kegg-mcp-server

search_reactions

Read-onlyIdempotent

Search KEGG reactions by keyword to find matching reaction names or descriptions, returning up to 100 results for metabolic analysis.

Instructions

Search KEGG reactions by keyword.

Args: query: Search term (reaction name or description). max_results: Maximum number of results to return (capped at 100).

Input Schema

Name	Required	Description	Default
`query`	Yes
`max_results`	No

Output Schema

Name	Required	Description	Default
`query`	Yes
`results`	Yes
`database`	Yes
`truncated`	No
`total_found`	Yes
`returned_count`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

Changed10 schema fields changedv0.5.0Oct 23, 2026

removedOutput schema / $defs

Removed value: -{
-  "ErrorResult": {
-    "description": "Structured error returned by a tool when the KEGG API fails.\n\nA tool returns this instead of raising so the model can reason about\nthe failure and decide whether to retry, change inputs, or give up.\nA point lookup that receives a 404 uses code ``not_found``; an empty search\nremains a successful result with no items.",
-    "properties": {
-      "code": {
-        "default": "kegg_api_error",
-        "title": "Code",
-        "type": "string"
-      },
-      "error": {
-        "title": "Error",
-        "type": "string"
-      },
-      "hint": {
-        "anyOf": [
-          {
-            "type": "string"
-          },
-          {
-            "type": "null"
-          }
-        ],
-        "default": null,
-        "title": "Hint"
-      },
-      "path": {
-        "anyOf": [
-          {
-            "type": "string"
-          },
-          {
-            "type": "null"
-          }
-        ],
-        "default": null,
-        "title": "Path"
-      },
-      "retryable": {
-        "default": false,
-        "title": "Retryable",
-        "type": "boolean"
-      },
-      "status": {
-        "anyOf": [
-          {
-            "type": "integer"
-          },
-          {
-            "type": "null"
-          }
-        ],
-        "default": null,
-        "title": "Status"
-      }
-    },
-    "required": [
-      "error"
-    ],
-    "title": "ErrorResult",
-    "type": "object"
-  },
-  "SearchResult": {
-    "properties": {
-      "database": {
-        "title": "Database",
-        "type": "string"
-      },
-      "query": {
-        "title": "Query",
-        "type": "string"
-      },
-      "results": {
-        "additionalProperties": {
-          "type": "string"
-        },
-        "title": "Results",
-        "type": "object"
-      },
-      "returned_count": {
-        "title": "Returned Count",
-        "type": "integer"
-      },
-      "total_found": {
-        "title": "Total Found",
-        "type": "integer"
-      },
-      "truncated": {
-        "default": false,
-        "title": "Truncated",
-        "type": "boolean"
-      }
-    },
-    "required": [
-      "query",
-      "database",
-      "total_found",
-      "returned_count",
-      "results"
-    ],
-    "title": "SearchResult",
-    "type": "object"
-  }
-}

addedOutput schema / properties / database

Added value: +{
+  "title": "Database",
+  "type": "string"
+}

addedOutput schema / properties / query

Added value: +{
+  "title": "Query",
+  "type": "string"
+}

removedOutput schema / properties / result

Removed value: -{
-  "anyOf": [
-    {
-      "$ref": "#/$defs/SearchResult"
-    },
-    {
-      "$ref": "#/$defs/ErrorResult"
-    }
-  ],
-  "title": "Result"
-}

addedOutput schema / properties / results

Added value: +{
+  "additionalProperties": {
+    "type": "string"
+  },
+  "title": "Results",
+  "type": "object"
+}

addedOutput schema / properties / returned_count

Added value: +{
+  "title": "Returned Count",
+  "type": "integer"
+}

addedOutput schema / properties / total_found

Added value: +{
+  "title": "Total Found",
+  "type": "integer"
+}

addedOutput schema / properties / truncated

Added value: +{
+  "default": false,
+  "title": "Truncated",
+  "type": "boolean"
+}

changedOutput schema / required

Previous value: -[
-  "result"
-]New value: +[
+  "query",
+  "database",
+  "total_found",
+  "returned_count",
+  "results"
+]

changedOutput schema / title

Previous value: -"search_reactionsOutput"New value: +"SearchResult"

First observedv0.1.0Jul 29, 2026

TDQS

B3.4/5.0

Behavior3/5

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

Annotations already declare readOnlyHint=true, openWorldHint=true, idempotentHint=true, and destructiveHint=false, covering the safety profile. The description adds only that max_results is capped at 100, with no further behavioral details such as ordering, pagination, or external-service 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?

The description is short and front-loaded, with the purpose stated first and parameter meanings following in a compact Args block. It is appropriately sized, though the Args formatting is slightly mechanical rather than fully narrative.

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 simple two-parameter search tool with rich annotations and an output schema, the description is sufficiently complete. It does not need to explain return values because an output schema exists, and it covers the key input semantics and result cap.

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 description coverage is 0%, so the description must carry parameter meaning. It documents both parameters: query as a reaction name or description, and max_results as capped at 100. It does not mention the default value of 25, but otherwise compensates well for the schema gap.

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 states a specific verb and resource: "Search KEGG reactions by keyword." This clearly distinguishes keyword-based reaction search from sibling detail tools like get_reaction_info, though it does not explicitly name the alternative.

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?

The description implies keyword search via "Search KEGG reactions by keyword" and defines the query as a reaction name or description. However, it gives no explicit guidance on when to use this tool versus get_reaction_info, get_pathway_reactions, or other search tools.

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