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reactome-mcp

reactome-mcp

by tc2fh
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Remote

get_entries

Batch fetch Reactome records for several stable identifiers in one call (up to 20). Returns count and matched entries.

Instructions

Batch-fetch records for several identifiers in one call (max 20).

Args:
    stable_ids: A list of identifiers, or a comma/whitespace-separated
        string (e.g. "R-HSA-69278, R-HSA-69620").

Returns:
    Dict `{count, entries}` where `entries` is the list of matched records.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "stable_ids": "<stable_ids>"
    },
    "name": "get_entries"
  }
}

Input Schema

NameRequiredDescriptionDefault
stable_idsYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A4.3/5.0
Behavior3/5

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

No annotations present, so the description carries the burden. It discloses the max 20 limit and the return format, but does not mention behavior for missing/invalid identifiers or ordering. It provides some context but not full behavioral disclosure.

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 compact and well-structured with Args and Returns sections. Every sentence is informative, and the example is concise yet valuable.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With one parameter and no output schema, the description adequately covers input and output. The max 20 limit is a useful constraint. It could be more complete with error behavior or a note about usage vs. get_entry, but overall it is sufficient.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 0%, yet the description fully explains the stable_ids parameter: it can be a list or a comma/whitespace-separated string, with a concrete example. This adds significant value beyond the raw schema.

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?

Clearly states 'Batch-fetch records for several identifiers in one call (max 20)', using a specific verb and resource. This distinguishes it from sibling tools like get_entry (singular) and search.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Implies usage for retrieving multiple records at once, and the max 20 limit is stated. However, it does not explicitly mention alternatives or exclusions, so it lacks a direct when/not comparison to get_entry or search.

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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