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MCP GeneLab Server

by sbl-sdsc

get_neo4j_schema

Read-onlyIdempotent

Retrieves Neo4j node labels, attributes, and relationships to map the graph schema for Cypher queries; suggests enabling APOC if the procedure is missing.

Instructions

List all nodes, their attributes and their relationships to other nodes in the neo4j database. If this fails with a message that includes "Neo.ClientError.Procedure.ProcedureNotFound" suggest that the user install and enable the APOC plugin.

Input Schema

NameRequiredDescriptionDefault
session_idNoSession id returned by `create_session()`. This server serves many users from one process; the session id is what keeps your output directory and generated plots private to you. Pass the SAME value on every tool call. If the server replies that the session is unknown or expired, call `create_session()` again and use the new id.

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changedv1.0.0
    • addedInput schema / properties / session_id
      Added value: +{
      +  "anyOf": [
      +    {
      +      "type": "string"
      +    },
      +    {
      +      "type": "null"
      +    }
      +  ],
      +  "default": null,
      +  "description": "Session id returned by `create_session()`. This server serves many users from one process; the session id is what keeps your output directory and generated plots private to you. Pass the SAME value on every tool call. If the server replies that the session is unknown or expired, call `create_session()` again and use the new id.",
      +  "title": "Session Id"
      +}
    • changedOutput schema / (root)
      Previous value: -{
      -  "$defs": {
      -    "Annotations": {
      -      "additionalProperties": true,
      -      "properties": {
      -        "audience": {
      -          "anyOf": [
      -            {
      -              "items": {
      -                "enum": [
      -                  "user",
      -                  "assistant"
      -                ],
      -                "type": "string"
      -              },
      -              "type": "array"
      -            },
      -            {
      -              "type": "null"
      -            }
      -          ],
      -          "default": null,
      -          "title": "Audience"
      -        },
      -        "priority": {
      -          "anyOf": [
      -            {
      -              "maximum": 1,
      -              "minimum": 0,
      -              "type": "number"
      -            },
      -            {
      -              "type": "null"
      -            }
      -          ],
      -          "default": null,
      -          "title": "Priority"
      -        }
      -      },
      -      "title": "Annotations",
      -      "type": "object"
      -    },
      -    "TextContent": {
      -      "additionalProperties": true,
      -      "description": "Text content for a message.",
      -      "properties": {
      -        "_meta": {
      -          "anyOf": [
      -            {
      -              "additionalProperties": true,
      -              "type": "object"
      -            },
      -            {
      -              "type": "null"
      -            }
      -          ],
      -          "default": null,
      -          "title": "Meta"
      -        },
      -        "annotations": {
      -          "anyOf": [
      -            {
      -              "$ref": "#/$defs/Annotations"
      -            },
      -            {
      -              "type": "null"
      -            }
      -          ],
      -          "default": null
      -        },
      -        "text": {
      -          "title": "Text",
      -          "type": "string"
      -        },
      -        "type": {
      -          "const": "text",
      -          "title": "Type",
      -          "type": "string"
      -        }
      -      },
      -      "required": [
      -        "type",
      -        "text"
      -      ],
      -      "title": "TextContent",
      -      "type": "object"
      -    }
      -  },
      -  "properties": {
      -    "result": {
      -      "items": {
      -        "$ref": "#/$defs/TextContent"
      -      },
      -      "title": "Result",
      -      "type": "array"
      -    }
      -  },
      -  "required": [
      -    "result"
      -  ],
      -  "title": "get_neo4j_schemaOutput",
      -  "type": "object"
      -}New value: +null
  2. First observedv0.4.0

TDQS

A3.7/5.0
Behavior4/5

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

Annotations already declare readOnlyHint, idempotentHint, and closed-world scope, so the safety profile is covered. The description adds genuine behavioral value beyond that by disclosing a concrete failure mode (Neo.ClientError.Procedure.ProcedureNotFound) and the remediation (install/enable APOC), which the agent cannot derive from structured fields.

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?

Two short sentences that are front-loaded with the primary purpose, with no filler. The second sentence has an awkward mid-sentence line break that slightly hurts readability but not meaning.

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 read-only introspection tool with no output schema, the description does enumerate what is returned (nodes, attributes, relationships). Combined with the error/remediation note and annotations covering safety, an agent has enough to call it correctly, though the granularity of the returned structure remains unspecified.

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?

There is only one parameter (session_id) and the schema description coverage is 100%, with a thorough explanation of session lifetime and reuse in the schema itself. The description adds nothing about the parameter, so the baseline of 3 applies.

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?

States a specific verb (list) and resource (nodes, attributes, relationships) in the neo4j database, which is clear and concrete. It does not explicitly differentiate itself from close siblings such as get_node_metadata, get_relationship_metadata, or visualize_schema, so an agent must infer that this returns the whole graph schema rather than a per-element view.

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?

There is no explicit when-to-use guidance versus alternatives like get_node_metadata or visualize_schema. The APOC plugin advice is conditional troubleshooting rather than usage routing, though it does give the agent a clear next step on a specific failure.

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