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reactome-mcp

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by reactome

reactome_export_pdf

Export Reactome pathway or reaction documentation to PDF by providing the stable ID, yielding a shareable file for reports and offline use.

Instructions

Export pathway or reaction documentation to PDF format.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
idYesPathway or reaction stable ID
Behavior2/5

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

No annotations are provided, so the description carries the full burden of disclosing behavioral traits. It does not mention how the PDF is returned (e.g., file download, base64), any file size limitations, authentication needs, or side effects. The lack of any such details for a tool with zero annotation coverage is a significant gap.

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 action and resource. No wasted words, and it earnestly conveys the core purpose.

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?

Despite the tool's simplicity, the description omits what the agent can expect in return (e.g., a PDF file, download URL, or binary content). With no output schema, this missing information is essential for correct invocation and handling of results.

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 only parameter 'id' is already fully described in the schema as 'Pathway or reaction stable ID' (100% coverage). The description adds no additional meaning beyond 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 clearly states the action (export), the resource (pathway or reaction documentation), and the format (PDF). This distinguishes it from sibling export tools like reactome_export_diagram (diagram format) and reactome_export_sbml (SBML format).

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. With many sibling export tools (diagram, reaction, SBGN, SBML, etc.), the description fails to explain when PDF documentation is preferred.

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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