kegg-mcp-server

get_pathway_info

Read-onlyIdempotent

Fetch detailed KEGG pathway data by pathway ID, choosing summary or full detail with linked genes, compounds, reactions, references, and xrefs.

Instructions

Get detailed information for a KEGG pathway.

Args: pathway_id: KEGG pathway ID (e.g. 'hsa00010', 'map00010'). detail_level: 'summary' (default, compact) or 'full' (complete flat-file parse with all linked genes, compounds, reactions, references, and xrefs).

Input Schema

Name	Required	Description	Default
`pathway_id`	Yes
`detail_level`	No		summary

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

Changed4 schema fields changedv0.5.0Oct 23, 2026

addedOutput schema / $defs / EntrySummary / properties / symbol

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "title": "Symbol"
+}

removedOutput schema / $defs / ErrorResult

Removed value: -{
-  "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"
-}

addedOutput schema / $defs / Reference / properties / sequence

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "title": "Sequence"
+}

changedOutput schema / properties / result / anyOf

Previous value: -[
-  {
-    "$ref": "#/$defs/PathwayInfo"
-  },
-  {
-    "$ref": "#/$defs/EntrySummary"
-  },
-  {
-    "$ref": "#/$defs/ErrorResult"
-  }
-]New value: +[
+  {
+    "$ref": "#/$defs/PathwayInfo"
+  },
+  {
+    "$ref": "#/$defs/EntrySummary"
+  }
+]

First observedv0.1.0Jul 29, 2026

TDQS

A3.8/5.0

Behavior4/5

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

Annotations already cover the safety profile (readOnly, idempotent, non-destructive, openWorld). The description adds genuinely useful behavior beyond that: it explains that 'full' performs a complete flat-file parse and returns all linked genes, compounds, reactions, references and xrefs, which signals response size and payload breadth.

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 purpose sentence is front-loaded and the Args block is tight with no filler. The docstring-style formatting is slightly verbose for two parameters but every line carries information.

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 an output schema present and all parameters explained, an agent has enough to invoke this correctly. The remaining gap is routing guidance relative to the pathway-specific siblings and what 'summary' actually contains.

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 carries the burden — and it does, giving pathway_id examples ('hsa00010', 'map00010') and defining both detail_level values plus the 'summary' default. It stops short of explaining the hsa vs map prefix semantics, which matters for organism-specific vs reference pathways.

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?

Specific verb+resource ("Get detailed information for a KEGG pathway") with a named identifier format. It does not, however, distinguish itself from the many pathway-scoped siblings (get_pathway_genes, get_pathway_compounds, get_pathway_reactions), which return subsets of what 'full' detail returns.

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 detail_level explanation implies usage ('summary' for compact, 'full' for everything), but there is no explicit when-to-use guidance and no mention of the alternative tools that return pathway genes/compounds/reactions individually or of search_pathways for discovery.

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