kegg-mcp-server

get_pathway_reactions

Read-onlyIdempotent

Retrieve all reactions for a specified KEGG pathway ID to map pathway steps and analyze metabolic reactions, with an optional result limit.

Instructions

Get all reactions in a KEGG pathway.

Args: pathway_id: KEGG pathway ID (e.g. 'hsa00010'). max_results: Maximum number of pairs to return (capped at 100).

Input Schema

Name	Required	Description	Default
`pathway_id`	Yes
`max_results`	No

Output Schema

Name	Required	Description	Default
`count`	Yes
`pairs`	Yes
`linked_db`	Yes
`truncated`	No
`pathway_id`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

Changed10 schema fields changedv0.5.0Oct 23, 2026

addedInput schema / properties / max_results

Added value: +{
+  "default": 100,
+  "title": "Max Results",
+  "type": "integer"
+}

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"
-  },
-  "PathwayLinks": {
-    "properties": {
-      "count": {
-        "title": "Count",
-        "type": "integer"
-      },
-      "linked_db": {
-        "title": "Linked Db",
-        "type": "string"
-      },
-      "pairs": {
-        "items": {
-          "maxItems": 2,
-          "minItems": 2,
-          "prefixItems": [
-            {
-              "type": "string"
-            },
-            {
-              "type": "string"
-            }
-          ],
-          "type": "array"
-        },
-        "title": "Pairs",
-        "type": "array"
-      },
-      "pathway_id": {
-        "title": "Pathway Id",
-        "type": "string"
-      }
-    },
-    "required": [
-      "pathway_id",
-      "linked_db",
-      "pairs",
-      "count"
-    ],
-    "title": "PathwayLinks",
-    "type": "object"
-  }
-}

addedOutput schema / properties / count

Added value: +{
+  "title": "Count",
+  "type": "integer"
+}

addedOutput schema / properties / linked_db

Added value: +{
+  "title": "Linked Db",
+  "type": "string"
+}

addedOutput schema / properties / pairs

Added value: +{
+  "items": {
+    "maxItems": 2,
+    "minItems": 2,
+    "prefixItems": [
+      {
+        "type": "string"
+      },
+      {
+        "type": "string"
+      }
+    ],
+    "type": "array"
+  },
+  "title": "Pairs",
+  "type": "array"
+}

addedOutput schema / properties / pathway_id

Added value: +{
+  "title": "Pathway Id",
+  "type": "string"
+}

removedOutput schema / properties / result

Removed value: -{
-  "anyOf": [
-    {
-      "$ref": "#/$defs/PathwayLinks"
-    },
-    {
-      "$ref": "#/$defs/ErrorResult"
-    }
-  ],
-  "title": "Result"
-}

addedOutput schema / properties / truncated

Added value: +{
+  "default": false,
+  "title": "Truncated",
+  "type": "boolean"
+}

changedOutput schema / required

Previous value: -[
-  "result"
-]New value: +[
+  "pathway_id",
+  "linked_db",
+  "pairs",
+  "count"
+]

changedOutput schema / title

Previous value: -"get_pathway_reactionsOutput"New value: +"PathwayLinks"

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 the useful cap of 100 results, but does not explain truncation behavior beyond that cap or whether results are complete or sampled.

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 short and front-loaded, with the core action in the first sentence and parameter details in a compact Args block. Every sentence adds value.

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 annotations covering safety, the description need not explain return values. It covers both parameters and the result cap, leaving only alternative-tool routing as a minor gap for this simple retrieval 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 compensate. It documents both parameters: pathway_id with a concrete KEGG ID example and max_results with the 100 cap. The term 'pairs' is slightly ambiguous, but overall it meaningfully supplements the bare schema.

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: 'Get all reactions in a KEGG pathway.' This clearly distinguishes it from pathway siblings like get_pathway_genes and get_pathway_compounds by resource type, though it does not explicitly differentiate it from search_reactions.

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 implied by the name and resource scope, but there is no explicit guidance on when to use this versus search_reactions or get_reaction_info. No alternatives or exclusions are named.

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