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reactome

reactome-mcp

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by reactome

reactome_search_pathways_of

Find all biological pathways containing a specific entity by its Reactome database ID. Filter by species, direct participation, or interactors.

Instructions

Find all pathways that contain a specific entity by its database ID.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
db_idYesReactome database ID of the entity
speciesNoFilter by species
direct_onlyNoOnly pathways where entity appears directly in diagram
include_interactorsNoInclude interactor pathways
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 for behavioral disclosure. It only states the tool 'finds' pathways, but does not mention read-only semantics, return format, pagination, or any limitations. The description is too thin to convey meaningful behavioral context.

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 immediately states the tool's purpose. There is no redundant or filler content, making it appropriately concise and front-loaded.

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?

With no output schema and lacking annotations, the description is incomplete for a tool with four parameters and several close siblings. It does not explain return values, the distinction between direct and indirect containment, or how include_interactors changes behavior, making it hard for an agent to use correctly without additional context.

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 coverage is 100%, so the baseline is 3. The description adds no additional meaning to the parameters beyond what the schema already provides. It only references the database ID without elaborating on species, direct_only, or include_interactors, which is acceptable since the schema descriptions are present.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool finds pathways containing a specific entity by database ID, which is specific and informative. However, it does not differentiate from closely related siblings like reactome_pathways_for_entity or reactome_diagram_pathways_for_entity, so it loses a point for missing sibling distinction.

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?

The description provides no guidance on when to use this tool versus alternatives. With multiple overlapping siblings, the agent is left without clear selection criteria, so this is essentially missing usage guidance.

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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