Skip to main content
Glama
Sign In
kegg-mcp-server

kegg-mcp-server

by Lucas-Servi
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Hybrid

get_gene_info

Read-onlyIdempotent

Retrieve detailed KEGG gene entry information by gene ID, choosing summary or full detail and optionally including amino acid and nucleotide sequences.

Instructions

Get detailed information for a KEGG gene entry.

Args: gene_id: KEGG gene ID in format 'organism:gene' (e.g. 'hsa:1956' for EGFR). detail_level: 'summary' (default, compact) or 'full' (complete parse with linked orthologs, pathways, xrefs, and references). include_sequence: If True and detail_level='full', fetches amino acid and nucleotide sequences.

Input Schema

NameRequiredDescriptionDefault
gene_idYes
detail_levelNosummary
include_sequenceNo

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed5 schema fields changedv0.5.0
    • 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 / GeneInfo / properties / symbol
      Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "title": "Symbol"
+}
    • 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": "#/$defs/GeneInfo"
-  },
-  {
-    "$ref": "#/$defs/EntrySummary"
-  },
-  {
-    "$ref": "#/$defs/ErrorResult"
-  }
-]New value: +[
+  {
+    "$ref": "#/$defs/GeneInfo"
+  },
+  {
+    "$ref": "#/$defs/EntrySummary"
+  }
+]
  2. First observedv0.1.0

TDQS

A3.9/5.0
Behavior4/5

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 genuinely new behavioral context: what 'full' parses (orthologs, pathways, xrefs, references) and that include_sequence is only honored when detail_level='full' — a dependency an agent could not infer from the schema.

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 each parameter note earns its place with no filler. The Args block style is structured and scan-friendly, though marginally more verbose than a single tight paragraph would be.

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

Completeness5/5

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, annotations cover the safety profile, and all three parameters are explained including their interaction. An agent has everything needed to call this correctly on the first attempt.

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 full burden and mostly succeeds: it gives the gene_id format with a worked example, defines both 'summary' and 'full' semantically rather than just repeating the enum, and states the conditional gate on include_sequence. Only the amino-acid/nucleotide sequence distinction is left slightly thin.

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 detailed information for a KEGG gene entry'), which is clearly distinct from lookup-adjacent siblings like search_genes or get_gene_orthologs. It does not explicitly name those siblings or say when to prefer them, so it stops short of full differentiation.

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 through the required ID format ('organism:gene', with a concrete example 'hsa:1956') and through the detail_level tradeoff, which tells an agent to start with 'summary'. However, there is no explicit 'use this instead of X' routing against search_genes or get_gene_orthologs.

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

Deploy Server

Other Tools