kegg-mcp-server

search_compounds

Read-onlyIdempotent

Find KEGG compounds by name, molecular formula, exact mass, or molecular weight to identify chemical entries and retrieve up to 100 matches.

Instructions

Search KEGG compounds by name or chemical property.

Args: query: Search term (compound name, formula, or mass). search_type: 'name' (default), 'formula', 'exact_mass', 'mol_weight', or 'nop'. max_results: Maximum number of results to return (capped at 100).

Input Schema

Name	Required	Default
`query`	Yes
`max_results`	No
`search_type`	No	name

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.

Changed11 schema fields changedv0.5.0Oct 23, 2026

addedInput schema / properties / search_type / enum

Added value: +[
+  "name",
+  "formula",
+  "exact_mass",
+  "mol_weight",
+  "nop"
+]

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_compoundsOutput"New value: +"SearchResult"

First observedv0.1.0Jul 29, 2026

TDQS

A3.5/5.0

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 safety is covered. The description adds only the useful 100-result cap and defaults; it says nothing about pagination, result ordering, or remote/network 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?

One lead sentence plus a compact Args block; the core action is front-loaded and nothing is padded. The terseness of the enum descriptions costs a little clarity.

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 shape needn't be described, and all three params are addressed. The residual gap is the undocumented 'nop' mode and unit/format specifics for mass and formula searches.

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?

Schema description coverage is 0%, so the description carries the load. It documents all three parameters and the enum's intent, which is solid, but leaves 'nop' undefined and doesn't clarify mass units or formula syntax.

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?

States a specific verb and resource ('Search KEGG compounds') and the axes it searches on (name or chemical property). This distinguishes it from retrieval siblings like get_compound_info, though it doesn't name them explicitly.

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 search_type enumeration implies when to use each mode and query's parenthetical gives formats, but there is no explicit guidance on choosing exact_mass vs mol_weight, no explanation of 'nop', and no mention of when to prefer get_compound_info over searching.

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