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syntheticgio

ncbi-datasets-mcp

by syntheticgio

taxonomy_download

Download a taxonomy data package by specifying a taxon name or NCBI tax ID. Saves the package to your chosen output directory.

Instructions

Download a taxonomy data package for a given taxon.

Args: taxon: Taxon name or NCBI tax ID output_dir: Directory for the download

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
taxonYes
output_dirNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior2/5

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

Without annotations, the description should carry the burden of behavioral disclosure. It only says 'download,' implying a network operation, but does not mention file size, permissions, side effects, or whether the tool modifies any state.

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?

Very short, with the main action front-loaded. The parameter listing is concise, but could be more structured (e.g., bullet points) for clarity. No wasted words.

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

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the presence of an output schema, the description does not explain return values or the nature of the download (e.g., file format, size). Sibling tools exist but no context is provided. Incomplete for a network-bound tool.

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

Parameters2/5

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 adds basic meaning: 'taxon' is a name or NCBI ID, 'output_dir' is a directory. However, no details on formats, defaults, or constraints beyond what is in the schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool downloads a taxonomy data package for a given taxon, which is a specific verb+resource. It distinguishes from sibling tools like genome_download_by_taxon, which downloads genome data, by specifying 'taxonomy' data package.

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?

No guidance on when to use this tool versus alternatives. For example, when to use taxonomy_download vs taxonomy_summary or genome_download_by_taxon is not explained. No mention of prerequisites or context.

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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