Skip to main content
Glama

search_gene

Read-onlyIdempotent

Search the NCBI Gene database to find gene symbols, aliases, functions, and chromosome locations. Filter by organism to identify genes by name or function.

Instructions

Search NCBI Gene database for gene information.

═══════════════════════════════════════════════════════════════ USE CASES: ═══════════════════════════════════════════════════════════════

  • Look up gene function and description

  • Find gene aliases and official symbols

  • Get chromosome location

  • Find genes by name or function

Args: query: Gene name, symbol, or function keyword organism: Filter by organism (e.g., "human", "Homo sapiens", "mouse") limit: Maximum results (1-50)

Returns: JSON with gene records including symbols, names, locations

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNo
queryYes
organismNo

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed4 schema fields changedv0.7.7
    • addedInput schema / properties / limit / anyOf
      Added value: +[
      +  {
      +    "default": 10,
      +    "maximum": 50,
      +    "minimum": 1,
      +    "title": "Limit",
      +    "type": "integer"
      +  },
      +  {
      +    "description": "ASCII decimal integer; the integer branch's bounds apply after conversion.",
      +    "maxLength": 32,
      +    "pattern": "^[ \\t\\r\\n]*-?(?:0|[1-9][0-9]*)[ \\t\\r\\n]*$",
      +    "type": "string"
      +  }
      +]
    • removedInput schema / properties / limit / maximum
      Removed value: -50
    • removedInput schema / properties / limit / minimum
      Removed value: -1
    • removedInput schema / properties / limit / type
      Removed value: -"integer"
  2. Changed9 schema fields changedv0.7.2
    • addedInput schema / additionalProperties
      Added value: +false
    • removedInput schema / properties / limit / anyOf
      Removed value: -[
      -  {
      -    "type": "integer"
      -  },
      -  {
      -    "type": "string"
      -  }
      -]
    • addedInput schema / properties / limit / maximum
      Added value: +50
    • addedInput schema / properties / limit / minimum
      Added value: +1
    • addedInput schema / properties / limit / type
      Added value: +"integer"
    • changedInput schema / properties / organism / anyOf
      Previous value: -[
      -  {
      -    "type": "string"
      -  },
      -  {
      -    "type": "null"
      -  }
      -]New value: +[
      +  {
      +    "maxLength": 200,
      +    "minLength": 1,
      +    "type": "string"
      +  },
      +  {
      +    "type": "null"
      +  }
      +]
    • addedInput schema / properties / query / maxLength
      Added value: +500
    • addedInput schema / properties / query / minLength
      Added value: +1
    • changedOutput schema / (root)
      Previous value: -{
      -  "properties": {
      -    "result": {
      -      "title": "Result",
      -      "type": "string"
      -    }
      -  },
      -  "required": [
      -    "result"
      -  ],
      -  "title": "search_geneOutput",
      -  "type": "object"
      -}New value: +null
  3. First observedv0.5.16

TDQS

A4/5.0
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 value beyond that by disclosing the return shape ('JSON with gene records including symbols, names, locations') and the result-count range, which the annotations cannot convey.

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?

Content is front-loaded (purpose first, then use cases, args, returns) and each content line is short and useful. The triple-line box-drawing banners are pure decoration that consume tokens without adding 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 no output schema, the description supplies a brief return summary, and annotations cover behavior for this read-only search. The remaining gap is routing relative to get_gene_details and get_gene_literature, plus any note on result ordering or pagination.

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 param burden and largely does: query is described as 'Gene name, symbol, or function keyword', and organism includes concrete accepted values ('human', 'Homo sapiens', 'mouse'), which is genuinely useful for a taxonomy-filtered API. The limit line only restates the schema's 1-50 bound and adds no ranking or sorting semantics.

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 clear verb and resource: 'Search NCBI Gene database for gene information,' with a use-case list that scopes what it retrieves (function, aliases, symbols, location). It does not distinguish itself from siblings like get_gene_details or get_gene_literature, so an agent must infer search-vs-fetch 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 Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The USE CASES block gives concrete retrieval scenarios (look up gene function, find aliases/symbols, get chromosome location, search by name or function keyword), which is clear usage context. It stops short of exclusions or naming the alternative tools to use when you already have a gene ID or want literature about a gene.

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