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reactome-mcp

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by reactome

reactome_interactor_pathways

Find Reactome pathways that include the interactors of a given protein by entering its accession.

Instructions

Find Reactome pathways where the interactors of a protein are found.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
accessionYesProtein accession
Behavior2/5

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

No annotations are provided, so the description must convey behavioral traits. It states that the tool finds pathways based on interactors, but it does not disclose whether this is read-only, what the response format is, how empty results are handled, or any edge cases. The behavioral transparency is limited to the basic query intent.

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, front-loaded sentence that communicates the tool's core purpose without any filler. It is appropriately sized for the tool's simplicity and earns its place entirely.

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 (one parameter, no output schema, no annotations), and the description states the primary function. However, it omits details about the return value (e.g., pathway identifiers, names, or metadata) and behavior for proteins with no interactors. This is adequate for selection but not fully complete for understanding expected output.

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 has 100% description coverage for the single 'accession' parameter ('Protein accession'). The description adds minimal extra meaning beyond the schema, just clarifying that the protein is the starting point for interactor lookup. Baseline 3 is appropriate because the schema already documents the parameter adequately.

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 uses a specific verb ('Find') and names a clear resource (Reactome pathways) scoped by the concept of protein interactors. This distinguishes it from sibling tools like reactome_pathways_for_entity, though it does not explicitly contrast with them.

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 when to use the tool (when you need pathways associated with a protein's interactors) but does not explicitly state alternatives, exclusions, or prerequisites. There is no 'Use this when...' guidance, so it relies on the user inferring appropriate usage.

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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