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syntheticgio

ncbi-datasets-mcp

by syntheticgio

genome_download_by_accession

Download genome data packages for one or more assembly accessions. Returns the local path to the downloaded ZIP file, with options to select data types like genome, RNA, and annotations.

Instructions

Download a genome data package for one or more assembly accessions.

Returns the local path to the downloaded ZIP file.

Args: accessions: RefSeq/GenBank assembly accessions include: Data types — genome, rna, protein, cds, gff3, gbff, seq-report. Defaults to ["genome"]. output_dir: Directory for the download. Uses NCBI_DOWNLOAD_DIR if omitted. dehydrated: Download a lightweight dehydrated package (use rehydrate_genome_package to fetch the actual sequence files).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
accessionsYes
includeNo
output_dirNo
dehydratedNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior4/5

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

Without annotations, the description discloses key behaviors: returns local path, dehydrated packages need rehydration. It does not mention authentication or rate limits, but covers the main functional traits adequately.

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 description is front-loaded with the main verb and result, then details in a structured Args section. It is efficient but the Args block could be slightly more streamlined without losing clarity.

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?

Given the tool's complexity and the presence of an output schema, the description covers all necessary aspects: input parameters, output location, and the dehydrated workflow. It is fully complete for an agent to invoke correctly.

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?

With 0% schema coverage, the description fully explains each parameter: accessions format, include data types with defaults, output_dir fallback, and dehydrated's purpose. This adds critical meaning beyond 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 it downloads a genome data package for assembly accessions and returns the local path. It differentiates from siblings like genome_download_by_taxon and genome_summary_by_accession through its specific verb 'download' and resource 'genome 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 Guidelines4/5

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

The description provides clear parameter explanations with defaults and notes the dehydrated option's follow-up tool. It implicitly guides usage but lacks explicit when-to-use vs sibling tools, which would make it a 5.

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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