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reactome

reactome-mcp

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by reactome

reactome_search

Search Reactome's knowledgebase for pathways, reactions, proteins, genes, compounds, and other entities. Filter results by species, type, compartment, or keywords.

Instructions

Search the Reactome knowledgebase for pathways, reactions, proteins, genes, compounds, and other entities.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
rowsNoNumber of results to return
queryYesSearch term (gene name, protein, pathway name, disease, etc.)
typesNoFilter by type (Pathway, Reaction, Protein, Gene, Complex, etc.)
clusterNoCluster related results
speciesNoFilter by species (e.g., 'Homo sapiens', 'Mus musculus')
keywordsNoFilter by keywords
compartmentsNoFilter by cellular compartment
Behavior2/5

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

With no annotations provided, the description carries the full burden of behavioral disclosure, but it only says 'Search the Reactome knowledgebase.' It does not mention result clustering, pagination, default row count, return format, or any other behavioral traits, which is a significant gap for a search tool with multiple adjustable parameters.

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 clearly states the tool's purpose without any filler. It is appropriately concise for a generic search operation.

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?

The tool has 7 parameters and no output schema or annotations, yet the description is minimal. It does not explain what the search results look like, how pagination works, what the clustering option does, or when to use this tool instead of more specialized search siblings. This leaves significant gaps for an agent to understand the tool's full 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 description coverage is 100%, so the baseline is 3. The description itself adds no parameter-level meaning, but the schema already documents all seven parameters (query, rows, types, cluster, species, keywords, compartments), so the agent has sufficient information without additional description.

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's function: searching the Reactome knowledgebase for multiple entity types (pathways, reactions, proteins, genes, compounds, and other entities). It uses a specific verb and resource, but it does not explicitly distinguish itself from sibling search tools like reactome_search_paginated, reactome_search_suggest, or reactome_search_facets, so it falls short of a 5.

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 given on when to use this tool versus the many search-related siblings. There is no mention of alternatives, exclusions, or preferred scenarios, leaving the agent to infer appropriate usage from tool names alone.

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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