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reactome-mcp

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by reactome

reactome_export_analysis_report

Generate a PDF report from a biological pathway analysis token. Configure species, resource filter, and number of top pathways.

Instructions

Generate a PDF report for an analysis result.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
tokenYesAnalysis token
speciesNoSpecies for the reportHomo sapiens
resourceNoResource filterTOTAL
num_pathwaysNoNumber of top pathways to include
Behavior2/5

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

No annotations are provided, so the description must disclose behavior. It only states the action without detailing output format, download mechanism, required permissions, or side effects. Minimal behavioral disclosure beyond the one-liner.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Single sentence, no fluff. Front-loaded with action. Lacks extra info but is compact.

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?

With no output schema and no annotations, the description must explain report contents, output format, and prerequisites. It only provides the basic purpose, leaving questions about what the report contains and how to obtain the file.

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 covers 100% of parameters with descriptions and defaults, so the schema does the heavy lifting. The description adds no parameter-specific insight beyond what's in the schema, hence baseline 3.

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 a specific verb ('Generate'), resource ('PDF report'), and subject ('analysis result'). It distinguishes from CSV/JSON exports by mentioning PDF, but does not explicitly differentiate from sibling 'reactome_export_pdf', leaving slight ambiguity.

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 context for when to use this tool versus alternatives. It doesn't mention that it exports analysis reports specifically, nor does it point to CSV/JSON variants for data-oriented outputs.

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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