kegg-mcp-server

search_ko_entries

Read-onlyIdempotent

Search KEGG Orthology entries by keyword to retrieve gene function annotations and related KO identifiers.

Instructions

Search KEGG Orthology (KO) entries by keyword.

Args: query: Gene function (e.g. 'hexokinase', 'ribosomal protein', 'cytochrome'). 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_ko_entriesOutput"New value: +"SearchResult"

First observedv0.1.0Jul 29, 2026

TDQS

A3.7/5.0

Behavior3/5

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

Annotations already declare readOnlyHint, idempotentHint, openWorldHint, and destructiveHint=false, so the safety profile is covered. The description adds a useful cap of 100 results, but does not discuss ranking, pagination, or return behavior beyond what annotations and output schema provide.

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 description is front-loaded with the main purpose and then efficiently documents the two arguments. There is no unnecessary text, and the examples and cap are directly useful.

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?

With rich annotations and an output schema present, the description is nearly complete for a two-parameter search tool. The main remaining gap is explicit routing guidance versus get_ko_info or other KO-related tools.

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 does this well for both parameters: query is defined as a gene-function keyword with examples, and max_results is explained as a capped result limit.

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 Orthology (KO) entries by keyword. It is clear what the tool does, but it does not explicitly distinguish itself from siblings such as get_ko_info or other search_* tools.

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?

The query examples imply that this is a keyword search for gene functions, but the description does not state when to use this tool instead of get_ko_info or related search tools. Usage is implied rather than explicitly guided.

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