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ebi-pdbe-graph_example_queries

Read-onlyIdempotent

Retrieve example Cypher queries for exploring the PDBe graph database, with each query paired to a question so you can learn how to query protein structure data.

Instructions

Retrieves example Cypher queries for exploring the PDBe (PDBe-KB) graph database.
This tool can be used to get sample queries that demonstrate how to interact with the PDBe graph database using Cypher.
The tool returns a list of example queries, each with an question describing the purpose of the query and the corresponding Cypher query string.
Expected Output Format (text):
Question: Give me all the structures that are released in 2025.
Query:
MATCH (entry:Entry)
WHERE entry.PDB_REV_DATE STARTS WITH '2025'
RETURN entry.ID as PDB_ID,
    entry.TITLE as Title,
    entry.PDB_REV_DATE as Release_Date,
    entry.RESOLUTION as Resolution,
    entry.METHOD as Experimental_Method,
    entry.STATUS_CODE as Status
ORDER BY entry.PDB_REV_DATE DESC
(Additional example queries follow the same format...)

Input Schema

NameRequiredDescriptionDefault

No arguments

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv2.0.1

TDQS

A3.8/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true, idempotentHint=true, and destructiveHint=false, so the safety profile is covered. The description goes beyond that by disclosing the return shape: a list of example queries, each pairing a natural-language question with a Cypher query string, backed by a concrete output sample. It does not say how many examples are returned or whether they are curated/static, which keeps it below a 5.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The purpose is front-loaded in the first sentence, and the output-format block with a real query example is genuinely informative rather than filler. The second sentence largely restates the first ('This tool can be used to get sample queries...'), which is the one piece of waste in an otherwise tight description.

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 no output schema, the description must explain the return value, and it does so thoroughly via the 'Question:'/'Query:' format plus a full worked example. For a zero-parameter, read-only lookup tool that is essentially complete; only the absence of any note on how to use the returned queries (e.g., run them elsewhere) is a minor gap.

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

Parameters4/5

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

The tool takes zero parameters, so the schema carries no semantics to supplement; the baseline for a 0-parameter tool applies. The description correctly adds no parameter prose, and there is nothing misleading about invocation.

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 opens with a specific verb and resource: 'Retrieves example Cypher queries for exploring the PDBe (PDBe-KB) graph database.' It is clear this returns static sample queries rather than executing anything, which implicitly separates it from graph_nodes, graph_edges, and graph_node_relationships, but no sibling is named explicitly.

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?

It states the tool 'can be used to get sample queries that demonstrate how to interact with the PDBe graph database,' which implies the use case of learning the graph model or bootstrapping a Cypher query. There is no explicit when-not guidance and no pointer to the actual query-execution or schema-inspection siblings, so an agent must infer the routing.

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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