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reactome

reactome-mcp

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by reactome

reactome_diagram_pathways_for_entity

Find pathway diagrams containing a specific entity using its stable or database ID. Visualize which pathways include it.

Instructions

Find pathways with diagrams that contain a specific entity. Useful for visualization.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
idYesEntity stable ID or database ID
all_formsNoInclude all forms of the entity
Behavior2/5

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

No annotations are provided, so the description must carry the burden of behavioral disclosure, but it only states the core lookup behavior. It does not disclose the effect of the 'all_forms' parameter, the structure of the return value, or any limitations, leaving meaningful behavioral context undocumented.

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 two short sentences with no filler. The primary purpose is front-loaded, and every phrase contributes to understanding the tool's function and context.

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 description is adequate for a simple lookup tool with a well-specified schema, but it lacks an explicit comparison to the sibling 'reactome_pathways_for_entity' and does not mention any return format or behavior details, which would be helpful given there is no output schema.

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 description coverage is 100%, so the schema already documents both parameters ('id' and 'all_forms') with descriptions. The tool description adds no semantic detail beyond 'a specific entity', which is already implied by the parameter name and the first sentence.

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 ('Find') and clearly identifies the resource ('pathways with diagrams that contain a specific entity'), distinguishing it from the sibling tool 'reactome_pathways_for_entity' by adding the diagram constraint. The phrase 'useful for visualization' reinforces the intended 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 through 'useful for visualization' but does not explicitly state when to prefer this tool over the similar 'reactome_pathways_for_entity' or any other alternatives. There are no exclusions or when-not-to-use instructions.

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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