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reactome

reactome-mcp

Official
by reactome

reactome_search_diagram

Search for genes, proteins, or chemicals within a Reactome pathway diagram by providing a stable pathway ID and query. Finds matching entities to help locate components.

Instructions

Search for entities within a specific pathway diagram.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYesSearch term
diagramYesPathway stable ID for the diagram
include_interactorsNoInclude interactors
Behavior2/5

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

There are no annotations, so the description carries full responsibility for behavioral disclosure. It only states the search action and scope but does not disclose output format, pagination, how interactors are handled, limitations, or any authentication or data requirements. This is a significant gap for a tool with no structured behavioral metadata.

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 with no filler or redundant information. It is front-loaded with the action and resource, making it quick to parse.

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?

Given the moderate complexity of the tool (three parameters, no output schema, no annotations), the description is sufficient for basic understanding but lacks deeper context about query behavior, return format, or edge cases. The schema provides parameter names and types, but the overall contextual package is thin.

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 input schema provides complete descriptions for all three parameters (100% coverage), so the schema already does the heavy lifting. The description adds no additional parameter context, but per the baseline rule, schema coverage high yields a passing score.

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 action ('Search for') and a specific resource ('entities within a specific pathway diagram'), clearly distinguishing it from sibling search tools like reactome_search or reactome_search_paginated. The scope is explicit and immediately understandable.

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 alternative search tools, nor are any prerequisites or exclusions mentioned. The description simply states what it does without contextualizing its use case or contrasting it with available alternatives.

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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