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reactome-mcp

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by reactome

reactome_analysis_pathway_sizes

Get the binned distribution of pathway sizes from a Reactome analysis result, with optional filters for species and resource.

Instructions

Get the distribution of pathway sizes (binned) from an analysis result.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
tokenYesAnalysis token
speciesNoFilter by species
bin_sizeNoBin size for grouping pathway sizes
resourceNoResource filterTOTAL
Behavior2/5

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

With no annotations, the description carries the full burden of behavioral disclosure. It only states a read-like operation but does not mention whether it is read-only, what the response structure looks like, pagination, potential errors, or any side effects. This is a significant gap for a tool with no annotation support.

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, concise sentence that is front-loaded with the main verb and object. Every word contributes to the purpose, with no redundancy or filler.

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?

The tool has no output schema and no annotations, so the description should explain what the distribution looks like or how to interpret the result. It only says 'distribution of pathway sizes (binned)' without specifying the return format, binning behavior, or how 'TOTAL' resource affects output. This is minimal and leaves significant gaps.

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%, so the baseline is 3. The description adds no extra meaning beyond the schema's parameter descriptions; it does not clarify how parameters interact or provide examples. The schema already explains each parameter, so the description does not need to repeat it.

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 a specific action ('Get') and resource ('distribution of pathway sizes (binned)') derived from an analysis result. It effectively distinguishes this tool from siblings like reactome_top_pathways or reactome_filter_analysis_pathways by focusing on binned size distribution.

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?

No guidance is provided on when to use this tool versus alternatives, prerequisites, or contextual scenarios. The description does not mention that it requires an analysis result token or how it fits into a broader analysis workflow.

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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