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Ncbi Genome Reports

ncbi_genome_reports
Read-onlyIdempotent

List the genome assemblies NCBI holds for an organism (or fetch one by accession), with assembly level, total length, contig and scaffold N50, GC percent, submitter, release date, BioProject, and the paired RefSeq/GenBank accession. AUTHORITATIVE for "what is the reference genome for X and how good is it" — PREFER OVER WEB SEARCH, which returns papers rather than current assembly metadata. Defaults to reference genomes only, because the unfiltered report for a well-sequenced organism runs to hundreds of thousands of rows (E. coli: 492,559) and its first page is not the reference. Set reference_only false to see every deposited assembly.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNoMaximum assemblies to return, 1-100 (default 10).
taxonNoTax id, scientific name or common name — "9606", "Homo sapiens" and "human" all work. Ignored if accession is given.
accessionNoA specific assembly accession, e.g. GCF_000001405.40 or GCA_000001405.29. Overrides taxon and disables the reference-only default.
assembly_levelNoRestrict by completeness: complete_genome, chromosome, scaffold, or contig.
reference_onlyNoRestrict to NCBI reference/representative genomes. Defaults to true for a taxon lookup; set false to list every assembly.

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.2/5.0
Behavior3/5

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

Annotations already declare read-only, idempotent, open-world and non-destructive behavior, so the safety profile is covered without the description. The description adds genuine value by disclosing the reference-only default, why it exists (row counts up to 492,559 and the non-reference first page), and that accession disables that default. However it does not describe pagination or result-shape behavior.

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 purpose, authority claim and default-scoping rationale are front-loaded, and every sentence carries information. The E. coli row-count aside is illustrative but slightly padded for the space it occupies.

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 no output schema, the description compensates by enumerating the returned fields (assembly level, N50, GC percent, BioProject, paired accessions). Combined with the default-behavior disclosure and the accession note, an agent has everything needed to call it correctly.

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 the schema already documents all five parameters, making 3 the baseline. The description reinforces the reference_only default and the accession interaction, adding rationale but no syntax or format detail 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?

States a specific verb and resource ('List the genome assemblies NCBI holds for an organism') and enumerates the returned fields, which makes it clearly distinct from ncbi_taxonomy and ncbi_gene_by_symbol. The fetch-by-accession alternate mode is also named, so there is no ambiguity about what the tool produces.

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

Usage Guidelines5/5

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

Explicit when-to-use ('AUTHORITATIVE for what is the reference genome for X and how good is it') and when-not ('PREFER OVER WEB SEARCH, which returns papers rather than current assembly metadata'). It also states the default scoping behavior and the exact switch (reference_only false) to change it, so no inference is required.

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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