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reactome

reactome-mcp

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by reactome

reactome_get_pathway

Retrieve detailed information about a biological pathway or reaction by providing its Reactome ID.

Instructions

Get detailed information about a specific pathway or reaction by its Reactome ID.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
idYesReactome stable ID (e.g., R-HSA-109582) or database ID
Behavior2/5

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

There are no annotations, so the description carries the full burden. It only says 'Get detailed information' without disclosing what 'detailed' includes, the return format, whether any special permissions are required, or any side effects. For a fetch operation, this is a notable gap in setting expectations.

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 sentence with a clear verb-object structure. It is front-loaded with the action and resource, contains no redundant phrases, and is appropriately sized for a tool with one parameter.

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 is simple with one parameter and no output schema, so the description does not need to be lengthy. However, the phrase 'detailed information' is vague—it does not specify whether the response includes full pathway structure, participants, or just metadata. Given the context of many siblings, a bit more detail would improve completeness, but it is adequate for a basic fetch.

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 describes the sole parameter 'id' with full coverage (100%), specifying format and examples. The tool description only repeats 'Reactome ID', adding no additional meaning. According to the rubric, the baseline is 3 when schema coverage is high, and there is no extra information to raise it.

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 a specific verb ('Get'), a resource ('pathway or reaction'), and the identifier type ('Reactome ID'). It distinguishes from many sibling tools that focus on analysis, export, or querying, but it does not explicitly contrast with close relatives like reactome_get_entity, which could cause ambiguity.

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 the usage context: when you need detailed information about a specific pathway/reaction given an ID. However, it provides no explicit guidance on when to use this tool versus alternatives, nor does it mention exclusions or prerequisites. This is acceptable but not as strong as an explicit recommendation.

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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