kegg-mcp-server

search_genes

Read-onlyIdempotent

Search KEGG organism databases for genes by name, symbol, or description using an organism code, with optional result limits.

Instructions

Search for genes in a KEGG organism database.

Args: query: Search term (gene name, symbol, or description). organism_code: KEGG organism code (e.g. 'hsa' human, 'mmu' mouse, 'eco' E. coli). max_results: Maximum number of results to return (capped at 100).

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "query": "<query>"
    },
    "name": "search_genes"
  }
}

Input Schema

Name	Required	Default
`query`	Yes
`max_results`	No
`organism_code`	No	hsa

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_genesOutput"New value: +"SearchResult"

First observedv0.1.0Jul 29, 2026

TDQS

A3.6/5.0

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 structurally. The description adds the useful constraint that max_results is capped at 100, but says nothing about permissions, result ordering, or matching behavior (exact vs substring), which materially affect how a search is issued.

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?

Front-loaded with a one-line purpose, then a compact Args block with no filler. Some of the Args lines restate schema property titles, but each carries additional semantics, so the space is largely earned.

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?

An output schema exists, so return values need not be described. All three parameters are explained and the organism scoping is clear, leaving only minor gaps: the default organism when omitted and how this differs from the ID-based gene lookups.

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 0%, so the description must carry the load, and it does: it explains all three parameters, clarifies that query covers gene name, symbol, or description, and gives concrete organism codes ('hsa', 'mmu', 'eco'). It also adds a cap of 100 on max_results that is absent from the schema, though it never states the default (hsa / 25) that the schema implies.

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?

Names a specific verb and resource ('Search for genes') and scopes it to a KEGG organism database, so the agent knows exactly what is being queried. It does not distinguish itself from siblings such as get_gene_info, search_ko_entries, or get_gene_orthologs, leaving selection partly to inference.

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?

Usage is only implied: the word 'search' plus a free-text query term suggests this is for discovery when IDs are unknown, with organism_code scoping the space. There is no explicit statement of when to prefer this over get_gene_info (fetch by ID) or get_gene_orthologs, and no exclusions or prerequisites are given.

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