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reactome

reactome-mcp

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by reactome

reactome_cypher_sample

Retrieve a small sample of nodes for a given label to inspect their shape and typical property values.

Instructions

Return a small sample of nodes for a given label, to inspect shape and typical property values.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
labelYesNode label to sample (e.g. 'Pathway', 'ReactionLikeEvent', 'PhysicalEntity')
limitNoNumber of nodes to return (default 5, max 50)
Behavior3/5

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

With no annotations, the description carries the burden of behavioral disclosure. It states it returns a 'small sample' of nodes, which conveys the read-only, limited nature of the operation. However, it does not disclose behaviors like randomness, error handling for non-existent labels, or whether the returned nodes are representative in any particular way. These gaps are notable but not critical for a simple sampling tool.

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, well-structured sentence that delivers the key information upfront: 'Return a small sample of nodes for a given label, to inspect shape and typical property values.' No wasted words or redundant details.

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 is simple, with only two parameters and no output schema. The description sufficiently explains the tool's purpose and output ('nodes') while the schema covers parameter details. It is complete enough for an agent to understand what to expect, though it could mention that the sample is intended for quick data inspection rather than querying.

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 provides descriptions for both parameters (label and limit), so schema coverage is 100%. The description adds minimal extra meaning beyond saying 'given label' and 'small sample', which aligns with the parameters. It does not introduce any new parameter-specific semantics, so a 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 clearly states the tool's function with a specific verb ('Return') and resource ('nodes for a given label'), and adds the purpose ('to inspect shape and typical property values'). This effectively distinguishes it from sibling tools like reactome_cypher_query (which runs arbitrary queries) and reactome_cypher_schema (which returns schema).

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

Usage Guidelines4/5

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

The description implies when to use this tool: when you need to inspect the shape and typical values of nodes for a label. It provides a clear context but does not explicitly name alternatives or state when not to use it. However, the purpose is clear enough for an agent to infer the appropriate use case.

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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