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STRING Database MCP Server

by org.string-db
OverviewDiscussionsAdmin

STRING: Help / FAQ

string_help

Provides explanatory text for STRING features and limitations.

Use this tool when the user question involves:

  • What is STRING is or how to use the tool (how_to_use_string, cytoscape)

  • functionality not available via MCP tools (e.g. GSEA or large datasets).

  • meaning of network edges and their visual encoding (network_edge_legend)

  • interpretation of enrichment strength and signal (enrichment_scores)

  • grouping of terms in enrichment figures (enrichment_grouping)

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
topicNoHelp topic to display. If omitted, returns the available topics.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changed
    • changedInput schema / properties / topic / anyOf
      Previous value: -[
-  {
-    "anyOf": [
-      {
-        "enum": [
-          "gsea",
-          "enrichment_scores",
-          "large_input",
-          "cytoscape",
-          "scores",
-          "missing_proteins",
-          "missing_species",
-          "proteome_annotation",
-          "regulatory_networks",
-          "how_to_use_string",
-          "network_edge_legend",
-          "version_and_citation",
-          "line_colors",
-          "enrichment",
-          "signal_strength"
-        ],
-        "type": "string"
-      },
-      {
-        "type": "null"
-      }
-    ],
-    "description": "Help topic to display. If omitted, returns the available topics."
-  },
-  {
-    "type": "null"
-  }
-]New value: +[
+  {
+    "enum": [
+      "gsea",
+      "enrichment_scores",
+      "enrichment_grouping",
+      "large_input",
+      "cytoscape",
+      "scores",
+      "missing_proteins",
+      "missing_species",
+      "proteome_annotation",
+      "regulatory_networks",
+      "how_to_use_string",
+      "network_edge_legend",
+      "version_and_citation",
+      "line_colors",
+      "enrichment",
+      "signal_strength"
+    ],
+    "type": "string"
+  },
+  {
+    "type": "null"
+  }
+]
    • addedInput schema / properties / topic / description
      Added value: +"Help topic to display. If omitted, returns the available topics."
  2. Changed1 schema field changed
    • changedInput schema / properties / topic / anyOf
      Previous value: -[
-  {
-    "anyOf": [
-      {
-        "enum": [
-          "gsea",
-          "large_input",
-          "cytoscape",
-          "scores",
-          "missing_proteins",
-          "missing_species",
-          "proteome_annotation",
-          "regulatory_networks",
-          "how_to_use_string",
-          "line_colors",
-          "version_and_citation"
-        ],
-        "type": "string"
-      },
-      {
-        "type": "null"
-      }
-    ],
-    "description": "Optional. Help topic to display. If omitted, returns the available topics."
-  },
-  {
-    "type": "null"
-  }
-]New value: +[
+  {
+    "anyOf": [
+      {
+        "enum": [
+          "gsea",
+          "enrichment_scores",
+          "large_input",
+          "cytoscape",
+          "scores",
+          "missing_proteins",
+          "missing_species",
+          "proteome_annotation",
+          "regulatory_networks",
+          "how_to_use_string",
+          "network_edge_legend",
+          "version_and_citation",
+          "line_colors",
+          "enrichment",
+          "signal_strength"
+        ],
+        "type": "string"
+      },
+      {
+        "type": "null"
+      }
+    ],
+    "description": "Help topic to display. If omitted, returns the available topics."
+  },
+  {
+    "type": "null"
+  }
+]
  3. Changed2 schema fields changed
    • removedInput schema / $defs
      Removed value: -{
-  "HelpTopic": {
-    "enum": [
-      "gsea",
-      "large_input",
-      "cytoscape",
-      "scores",
-      "missing_proteins",
-      "missing_species",
-      "proteome_annotation",
-      "regulatory_networks",
-      "how_to_use_string",
-      "line_colors",
-      "version_and_citation"
-    ],
-    "type": "string"
-  }
-}
    • changedInput schema / properties / topic / anyOf
      Previous value: -[
-  {
-    "anyOf": [
-      {
-        "$ref": "#/$defs/HelpTopic"
-      },
-      {
-        "type": "null"
-      }
-    ],
-    "description": "Optional. Help topic to display. If omitted, returns the available topics."
-  },
-  {
-    "type": "null"
-  }
-]New value: +[
+  {
+    "anyOf": [
+      {
+        "enum": [
+          "gsea",
+          "large_input",
+          "cytoscape",
+          "scores",
+          "missing_proteins",
+          "missing_species",
+          "proteome_annotation",
+          "regulatory_networks",
+          "how_to_use_string",
+          "line_colors",
+          "version_and_citation"
+        ],
+        "type": "string"
+      },
+      {
+        "type": "null"
+      }
+    ],
+    "description": "Optional. Help topic to display. If omitted, returns the available topics."
+  },
+  {
+    "type": "null"
+  }
+]
  4. First observed

TDQS

A4.2/5.0
Behavior3/5

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

No annotations are provided, so the description carries the full burden. It implies a safe, read-only help lookup and mentions limitations, but does not explicitly disclose side effects, permissions, or rate-limit behavior.

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

Conciseness5/5

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

The purpose is stated in the first sentence, followed by a compact, well-structured bullet list of usage conditions. The format is front-loaded and every item helps an agent select the right topic.

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?

The definition is complete enough for a one-parameter help tool with an output schema, and it covers the main question categories. It leaves a small gap by not explicitly stating the read-only/no-side-effect behavior absent annotations.

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?

Schema coverage is 100%, so the enum and optional topic parameter are already documented. The description adds useful meaning by mapping user-question types to specific help topics such as how_to_use_string, network_edge_legend, and enrichment_scores.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb and resource: provides explanatory text for STRING features and limitations. It clearly distinguishes this help/FAQ tool from the data-query and analysis siblings by scoping it to interpretation, usage, and unsupported functionality.

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?

The bullet list gives clear contexts for when to use the tool, including unavailable functionality and interpretation questions. It does not explicitly name sibling alternatives to use instead, but the conditions are specific enough for 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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