriate.

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 uses a specific verb 'summarize' and identifies distinct resources (Reactome pathways, STRING network hubs) applied to a gene set. It clearly distinguishes from sibling tools like 'pathway_analysis' which likely performs standard enrichment, and 'find_protein' which focuses on individual proteins.

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?

The description implies the tool is for summarizing network-level insights, but it does not explicitly state when to use it versus alternatives such as 'pathway_analysis' or 'verify_biological_claim'. No when-not or clear context for selection is provided.

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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