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by PDBeurope

ebi-pdbe-graph_indexes

Read-onlyIdempotent

Retrieves PDBe Neo4j graph index metadata, listing indexed node labels and properties to help write Cypher queries that use indexes properly.

Instructions

Retrieves metadata about all indexes defined in the PDBe (PDBe-KB) Neo4j graph database schema.
This tool can be used to understand which node properties are indexed in the graph database, which is helpful
when writing Cypher queries to ensure indexes are properly utilized for optimal performance.

This tool returns detailed information about each index in the graph database. For every index, it includes:
- The node label that the index applies to (e.g., 'Entry', 'Pfam', 'UniProt')
- The property name that is indexed (e.g., 'ID', 'PFAM_ACCESSION', 'ACCESSION')

Expected Output Format (text):
Node: Entry
Property: ID

Node: Pfam
Property: PFAM_ACCESSION

Node: UniProt
Property: ACCESSION

(Additional indexes 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
Behavior3/5

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

The annotations already declare readOnlyHint, idempotentHint and destructiveHint=false, so the safety profile is covered without the description. The description adds useful behavioral detail by spelling out the exact return format (Node/Property pairs per index) in the absence of an output schema. It does not mention result size, whether indexes include relationship indexes, or empty-result behavior.

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?

Purpose and use case are front-loaded in the first two sentences, and the output sample is directly informative given there is no output schema. Minor redundancy exists — 'returns detailed information about each index' restates the opening sentence, and the trailing parenthetical explaining that more indexes follow adds little.

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?

For a zero-parameter, read-only metadata tool with no output schema, the description covers what an agent needs: what is returned and the shape of the result. It could go further by noting whether only node indexes are covered and how to pair this with example-query or node-listing siblings.

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 there is nothing for the description to disambiguate and the baseline is 4. The description correctly implies no inputs are needed, consistent with the empty schema.

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 names a specific verb and resource: retrieving metadata about all indexes in the PDBe Neo4j graph schema. It clearly frames the tool as schema-introspection rather than data retrieval, which distinguishes it in spirit from data-returning siblings. However, it never explicitly names the adjacent introspection siblings (search_schema, graph_nodes, graph_edges) to sharpen the boundary.

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?

It states a concrete use case — understanding which node properties are indexed so Cypher queries can use indexes for performance. That is a clear when-to-use signal. It stops short of explicit alternatives or exclusions, e.g. directing the agent to search_schema for a broader schema overview or graph_example_queries for query patterns.

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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