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syntheticgio

ncbi-datasets-mcp

by syntheticgio

genome_summary_by_taxon

Search NCBI for genome assemblies by taxon name or ID. Retrieve assembly metadata including accession numbers, organism info, and annotation status.

Instructions

Search NCBI for genome assemblies matching a taxon name or tax ID.

Returns assembly metadata including accession numbers, organism info, assembly statistics, annotation status, and submission details.

Args: taxon: Taxon name (e.g. "human", "Mus musculus") or NCBI tax ID assembly_level: Filter by level — chromosome, complete_genome, contig, scaffold assembly_source: Filter by source — all, genbank, refseq reference_only: Return only reference/representative genomes annotated_only: Return only annotated genomes limit: Maximum number of assemblies to return (capped by server config)

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
taxonYes
assembly_levelNo
assembly_sourceNo
reference_onlyNo
annotated_onlyNo
limitNo

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 full burden. It states that it returns assembly metadata but does not explicitly confirm it is a read-only operation, mention authentication needs, or rate limits. The search nature implies safety, but not fully transparent.

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 concise with a clear front-loaded purpose and a structured Args section. Every sentence adds value, though it could be slightly tighter without losing information.

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?

With 6 parameters (1 required) and an output schema, the description covers all inputs and states the return type (assembly metadata). It provides enough context for an AI agent to understand the tool's scope and usage.

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?

Schema description coverage is 0%, so description must add meaning. It includes an 'Args' section explaining each parameter with examples (e.g., 'human' for taxon) and possible values (e.g., 'chromosome' for assembly_level). The limit parameter notes server cap. This adds significant value beyond the schema defaults.

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 states a specific verb ('Search') and resource ('NCBI genome assemblies') with clear matching criteria ('taxon name or tax ID'). It distinguishes from sibling tools like genome_summary_by_accession (different lookup method) and genome_download_by_taxon (download vs summary).

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

Usage Guidelines3/5

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

The description explains what the tool does but does not provide explicit guidance on when to use it versus alternatives like genome_summary_by_accession. No when-not-to-use or preference suggestions are given.

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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