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reactome-mcp

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by reactome

reactome_export_sbgn

Export a Reactome pathway or reaction to SBGN XML format for systems biology visualization and analysis.

Instructions

Export a pathway or reaction to SBGN (Systems Biology Graphical Notation) XML 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. It states the export action and format, but does not disclose whether the result is a file, a string, or generated asynchronously, nor any side effects or permissions. This is minimal behavioral disclosure.

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, front-loaded sentence with no redundant words. It efficiently states the action, resource, and output format.

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?

For a low-complexity tool with one well-documented parameter, the description is mostly sufficient: it identifies the input and the output format. However, without an output schema or annotations, some return-value details are missing, but this is partially mitigated by the simple nature of the export operation.

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 schema already fully describes the single 'id' parameter as a 'Pathway or reaction stable ID', and the description repeats that same context. With 100% schema coverage, the description adds no additional parameter semantics beyond the tool's output format.

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 ('Export') with a clear resource ('a pathway or reaction') and a specific output format ('SBGN XML'). It distinguishes this tool from siblings like export_sbml or export_pdf by format.

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 clearly implies this tool is used when SBGN XML output is needed, but it does not explicitly mention when not to use it or contrast it with alternative export tools. This is clear context without exclusions.

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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