Skip to main content
Glama
PDBe MCP Servers

PDBe MCP Servers

Official
by PDBeurope

ebi-pdbe-graph_edges

Read-onlyIdempotent

Retrieve metadata for all relationship types in the PDBe graph database schema, including labels, directions, and properties, to understand connectivity and write accurate Cypher queries.

Instructions

Retrieves metadata about all relationship types (edges) defined in the PDBe (PDBe-KB) graph database schema.
This tool can be used to understand the different types of relationships represented in the PDBe graph database, along with
their start and end nodes, properties and descriptions and then can be used to explore the graph more effectively by writing Cypher queries.
This tool returns detailed information about each relationship (edge) in the graph. For every relationship type, it includes:
- The relationship label (e.g., 'HAS_OUTLIER', 'CONNECTS_TO')
- A human-readable description of the relationship
- The 'from' node label and 'to' node label, defining the direction and connectivity
- A list of properties associated with the relationship
- For each property: the name and a brief description

Expected Output Format (text):
Label: HAS_OUTLIER
Description: Indicates a structure has validation outliers
From: Structure
To: ValAngleOutlier
Properties:
  - since: The date when the outlier was detected
  - severity: The severity level of the outlier

(Additional relationship types 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, idempotentHint, and destructiveHint=false, so the safety profile is covered. Beyond that, the description usefully discloses that this is a schema-introspection call returning full detail for every edge type, and it supplies the expected output shape, which matters because there is no output schema. It stops short of stating result size or ordering guarantees, but the behavioral picture is solid.

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

Conciseness3/5

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

The opening sentence is well front-loaded, but the description is verbose: the bulleted field list is then repeated almost verbatim in the worked 'Expected Output Format' example. The example is genuinely useful given there is no output schema, but the duplication makes it longer than it needs to be.

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

Completeness5/5

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

For a zero-parameter, read-only introspection tool with no output schema, the description covers everything an agent needs: what it returns, the exact field semantics, and a concrete example of the response format. Nothing required to call it correctly or interpret results is missing.

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 per the baseline this scores 4. The description correctly presents the call as unconditional and global over the whole schema, leaving no parameter semantics to clarify.

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: it retrieves metadata about all relationship types (edges) in the PDBe graph database schema, and it enumerates exactly what is returned (label, description, from/to node labels, properties). This clearly separates it from node-oriented siblings, but it never explicitly distinguishes itself from the closely related graph_nodes or graph_node_relationships tools by name.

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?

Usage is only implied: the description says the tool can be used to 'understand the different types of relationships' and 'then... explore the graph more effectively by writing Cypher queries.' There is no explicit when-to-use versus when-not, and no direct pointer to graph_nodes, graph_indexes, or graph_example_queries as alternatives, so the agent must infer the routing itself.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

Deploy Server

Other Tools