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syntheticgio

ncbi-datasets-mcp

by syntheticgio

genome_download_by_taxon

Download genome assemblies for a given taxon by name or ID, optionally limiting to reference genomes or using dehydrated packages for large datasets.

Instructions

Download genome data packages for assemblies matching a taxon.

For taxa with many assemblies, use dehydrated=True first, then call rehydrate_genome_package to fetch only the data you need.

Args: taxon: Taxon name or NCBI tax ID include: Data types — genome, rna, protein, cds, gff3, gbff, seq-report output_dir: Directory for the download dehydrated: Download a dehydrated package (recommended for large taxa) reference_only: Download only the reference/representative genome

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
taxonYes
includeNo
output_dirNo
dehydratedNo
reference_onlyNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior3/5

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

No annotations are provided, so the description carries the full burden. It explains the dehydrated option and parameter purposes, but does not disclose that the tool writes files to the output directory, any potential side effects, or success/failure responses. The behavior is partially transparent but missing details about file creation.

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 concise with an introductory sentence, a usage tip, and a well-structured Args list. No unnecessary words; 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?

Given the tool downloads files and has an output schema (not shown), the description covers the main purpose and all parameters adequately. It could mention that the download creates files in the output directory, but it is reasonably complete for a download tool.

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

Parameters5/5

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

The schema has 0% description coverage, so the description must add meaning. It includes an Args section explaining each parameter beyond the schema: taxon (name or ID), include (data types list), output_dir (directory), dehydrated (recommended for large taxa), reference_only (only reference/representative). This provides excellent semantic detail.

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 it downloads genome data packages for assemblies matching a taxon, specifying the verb 'download', the resource 'genome data packages', and the condition 'for assemblies matching a taxon'. It differentiates from siblings by mentioning the dehydrated workflow and referencing rehydrate_genome_package.

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 description provides explicit guidance for large taxa (use dehydrated=True then rehydrate_genome_package). It does not explicitly compare to genome_download_by_accession, but the different purpose is inferred. The recommendation for dehydrated packages is clear and actionable.

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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