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MCP GeneLab Server

MCP GeneLab Server

by sbl-sdsc
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Hybrid

visualize_schema

Read-onlyIdempotent

Visualize the NASA GeneLab Knowledge Graph schema as a Mermaid class diagram to clarify entity relationships before writing Cypher queries.

Instructions

Prompt for visualizing the knowledge graph schema using a Mermaid class diagram.

Tool call template

This tool declares no required parameters. Add optional parameters from the input schema as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {},
    "name": "visualize_schema"
  }
}

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": "visualize_schemaOutput",
-  "type": "object"
-}New value: +null
  2. First observedv0.4.0

TDQS

B3.2/5.0
Behavior3/5

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

Annotations already declare readOnlyHint, idempotentHint, and openWorldHint=false, so the safety profile is covered. The description adds that the tool yields a prompt rather than a rendered image, but it does not say what consumes the prompt or what the returned text looks like.

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?

A single front-loaded sentence with no filler. It is efficient, though the brevity leaves room for a clarifying clause about the prompt-only nature.

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

Completeness3/5

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

With no output schema, the description should explain what is returned and how it is used. Saying 'Prompt for visualizing' hints at text output but does not tell the agent whether it must forward the prompt to an LLM or render the Mermaid itself.

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?

The single session_id parameter has 100% schema coverage with a thorough description of its privacy role and re-creation behavior. The tool description adds nothing about parameters, so the baseline 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?

The description pairs a clear action with its resource and output format: producing a prompt that visualizes the knowledge graph schema as a Mermaid class diagram. It is distinguishable from get_neo4j_schema, though it never names that sibling or clarify why a separate schema tool exists.

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

Usage Guidelines2/5

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

No when-to-use guidance, no prerequisites, and no mention of the obvious alternative get_neo4j_schema or clean_mermaid_diagram. The agent must infer that this is the diagram-oriented path versus the raw schema lookup.

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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