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reactome-mcp

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by reactome

reactome_export_sbml

Export any Reactome pathway or reaction to SBML format using its stable ID, enabling standard exchange and analysis of biological models.

Instructions

Export a pathway or reaction to SBML (Systems Biology Markup Language) 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, and the description only states 'Export' without detailing behavior such as whether the output is a file download or inline SBML XML, any authentication requirements, or side effects. Since the description carries the full burden for transparency, this lack of disclosure 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 clear sentence that is front-loaded with the action and target. Every word earns its place, with no redundant or vague phrasing. This is appropriately concise for a simple export tool.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

The tool has a simple structure with one well-described parameter, but the lack of an output schema and annotations means the description should explain the return value or output format. It does not, leaving the agent to guess whether SBML content is returned directly or as a download. However, given the low complexity, this is a clear but tolerable gap.

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 provides 100% coverage for the single parameter 'id', describing it as a 'Pathway or reaction stable ID'. The tool description repeats the same resource types but adds no new semantics. With full schema coverage, the baseline of 3 applies.

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 exports a pathway or reaction to SBML format. The verb 'Export' combined with the specific resource type and output format distinguishes it from other export tools like export_sbgn or export_diagram. This is a precise and unambiguous purpose.

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

Usage Guidelines3/5

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

The description implies usage when SBML format is needed, but it does not explicitly compare with alternative export tools such as export_sbgn or export_pdf. There is no mention of when to prefer this tool over others, nor any exclusions or prerequisites. The context is minimal, making it merely adequate.

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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