amr-mcp

search_amr_genes

Read-only

Search the NCBI Reference Gene Catalog for AMR, stress and virulence genes and point mutations by name, drug class, subclass or organism to identify resistance determinants.

Instructions

Search the NCBI Reference Gene Catalog of AMR, stress and virulence genes and point mutations.

Tool call template

This tool declares no required parameters. Add optional parameters from the input schema as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {},
    "name": "search_amr_genes"
  }
}

Input Schema

Name	Required	Description
`limit`	No	Max entries, or max families when grouping
`query`	No	Text in allele, gene family, product name or synonyms, e.g. 'KPC', 'mcr', 'carbapenemase'
`organism`	No	Drop entries the catalog restricts to other taxa, e.g. 'Klebsiella pneumoniae'. Most acquired genes have no restriction, so this does not show where a gene has been found: use get_protein_hosts for that
`subclass`	No	e.g. CARBAPENEM, CEPHALOSPORIN
`drug_class`	No	e.g. BETA-LACTAM, COLISTIN, AMINOGLYCOSIDE
`element_type`	No	Element type
`group_by_family`	No	Return one row per gene family with its entry count; use for broad searches

Output Schema

Name	Required	Description	Default
No arguments

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.3Nov 5, 2026

TDQS

C2.9/5.0

Behavior2/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true, so safety and external-data traits are covered. Beyond catalog scope, the description discloses nothing about result ordering, empty-result behavior, or how filters combine, which matters for a search tool over a curated reference database.

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?

A single front-loaded sentence with no filler or repetition. It is efficient, though the brevity comes at the cost of the guidance and behavior detail noted elsewhere.

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 and the parameters are fully documented, so the description needn't explain return values or fields. However, a seven-parameter, all-optional search tool with no stated defaults-for-use or query-construction advice leaves the agent to derive invocation strategy from the schema alone.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so every one of the seven parameters is already documented with examples and caveats (including the important warning that organism filtering does not indicate where a gene was found). The description adds no parameter meaning beyond that, so the baseline 3 applies.

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 names a specific verb ("Search") and a specific resource ("the NCBI Reference Gene Catalog of AMR, stress and virulence genes and point mutations"), which tells an agent exactly what corpus is being queried. It stops short of differentiating from siblings such as get_amr_gene or fetch_sequence, so the agent has to infer the boundary itself.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

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

There is no when-to-use guidance, no exclusions, and no mention of alternatives like get_amr_gene (single-record lookup) or get_protein_hosts (host distribution). Some routing hints live inside parameter descriptions (e.g. the organism field pointing to get_protein_hosts), but the tool-level description contributes none.

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

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