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kegg-mcp-server

kegg-mcp-server

by Lucas-Servi

search_modules

Read-onlyIdempotent

Search KEGG modules by keyword or pathway block and return up to a specified number of matching results.

Instructions

Search KEGG modules by keyword.

Args: query: Module name or pathway block (e.g. 'glycolysis', 'TCA cycle'). max_results: Maximum number of results to return (capped at 100).

Input Schema

NameRequiredDescriptionDefault
queryYes
max_resultsNo

Output Schema

NameRequiredDescriptionDefault
queryYes
resultsYes
databaseYes
truncatedNo
total_foundYes
returned_countYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed10 schema fields changedv0.5.0
    • 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_modulesOutput"New value: +"SearchResult"
  2. First observedv0.1.0

TDQS

A3.5/5.0
Behavior3/5

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

Annotations already declare read-only, idempotent, non-destructive, open-world behavior, so the safety burden is covered. The description adds one genuinely useful behavioral fact not present in structured data: results are capped at 100. It says nothing about matching semantics (term vs. ID matching, substring vs. fuzzy) or behavior on empty results.

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?

Short and front-loaded, with the purpose in the first sentence and parameters in a compact Args block. Minor waste from the Args formatting duplicating schema field names, but nothing extraneous.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

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 explained, and the simple two-parameter read operation is largely covered. Still missing the relationship to get_module_info and any note on what the query actually matches against (module names, IDs, or pathway blocks), which matters for a keyword search tool.

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, and it does: query is defined as a module name or pathway block with concrete examples ('glycolysis', 'TCA cycle'), and max_results is explained along with its hard cap of 100, which the schema's default of 25 does not convey.

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+resource ("Search KEGG modules") which is unambiguous and clearly distinct from the get_* siblings such as get_module_info. However, it does not distinguish itself from the many other search_* siblings (search_pathways, search_ko_entries, search_genes), leaving scope at the KEGG module database to be inferred from the name alone.

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 description implies discovery usage by describing the query as a keyword, but gives no explicit when-to-use or when-not guidance and never names the natural follow-up (get_module_info) for retrieving full details. An agent must infer the search-then-fetch workflow from the sibling list.

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